/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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trunk/esys2/finley/src/CPPAdapter/MeshAdapter.cpp revision 82 by jgs, Tue Oct 26 06:53:54 2004 UTC trunk/finley/src/CPPAdapter/MeshAdapter.cpp revision 3546 by jfenwick, Thu Jul 28 01:32:20 2011 UTC
# Line 1  Line 1 
1  /*  
2   ******************************************************************************  /*******************************************************
3   *                                                                            *  *
4   *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  * Copyright (c) 2003-2010 by University of Queensland
5   *                                                                            *  * Earth Systems Science Computational Center (ESSCC)
6   * This software is the property of ACcESS. No part of this code              *  * http://www.uq.edu.au/esscc
7   * may be copied in any form or by any means without the expressed written    *  *
8   * consent of ACcESS.  Copying, use or modification of this software          *  * Primary Business: Queensland, Australia
9   * by any unauthorised person is illegal unless that person has a software    *  * Licensed under the Open Software License version 3.0
10   * license agreement with ACcESS.                                             *  * http://www.opensource.org/licenses/osl-3.0.php
11   *                                                                            *  *
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());     }
74      //   cout << "Finished dealloc." << endl;  }
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];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
119    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
120    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
121    checkFinleyError();     checkFinleyError();
122       TMPMEMFREE(fName);
123  }  }
124    
125  // void MeshAdapter::getTagList(int functionSpaceType,  void MeshAdapter::Print_Mesh_Info(const bool full) const
126  //                  int* numTags) const  {
127  // {     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
128  //   Finley_Mesh_tagList(m_finleyMesh.get(),functionSpaceType,tagList,numTags);  }
129  //   return;  
130  // }  void MeshAdapter::dump(const string& fileName) const
131    {
132    #ifdef USE_NETCDF
133       const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
134       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::getDiracDeltaFunctionsCode() 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=0;     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 277  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                                   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 escript::Data& d, const escript::Data& y,
774                                     const escript::Data& d_contact,const escript::Data& y_contact,
775                                     const escript::Data& d_dirac,const escript::Data& y_dirac) const
776    {
777       SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
778       if (smat==0)
779       {
780        throw FinleyAdapterException("finley only supports its own system matrices.");
781       }
782       escriptDataC _rhs=rhs.getDataC();
783       escriptDataC _A  =A.getDataC();
784       escriptDataC _B=B.getDataC();
785       escriptDataC _C=C.getDataC();
786       escriptDataC _D=D.getDataC();
787       escriptDataC _X=X.getDataC();
788       escriptDataC _Y=Y.getDataC();
789       escriptDataC _d=d.getDataC();
790       escriptDataC _y=y.getDataC();
791       escriptDataC _d_contact=d_contact.getDataC();
792       escriptDataC _y_contact=y_contact.getDataC();
793       escriptDataC _d_dirac=d_dirac.getDataC();
794       escriptDataC _y_dirac=y_dirac.getDataC();
795    
796     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
797     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getFinley_SystemMatrix(),&(rhs.getDataC()),  
798                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
799       checkFinleyError();
800    
801       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
802       checkFinleyError();
803    
804       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
805       checkFinleyError();
806    
807        Finley_Assemble_PDE(mesh->Nodes,mesh->Points, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
808     checkFinleyError();     checkFinleyError();
809  }  }
810    
811    void  MeshAdapter::addPDEToLumpedSystem(
812                                            escript::Data& mat,
813                                            const escript::Data& D,
814                                            const escript::Data& d,
815                                            const escript::Data& d_dirac,
816                                            const bool useHRZ) const
817    {
818       escriptDataC _mat=mat.getDataC();
819       escriptDataC _D=D.getDataC();
820       escriptDataC _d=d.getDataC();
821       escriptDataC _d_dirac=d_dirac.getDataC();
822    
823       Finley_Mesh* mesh=m_finleyMesh.get();
824    
825       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D, useHRZ);
826       checkFinleyError();
827      
828       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d, useHRZ);
829       checkFinleyError();
830    
831       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Points,&_mat, &_d_dirac, useHRZ);
832       checkFinleyError();
833    
834    }
835    
836    
837  //  //
838  // adds Robin boundary conditions as natural boundary condition into a given stiffness matrix and right hand side:  // adds linear PDE of second order into the right hand side only
839  //  //
840  void MeshAdapter::addRobinConditionsToSystem(  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact,  const escript::Data& y_dirac) const
                      SystemMatrixAdapter& mat, Data& rhs,  
                      const Data& d, const Data& y) const  
841  {  {
842     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
843     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,  
844                    mat.getFinley_SystemMatrix(),     escriptDataC _rhs=rhs.getDataC();
845                    &(rhs.getDataC()),     escriptDataC _X=X.getDataC();
846                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _Y=Y.getDataC();
847                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _y=y.getDataC();
848       escriptDataC _y_contact=y_contact.getDataC();
849       escriptDataC _y_dirac=y_dirac.getDataC();
850    
851       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
852       checkFinleyError();
853    
854       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
855     checkFinleyError();     checkFinleyError();
856    
857       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
858       checkFinleyError();
859    
860       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs , 0, 0, 0, 0, 0, &_y_dirac );
861       checkFinleyError();
862    
863  }  }
864  //  //
865  // adds contact conditions as natural boundary condition into a given stiffness matrix and right hand side:  // adds PDE of second order into a transport problem
866  //  //
867  void MeshAdapter::addContactToSystem(  void MeshAdapter::addPDEToTransportProblem(
868                       SystemMatrixAdapter& mat, Data& rhs,                                             AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
869                       const Data& d_contact,const Data& y_contact) const                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,
870  {                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
871                                               const escript::Data& d, const escript::Data& y,
872                                               const escript::Data& d_contact,const escript::Data& y_contact,
873                                               const escript::Data& d_dirac, const escript::Data& y_dirac) const
874    {
875       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
876       if (tpa==0)
877       {
878        throw FinleyAdapterException("finley only supports its own transport problems.");
879       }
880    
881    
882       DataTypes::ShapeType shape;
883       source.expand();
884       escriptDataC _source=source.getDataC();
885       escriptDataC _M=M.getDataC();
886       escriptDataC _A=A.getDataC();
887       escriptDataC _B=B.getDataC();
888       escriptDataC _C=C.getDataC();
889       escriptDataC _D=D.getDataC();
890       escriptDataC _X=X.getDataC();
891       escriptDataC _Y=Y.getDataC();
892       escriptDataC _d=d.getDataC();
893       escriptDataC _y=y.getDataC();
894       escriptDataC _d_contact=d_contact.getDataC();
895       escriptDataC _y_contact=y_contact.getDataC();
896       escriptDataC _d_dirac=d_dirac.getDataC();
897       escriptDataC _y_dirac=y_dirac.getDataC();
898    
899    
900     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
901     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
902                    mat.getFinley_SystemMatrix(),  
903                    &(rhs.getDataC()),     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
904                                    &(d_contact.getDataC()),     checkFinleyError();
905                    &(y_contact.getDataC()),  
906                                    Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
907       checkFinleyError();
908    
909       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
910     checkFinleyError();     checkFinleyError();
911    
912       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
913       checkFinleyError();
914    
915       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, _tp->transport_matrix, &_source , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
916       checkFinleyError();
917    
918  }  }
919    
920  //  //
921  // interpolates data between different function spaces:  // interpolates data between different function spaces:
922  //  //
923  void MeshAdapter::interpolateOnDomain(Data& target,const Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
924  {  {
925    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
926    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
927    if (inDomain!=*this)     if (inDomain!=*this)  
928       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
929    if (targetDomain!=*this)     if (targetDomain!=*this)
930       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
931    
932    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
933    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
934       case(Nodes):     escriptDataC _in=in.getDataC();
935          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
936             case(Nodes):     case(Nodes):
937             case(ReducedDegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
938             case(DegreesOfFreedom):        case(Nodes):
939                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        case(ReducedNodes):
940                 break;        case(DegreesOfFreedom):
941             case(Elements):        case(ReducedDegreesOfFreedom):
942                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
943                 break;        break;
944             case(FaceElements):        case(Elements):
945                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        case(ReducedElements):
946                 break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
947             case(Points):        break;
948                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        case(FaceElements):
949                 break;        case(ReducedFaceElements):
950             case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
951                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
952                 break;        case(Points):
953             case(ContactElementsOne):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
954                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
955                 break;        case(ContactElementsZero):
956             default:        case(ReducedContactElementsZero):
957                 Finley_ErrorCode=TYPE_ERROR;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
958                 sprintf(Finley_ErrorMsg,"Interpolation on Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());        break;
959                 break;        case(ContactElementsOne):
960          }        case(ReducedContactElementsOne):
961          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
962       case(Elements):        break;
963          if (target.getFunctionSpace().getTypeCode()==Elements) {        default:
964             Finley_Assemble_CopyElementData(mesh->Elements,&(target.getDataC()),&(in.getDataC()));           stringstream temp;
965          } else {           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
966             Finley_ErrorCode=TYPE_ERROR;           throw FinleyAdapterException(temp.str());
967             sprintf(Finley_ErrorMsg,"No interpolation with data on elements possible.");           break;
968          }        }
969          break;        break;
970       case(FaceElements):     case(ReducedNodes):
971          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        switch(target.getFunctionSpace().getTypeCode()) {
972             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));        case(Nodes):
973          } else {        case(ReducedNodes):
974             Finley_ErrorCode=TYPE_ERROR;        case(DegreesOfFreedom):
975             sprintf(Finley_ErrorMsg,"No interpolation with data on face elements possible.");        case(ReducedDegreesOfFreedom):
976             break;        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
977         }        break;
978       case(Points):        case(Elements):
979          if (target.getFunctionSpace().getTypeCode()==Points) {        case(ReducedElements):
980             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
981          } else {        break;
982             Finley_ErrorCode=TYPE_ERROR;        case(FaceElements):
983             sprintf(Finley_ErrorMsg,"No interpolation with data on points possible.");        case(ReducedFaceElements):
984             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
985          }        break;
986          break;        case(Points):
987       case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
988       case(ContactElementsOne):        break;
989          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        case(ContactElementsZero):
990             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        case(ReducedContactElementsZero):
991          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
992             Finley_ErrorCode=TYPE_ERROR;        break;
993             sprintf(Finley_ErrorMsg,"No interpolation with data on contact elements possible.");        case(ContactElementsOne):
994             break;        case(ReducedContactElementsOne):
995          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
996          break;        break;
997       case(DegreesOfFreedom):        default:
998          switch(target.getFunctionSpace().getTypeCode()) {           stringstream temp;
999             case(ReducedDegreesOfFreedom):           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1000             case(DegreesOfFreedom):           throw FinleyAdapterException(temp.str());
1001             case(Nodes):           break;
1002                Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        }
1003                break;        break;
1004             case(Elements):     case(Elements):
1005                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Elements) {
1006                break;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1007             case(FaceElements):        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1008                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
1009                break;        } else {
1010             case(Points):           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
1011                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        }
1012                break;        break;
1013             case(ContactElementsZero):     case(ReducedElements):
1014             case(ContactElementsOne):        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1015                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1016               break;        } else {
1017             default:           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
1018               Finley_ErrorCode=TYPE_ERROR;        }
1019               sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());        break;
1020               break;     case(FaceElements):
1021          }        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
1022          break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1023       case(ReducedDegreesOfFreedom):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1024         switch(target.getFunctionSpace().getTypeCode()) {           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
1025            case(ReducedDegreesOfFreedom):        } else {
1026            case(Nodes):           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
1027               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        }
1028               break;        break;
1029            case(Elements):     case(ReducedFaceElements):
1030               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1031               break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1032            case(FaceElements):        } else {
1033               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.");
1034               break;        }
1035            case(Points):        break;
1036               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     case(Points):
1037               break;        if (target.getFunctionSpace().getTypeCode()==Points) {
1038            case(ContactElementsZero):           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1039            case(ContactElementsOne):        } else {
1040               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1041               break;        }
1042            case(DegreesOfFreedom):        break;
1043               Finley_ErrorCode=TYPE_ERROR;     case(ContactElementsZero):
1044               sprintf(Finley_ErrorMsg,"Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsOne):
1045               break;        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1046            default:           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1047               Finley_ErrorCode=TYPE_ERROR;        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1048               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);
1049               break;        } else {
1050         }           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1051         break;        }
1052       default:        break;
1053          Finley_ErrorCode=TYPE_ERROR;     case(ReducedContactElementsZero):
1054          sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",in.getFunctionSpace().getTypeCode());     case(ReducedContactElementsOne):
1055          break;        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1056    }           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1057    checkFinleyError();        } else {
1058             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1059          }
1060          break;
1061       case(DegreesOfFreedom):      
1062          switch(target.getFunctionSpace().getTypeCode()) {
1063          case(ReducedDegreesOfFreedom):
1064          case(DegreesOfFreedom):
1065          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1066          break;
1067      
1068          case(Nodes):
1069          case(ReducedNodes):
1070          if (getMPISize()>1) {
1071             escript::Data temp=escript::Data(in);
1072             temp.expand();
1073             escriptDataC _in2 = temp.getDataC();
1074             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1075          } else {
1076             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1077          }
1078          break;
1079          case(Elements):
1080          case(ReducedElements):
1081          if (getMPISize()>1) {
1082             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1083             escriptDataC _in2 = temp.getDataC();
1084             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1085          } else {
1086             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1087          }
1088          break;
1089          case(FaceElements):
1090          case(ReducedFaceElements):
1091          if (getMPISize()>1) {
1092             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1093             escriptDataC _in2 = temp.getDataC();
1094             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1095      
1096          } else {
1097             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1098          }
1099          break;
1100          case(Points):
1101          if (getMPISize()>1) {
1102             //escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1103             //escriptDataC _in2 = temp.getDataC();
1104          } else {
1105             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1106          }
1107          break;
1108          case(ContactElementsZero):
1109          case(ContactElementsOne):
1110          case(ReducedContactElementsZero):
1111          case(ReducedContactElementsOne):
1112          if (getMPISize()>1) {
1113             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1114             escriptDataC _in2 = temp.getDataC();
1115             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1116          } else {
1117             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1118          }
1119          break;
1120          default:
1121             stringstream temp;
1122             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1123             throw FinleyAdapterException(temp.str());
1124             break;
1125          }
1126          break;
1127       case(ReducedDegreesOfFreedom):
1128          switch(target.getFunctionSpace().getTypeCode()) {
1129          case(Nodes):
1130          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1131          break;
1132          case(ReducedNodes):
1133          if (getMPISize()>1) {
1134             escript::Data temp=escript::Data(in);
1135             temp.expand();
1136             escriptDataC _in2 = temp.getDataC();
1137             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1138          } else {
1139             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1140          }
1141          break;
1142          case(DegreesOfFreedom):
1143          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1144          break;
1145          case(ReducedDegreesOfFreedom):
1146          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1147          break;
1148          case(Elements):
1149          case(ReducedElements):
1150          if (getMPISize()>1) {
1151             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1152             escriptDataC _in2 = temp.getDataC();
1153             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1154          } else {
1155             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1156          }
1157          break;
1158          case(FaceElements):
1159          case(ReducedFaceElements):
1160          if (getMPISize()>1) {
1161             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1162             escriptDataC _in2 = temp.getDataC();
1163             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1164          } else {
1165             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1166          }
1167          break;
1168          case(Points):
1169          if (getMPISize()>1) {
1170             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1171             escriptDataC _in2 = temp.getDataC();
1172             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1173          } else {
1174             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1175          }
1176          break;
1177          case(ContactElementsZero):
1178          case(ContactElementsOne):
1179          case(ReducedContactElementsZero):
1180          case(ReducedContactElementsOne):
1181          if (getMPISize()>1) {
1182             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1183             escriptDataC _in2 = temp.getDataC();
1184             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1185          } else {
1186             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1187          }
1188          break;
1189          default:
1190             stringstream temp;
1191             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1192             throw FinleyAdapterException(temp.str());
1193             break;
1194          }
1195          break;
1196       default:
1197          stringstream temp;
1198          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1199          throw FinleyAdapterException(temp.str());
1200          break;
1201       }
1202       checkFinleyError();
1203  }  }
1204    
1205  //  //
1206  // copies the locations of sample points into x:  // copies the locations of sample points into x:
1207  //  //
1208  void MeshAdapter::setToX(Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1209  {  {
1210    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1211    if (argDomain!=*this)     if (argDomain!=*this)
1212       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1213    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1214    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1215    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1216       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1217    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1218       Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1219       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1220       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1221       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1222    }        // this is then interpolated onto arg:
1223    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1224       }
1225       checkFinleyError();
1226  }  }
1227    
1228  //  //
1229  // 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:
1230  //  //
1231  void MeshAdapter::setToNormal(Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1232  {  {
1233    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1234    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1235       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1236    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1237    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1238      case(Nodes):     escriptDataC _normal=normal.getDataC();
1239        Finley_ErrorCode=TYPE_ERROR;     switch(normal.getFunctionSpace().getTypeCode()) {
1240        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for nodes");     case(Nodes):
1241        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1242      case(Elements):     break;
1243        Finley_ErrorCode=TYPE_ERROR;     case(ReducedNodes):
1244        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");
1245        break;     break;
1246      case (FaceElements):     case(Elements):
1247        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1248        break;     break;
1249      case(Points):     case(ReducedElements):
1250        Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1251        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for point elements");     break;
1252        break;     case (FaceElements):
1253      case (ContactElementsOne):     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1254      case (ContactElementsZero):     break;
1255        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (ReducedFaceElements):
1256        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1257      case(DegreesOfFreedom):     break;
1258        Finley_ErrorCode=TYPE_ERROR;     case(Points):
1259        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");
1260        break;     break;
1261      case(ReducedDegreesOfFreedom):     case (ContactElementsOne):
1262        Finley_ErrorCode=TYPE_ERROR;     case (ContactElementsZero):
1263        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for reduced degrees of freedom.");     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1264        break;     break;
1265      default:     case (ReducedContactElementsOne):
1266        Finley_ErrorCode=TYPE_ERROR;     case (ReducedContactElementsZero):
1267        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);
1268       break;
1269       case(DegreesOfFreedom):
1270       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1271       break;
1272       case(ReducedDegreesOfFreedom):
1273       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1274       break;
1275       default:
1276          stringstream temp;
1277          temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1278          throw FinleyAdapterException(temp.str());
1279        break;        break;
1280    }     }
1281    checkFinleyError();     checkFinleyError();
1282  }  }
1283    
1284  //  //
1285  // interpolates data to other domain:  // interpolates data to other domain:
1286  //  //
1287  void MeshAdapter::interpolateACross(Data& target,const Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1288  {  {
1289    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1290    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1291       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1292          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1293    Finley_ErrorCode=SYSTEM_ERROR;  
1294    sprintf(Finley_ErrorMsg,"Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
   checkFinleyError();  
1295  }  }
1296    
1297  //  //
1298  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1299  //  //
1300  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1301  {  {
1302    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1303    if (argDomain!=*this)     if (argDomain!=*this)
1304       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1305    
1306    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1307    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1308       case(Nodes):     escriptDataC _temp;
1309          Finley_ErrorCode=TYPE_ERROR;     escript::Data temp;
1310          sprintf(Finley_ErrorMsg,"Integral of data on nodes is not supported.");     escriptDataC _arg=arg.getDataC();
1311          break;     switch(arg.getFunctionSpace().getTypeCode()) {
1312       case(Elements):     case(Nodes):
1313          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     temp=escript::Data( arg, escript::function(*this) );
1314          break;     _temp=temp.getDataC();
1315       case(FaceElements):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1316          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     break;
1317          break;     case(ReducedNodes):
1318       case(Points):     temp=escript::Data( arg, escript::function(*this) );
1319          Finley_ErrorCode=TYPE_ERROR;     _temp=temp.getDataC();
1320          sprintf(Finley_ErrorMsg,"Integral of data on points is not supported.");     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1321          break;     break;
1322       case(ContactElementsZero):     case(Elements):
1323          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1324          break;     break;
1325       case(ContactElementsOne):     case(ReducedElements):
1326          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1327          break;     break;
1328       case(DegreesOfFreedom):     case(FaceElements):
1329          Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1330          sprintf(Finley_ErrorMsg,"Integral of data on degrees of freedom is not supported.");     break;
1331          break;     case(ReducedFaceElements):
1332       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1333          Finley_ErrorCode=TYPE_ERROR;     break;
1334          sprintf(Finley_ErrorMsg,"Integral of data on reduced degrees of freedom is not supported.");     case(Points):
1335          break;     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1336       default:     break;
1337          Finley_ErrorCode=TYPE_ERROR;     case(ContactElementsZero):
1338          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]);
1339          break;     break;
1340    }     case(ReducedContactElementsZero):
1341    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1342       break;
1343       case(ContactElementsOne):
1344       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1345       break;
1346       case(ReducedContactElementsOne):
1347       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1348       break;
1349       case(DegreesOfFreedom):
1350       temp=escript::Data( arg, escript::function(*this) );
1351       _temp=temp.getDataC();
1352       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1353       break;
1354       case(ReducedDegreesOfFreedom):
1355       temp=escript::Data( arg, escript::function(*this) );
1356       _temp=temp.getDataC();
1357       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1358       break;
1359       default:
1360          stringstream temp;
1361          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1362          throw FinleyAdapterException(temp.str());
1363          break;
1364       }
1365       checkFinleyError();
1366       blocktimer_increment("integrate()", blocktimer_start);
1367  }  }
1368    
1369  //  //
1370  // calculates the gradient of arg:  // calculates the gradient of arg:
1371  //  //
1372  void MeshAdapter::setToGradient(Data& grad,const Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1373  {  {
1374    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1375    if (argDomain!=*this)     if (argDomain!=*this)
1376      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1377    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1378    if (gradDomain!=*this)     if (gradDomain!=*this)
1379       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1380    
1381    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1382    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1383         case(Nodes):     escriptDataC nodeDataC;
1384            Finley_ErrorCode=TYPE_ERROR;     escript::Data temp;
1385            sprintf(Finley_ErrorMsg,"Gradient at nodes is not supported.");     if (getMPISize()>1) {
1386            break;        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1387         case(Elements):           temp=escript::Data( arg,  continuousFunction(*this) );
1388            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1389            break;        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1390         case(FaceElements):           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1391            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1392            break;        } else {
1393         case(Points):           nodeDataC = arg.getDataC();
1394            Finley_ErrorCode=TYPE_ERROR;        }
1395            sprintf(Finley_ErrorMsg,"Gradient at points is not supported.");     } else {
1396            break;        nodeDataC = arg.getDataC();
1397         case(ContactElementsZero):     }
1398            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     switch(grad.getFunctionSpace().getTypeCode()) {
1399            break;     case(Nodes):
1400         case(ContactElementsOne):     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1401            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     break;
1402            break;     case(ReducedNodes):
1403         case(DegreesOfFreedom):     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1404            Finley_ErrorCode=TYPE_ERROR;     break;
1405            sprintf(Finley_ErrorMsg,"Gradient at degrees of freedom is not supported.");     case(Elements):
1406            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1407         case(ReducedDegreesOfFreedom):     break;
1408            Finley_ErrorCode=TYPE_ERROR;     case(ReducedElements):
1409            sprintf(Finley_ErrorMsg,"Gradient at reduced degrees of freedom is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1410            break;     break;
1411         default:     case(FaceElements):
1412            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1413            sprintf(Finley_ErrorMsg,"Gradient: Finley does not know anything about function space type %d",arg.getFunctionSpace().getTypeCode());     break;
1414            break;     case(ReducedFaceElements):
1415    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1416    checkFinleyError();     break;
1417       case(Points):
1418       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1419       break;
1420       case(ContactElementsZero):
1421       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1422       break;
1423       case(ReducedContactElementsZero):
1424       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1425       break;
1426       case(ContactElementsOne):
1427       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1428       break;
1429       case(ReducedContactElementsOne):
1430       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1431       break;
1432       case(DegreesOfFreedom):
1433       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1434       break;
1435       case(ReducedDegreesOfFreedom):
1436       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1437       break;
1438       default:
1439          stringstream temp;
1440          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1441          throw FinleyAdapterException(temp.str());
1442          break;
1443       }
1444       checkFinleyError();
1445  }  }
1446    
1447  //  //
1448  // returns the size of elements:  // returns the size of elements:
1449  //  //
1450  void MeshAdapter::setToSize(Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1451  {  {
1452    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1453    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1454    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1455         case(Nodes):     case(Nodes):
1456            Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1457            sprintf(Finley_ErrorMsg,"Size of nodes is not supported.");     break;
1458            break;     case(ReducedNodes):
1459         case(Elements):     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1460            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     break;
1461            break;     case(Elements):
1462         case(FaceElements):     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1463            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     break;
1464            break;     case(ReducedElements):
1465         case(Points):     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1466            Finley_ErrorCode=TYPE_ERROR;     break;
1467            sprintf(Finley_ErrorMsg,"Size of point elements is not supported.");     case(FaceElements):
1468            break;     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1469         case(ContactElementsZero):     break;
1470         case(ContactElementsOne):     case(ReducedFaceElements):
1471            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1472            break;     break;
1473         case(DegreesOfFreedom):     case(Points):
1474            Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1475            sprintf(Finley_ErrorMsg,"Size of degrees of freedom is not supported.");     break;
1476            break;     case(ContactElementsZero):
1477         case(ReducedDegreesOfFreedom):     case(ContactElementsOne):
1478            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1479            sprintf(Finley_ErrorMsg,"Size of reduced degrees of freedom is not supported.");     break;
1480            break;     case(ReducedContactElementsZero):
1481         default:     case(ReducedContactElementsOne):
1482            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1483            sprintf(Finley_ErrorMsg,"Element size: Finley does not know anything about function space type %d",size.getFunctionSpace().getTypeCode());     break;
1484            break;     case(DegreesOfFreedom):
1485    }     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1486    checkFinleyError();     break;
1487       case(ReducedDegreesOfFreedom):
1488       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1489       break;
1490       default:
1491          stringstream temp;
1492          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1493          throw FinleyAdapterException(temp.str());
1494          break;
1495       }
1496       checkFinleyError();
1497  }  }
1498  // sets the location of nodes:  
1499  void MeshAdapter::setNewX(const Data& new_x)  //
1500    // sets the location of nodes
1501    //
1502    void MeshAdapter::setNewX(const escript::Data& new_x)
1503  {  {
1504    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1505    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1506    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1507       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1508    Finley_NodeFile_setCoordinates(mesh->Nodes,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1509    checkFinleyError();     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1510  }         tmp = new_x.getDataC();
1511  // saves a data array in openDX format:         Finley_Mesh_setCoordinates(mesh,&tmp);
1512  void MeshAdapter::saveDX(const std::string& filename,const Data& arg) const     } else {
1513  {         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1514    Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),&(arg.getDataC()));         tmp = new_x_inter.getDataC();
1515    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1516  }     }
1517  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:     checkFinleyError();
1518  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  }
1519                        const int row_blocksize,  
1520                        const escript::FunctionSpace& row_functionspace,  //
1521                        const int column_blocksize,  // Helper for the save* methods. Extracts optional data variable names and the
1522                        const escript::FunctionSpace& column_functionspace,  // corresponding pointers from python dictionary. Caller must free arrays.
1523                        const int type,  //
1524                        const bool sym) const  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1525  {  {
1526      int reduceRowOrder=0;     numData = boost::python::extract<int>(arg.attr("__len__")());
1527      int reduceColOrder=0;     /* win32 refactor */
1528      // is the domain right?     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1529      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1530      if (row_domain!=*this)     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1531            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");  
1532      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     boost::python::list keys=arg.keys();
1533      if (col_domain!=*this)     for (int i=0; i<numData; ++i) {
1534            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");        string n=boost::python::extract<string>(keys[i]);
1535      // is the function space type right        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1536      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1537          reduceRowOrder=0;           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1538      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {        data[i] = d.getDataC();
1539          reduceRowOrder=1;        dataPtr[i] = &(data[i]);
1540      } else {        names[i] = TMPMEMALLOC(n.length()+1, char);
1541          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        strcpy(names[i], n.c_str());
1542       }
1543    }
1544    
1545    //
1546    // saves mesh and optionally data arrays in openDX format
1547    //
1548    void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1549    {
1550       int num_data;
1551       char **names;
1552       escriptDataC *data;
1553       escriptDataC **ptr_data;
1554    
1555       extractArgsFromDict(arg, num_data, names, data, ptr_data);
1556       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1557       checkFinleyError();
1558    
1559       /* win32 refactor */
1560       TMPMEMFREE(data);
1561       TMPMEMFREE(ptr_data);
1562       for(int i=0; i<num_data; i++)
1563       {
1564          TMPMEMFREE(names[i]);
1565       }
1566       TMPMEMFREE(names);
1567    
1568       return;
1569    }
1570    
1571    //
1572    // saves mesh and optionally data arrays in VTK format
1573    //
1574    void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1575    {
1576        boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1577        pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1578                  metadata, metadata_schema, arg);
1579    }
1580    
1581    bool MeshAdapter::ownSample(int fs_code, index_t id) const
1582    {
1583    #ifdef ESYS_MPI
1584        index_t myFirstNode=0, myLastNode=0, k=0;
1585        index_t* globalNodeIndex=0;
1586        Finley_Mesh* mesh_p=m_finleyMesh.get();
1587        if (fs_code == FINLEY_REDUCED_NODES)
1588        {
1589        myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1590        myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1591        globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1592      }      }
1593      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      else
1594          reduceColOrder=0;      {
1595      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1596          reduceColOrder=1;      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1597      } else {      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
         throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
1598      }      }
1599      // generate matrix:      k=globalNodeIndex[id];
1600      Finley_SystemMatrix* fsystemMatrix=Finley_SystemMatrix_alloc(getFinley_Mesh(),type,sym?1:0,      return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1601                                                                   row_blocksize,reduceRowOrder,  #endif
1602                                                                   column_blocksize,reduceColOrder);      return true;
1603      checkFinleyError();  }
1604      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1605    
1606    
1607    //
1608    // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1609    //
1610    ASM_ptr MeshAdapter::newSystemMatrix(
1611                                                     const int row_blocksize,
1612                                                     const escript::FunctionSpace& row_functionspace,
1613                                                     const int column_blocksize,
1614                                                     const escript::FunctionSpace& column_functionspace,
1615                                                     const int type) const
1616    {
1617       int reduceRowOrder=0;
1618       int reduceColOrder=0;
1619       // is the domain right?
1620       const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1621       if (row_domain!=*this)
1622          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1623       const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1624       if (col_domain!=*this)
1625          throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1626       // is the function space type right
1627       if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1628          reduceRowOrder=0;
1629       } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1630          reduceRowOrder=1;
1631       } else {
1632          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1633       }
1634       if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1635          reduceColOrder=0;
1636       } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1637          reduceColOrder=1;
1638       } else {
1639          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1640       }
1641       // generate matrix:
1642    
1643       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1644       checkFinleyError();
1645       Paso_SystemMatrix* fsystemMatrix;
1646       int trilinos = 0;
1647       if (trilinos) {
1648    #ifdef TRILINOS
1649          /* Allocation Epetra_VrbMatrix here */
1650    #endif
1651       }
1652       else {
1653          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1654       }
1655       checkPasoError();
1656       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1657       SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1658       return ASM_ptr(sma);
1659    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1660    }
1661    
1662    //
1663    // creates a TransportProblemAdapter
1664    //
1665    ATP_ptr MeshAdapter::newTransportProblem(
1666                                                             const bool useBackwardEuler,
1667                                                             const int blocksize,
1668                                                             const escript::FunctionSpace& functionspace,
1669                                                             const int type) const
1670    {
1671       int reduceOrder=0;
1672       // is the domain right?
1673       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1674       if (domain!=*this)
1675          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1676       // is the function space type right
1677       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1678          reduceOrder=0;
1679       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1680          reduceOrder=1;
1681       } else {
1682          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1683       }
1684       // generate matrix:
1685    
1686       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1687       checkFinleyError();
1688       Paso_TransportProblem* transportProblem;
1689       transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);
1690       checkPasoError();
1691       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1692       TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1693       return ATP_ptr(tpa);
1694    //   return TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1695  }  }
1696    
1697  //  //
1698  // vtkObject MeshAdapter::createVtkObject() const  // vtkObject MeshAdapter::createVtkObject() const
1699  // TODO:  // TODO:
1700  //  //
1701    
1702  //  //
1703  // 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:
1704  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1705  {  {
1706    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1707         case(Nodes):     case(Nodes):
1708         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1709         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1710       return false;
1711       break;
1712       case(Elements):
1713       case(FaceElements):
1714       case(Points):
1715       case(ContactElementsZero):
1716       case(ContactElementsOne):
1717       case(ReducedElements):
1718       case(ReducedFaceElements):
1719       case(ReducedContactElementsZero):
1720       case(ReducedContactElementsOne):
1721       return true;
1722       break;
1723       default:
1724          stringstream temp;
1725          temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1726          throw FinleyAdapterException(temp.str());
1727          break;
1728       }
1729       checkFinleyError();
1730       return false;
1731    }
1732    
1733    bool
1734    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1735    {
1736       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1737        class 1: DOF <-> Nodes
1738        class 2: ReducedDOF <-> ReducedNodes
1739        class 3: Points
1740        class 4: Elements
1741        class 5: ReducedElements
1742        class 6: FaceElements
1743        class 7: ReducedFaceElements
1744        class 8: ContactElementZero <-> ContactElementOne
1745        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1746    
1747       There is also a set of lines. Interpolation is possible down a line but not between lines.
1748       class 1 and 2 belong to all lines so aren't considered.
1749        line 0: class 3
1750        line 1: class 4,5
1751        line 2: class 6,7
1752        line 3: class 8,9
1753    
1754       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1755       eg hasnodes is true if we have at least one instance of Nodes.
1756       */
1757        if (fs.empty())
1758        {
1759            return false;
1760        }
1761        vector<int> hasclass(10);
1762        vector<int> hasline(4);
1763        bool hasnodes=false;
1764        bool hasrednodes=false;
1765        bool hascez=false;
1766        bool hasrcez=false;
1767        for (int i=0;i<fs.size();++i)
1768        {
1769        switch(fs[i])
1770        {
1771        case(Nodes):   hasnodes=true;   // no break is deliberate
1772        case(DegreesOfFreedom):
1773            hasclass[1]=1;
1774            break;
1775        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1776        case(ReducedDegreesOfFreedom):
1777            hasclass[2]=1;
1778            break;
1779        case(Points):
1780            hasline[0]=1;
1781            hasclass[3]=1;
1782            break;
1783        case(Elements):
1784            hasclass[4]=1;
1785            hasline[1]=1;
1786            break;
1787        case(ReducedElements):
1788            hasclass[5]=1;
1789            hasline[1]=1;
1790            break;
1791        case(FaceElements):
1792            hasclass[6]=1;
1793            hasline[2]=1;
1794            break;
1795        case(ReducedFaceElements):
1796            hasclass[7]=1;
1797            hasline[2]=1;
1798            break;
1799        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1800        case(ContactElementsOne):
1801            hasclass[8]=1;
1802            hasline[3]=1;
1803            break;
1804        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1805        case(ReducedContactElementsOne):
1806            hasclass[9]=1;
1807            hasline[3]=1;
1808            break;
1809        default:
1810            return false;
1811        }
1812        }
1813        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1814        // fail if we have more than one leaf group
1815    
1816        if (totlines>1)
1817        {
1818        return false;   // there are at least two branches we can't interpolate between
1819        }
1820        else if (totlines==1)
1821        {
1822        if (hasline[0]==1)      // we have points
1823        {
1824            resultcode=Points;
1825        }
1826        else if (hasline[1]==1)
1827        {
1828            if (hasclass[5]==1)
1829            {
1830            resultcode=ReducedElements;
1831            }
1832            else
1833            {
1834            resultcode=Elements;
1835            }
1836        }
1837        else if (hasline[2]==1)
1838        {
1839            if (hasclass[7]==1)
1840            {
1841            resultcode=ReducedFaceElements;
1842            }
1843            else
1844            {
1845            resultcode=FaceElements;
1846            }
1847        }
1848        else    // so we must be in line3
1849        {
1850            if (hasclass[9]==1)
1851            {
1852            // need something from class 9
1853            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1854            }
1855            else
1856            {
1857            // something from class 8
1858            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1859            }
1860        }
1861        }
1862        else    // totlines==0
1863        {
1864        if (hasclass[2]==1)
1865        {
1866            // something from class 2
1867            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1868        }
1869        else
1870        {   // something from class 1
1871            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1872        }
1873        }
1874        return true;
1875    }
1876    
1877    bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1878    {
1879       switch(functionSpaceType_source) {
1880       case(Nodes):
1881        switch(functionSpaceType_target) {
1882        case(Nodes):
1883        case(ReducedNodes):
1884        case(ReducedDegreesOfFreedom):
1885        case(DegreesOfFreedom):
1886        case(Elements):
1887        case(ReducedElements):
1888        case(FaceElements):
1889        case(ReducedFaceElements):
1890        case(Points):
1891        case(ContactElementsZero):
1892        case(ReducedContactElementsZero):
1893        case(ContactElementsOne):
1894        case(ReducedContactElementsOne):
1895        return true;
1896        default:
1897              stringstream temp;
1898              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1899              throw FinleyAdapterException(temp.str());
1900       }
1901       break;
1902       case(ReducedNodes):
1903        switch(functionSpaceType_target) {
1904        case(ReducedNodes):
1905        case(ReducedDegreesOfFreedom):
1906        case(Elements):
1907        case(ReducedElements):
1908        case(FaceElements):
1909        case(ReducedFaceElements):
1910        case(Points):
1911        case(ContactElementsZero):
1912        case(ReducedContactElementsZero):
1913        case(ContactElementsOne):
1914        case(ReducedContactElementsOne):
1915        return true;
1916        case(Nodes):
1917        case(DegreesOfFreedom):
1918        return false;
1919        default:
1920            stringstream temp;
1921            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1922            throw FinleyAdapterException(temp.str());
1923       }
1924       break;
1925       case(Elements):
1926        if (functionSpaceType_target==Elements) {
1927          return true;
1928        } else if (functionSpaceType_target==ReducedElements) {
1929          return true;
1930            } else {
1931            return false;            return false;
1932            }
1933       case(ReducedElements):
1934        if (functionSpaceType_target==ReducedElements) {
1935          return true;
1936        } else {
1937              return false;
1938        }
1939       case(FaceElements):
1940        if (functionSpaceType_target==FaceElements) {
1941                return true;
1942        } else if (functionSpaceType_target==ReducedFaceElements) {
1943                return true;
1944        } else {
1945                return false;
1946        }
1947       case(ReducedFaceElements):
1948        if (functionSpaceType_target==ReducedFaceElements) {
1949                return true;
1950        } else {
1951            return false;
1952        }
1953       case(Points):
1954        if (functionSpaceType_target==Points) {
1955                return true;
1956        } else {
1957                return false;
1958        }
1959       case(ContactElementsZero):
1960       case(ContactElementsOne):
1961        if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1962                return true;
1963        } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1964                return true;
1965        } else {
1966                return false;
1967        }
1968       case(ReducedContactElementsZero):
1969       case(ReducedContactElementsOne):
1970        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1971                return true;
1972        } else {
1973                return false;
1974        }
1975       case(DegreesOfFreedom):
1976        switch(functionSpaceType_target) {
1977        case(ReducedDegreesOfFreedom):
1978        case(DegreesOfFreedom):
1979        case(Nodes):
1980        case(ReducedNodes):
1981        case(Elements):
1982        case(ReducedElements):
1983        case(Points):
1984        case(FaceElements):
1985        case(ReducedFaceElements):
1986        case(ContactElementsZero):
1987        case(ReducedContactElementsZero):
1988        case(ContactElementsOne):
1989        case(ReducedContactElementsOne):
1990        return true;
1991        default:
1992            stringstream temp;
1993            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1994            throw FinleyAdapterException(temp.str());
1995        }
1996        break;
1997       case(ReducedDegreesOfFreedom):
1998       switch(functionSpaceType_target) {
1999        case(ReducedDegreesOfFreedom):
2000        case(ReducedNodes):
2001        case(Elements):
2002        case(ReducedElements):
2003        case(FaceElements):
2004        case(ReducedFaceElements):
2005        case(Points):
2006        case(ContactElementsZero):
2007        case(ReducedContactElementsZero):
2008        case(ContactElementsOne):
2009        case(ReducedContactElementsOne):
2010        return true;
2011        case(Nodes):
2012        case(DegreesOfFreedom):
2013        return false;
2014        default:
2015            stringstream temp;
2016            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
2017            throw FinleyAdapterException(temp.str());
2018        }
2019        break;
2020       default:
2021          stringstream temp;
2022          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
2023          throw FinleyAdapterException(temp.str());
2024          break;
2025       }
2026       checkFinleyError();
2027       return false;
2028    }
2029    
2030    bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
2031    {
2032       return false;
2033    }
2034    
2035    bool MeshAdapter::operator==(const AbstractDomain& other) const
2036    {
2037       const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2038       if (temp!=0) {
2039          return (m_finleyMesh==temp->m_finleyMesh);
2040       } else {
2041          return false;
2042       }
2043    }
2044    
2045    bool MeshAdapter::operator!=(const AbstractDomain& other) const
2046    {
2047       return !(operator==(other));
2048    }
2049    
2050    int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2051    {
2052       Finley_Mesh* mesh=m_finleyMesh.get();
2053       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2054       checkPasoError();
2055       return out;
2056    }
2057    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2058    {
2059       Finley_Mesh* mesh=m_finleyMesh.get();
2060       int out=Paso_TransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2061       checkPasoError();
2062       return out;
2063    }
2064    
2065    escript::Data MeshAdapter::getX() const
2066    {
2067       return continuousFunction(*this).getX();
2068    }
2069    
2070    escript::Data MeshAdapter::getNormal() const
2071    {
2072       return functionOnBoundary(*this).getNormal();
2073    }
2074    
2075    escript::Data MeshAdapter::getSize() const
2076    {
2077       return escript::function(*this).getSize();
2078    }
2079    
2080    const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2081    {
2082       int *out = NULL;
2083       Finley_Mesh* mesh=m_finleyMesh.get();
2084       switch (functionSpaceType) {
2085       case(Nodes):
2086       out=mesh->Nodes->Id;
2087       break;
2088       case(ReducedNodes):
2089       out=mesh->Nodes->reducedNodesId;
2090       break;
2091       case(Elements):
2092       out=mesh->Elements->Id;
2093       break;
2094       case(ReducedElements):
2095       out=mesh->Elements->Id;
2096       break;
2097       case(FaceElements):
2098       out=mesh->FaceElements->Id;
2099       break;
2100       case(ReducedFaceElements):
2101       out=mesh->FaceElements->Id;
2102       break;
2103       case(Points):
2104       out=mesh->Points->Id;
2105       break;
2106       case(ContactElementsZero):
2107       out=mesh->ContactElements->Id;
2108       break;
2109       case(ReducedContactElementsZero):
2110       out=mesh->ContactElements->Id;
2111       break;
2112       case(ContactElementsOne):
2113       out=mesh->ContactElements->Id;
2114       break;
2115       case(ReducedContactElementsOne):
2116       out=mesh->ContactElements->Id;
2117       break;
2118       case(DegreesOfFreedom):
2119       out=mesh->Nodes->degreesOfFreedomId;
2120       break;
2121       case(ReducedDegreesOfFreedom):
2122       out=mesh->Nodes->reducedDegreesOfFreedomId;
2123       break;
2124       default:
2125          stringstream temp;
2126          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2127          throw FinleyAdapterException(temp.str());
2128          break;
2129       }
2130       return out;
2131    }
2132    int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2133    {
2134       int out=0;
2135       Finley_Mesh* mesh=m_finleyMesh.get();
2136       switch (functionSpaceType) {
2137       case(Nodes):
2138       out=mesh->Nodes->Tag[sampleNo];
2139       break;
2140       case(ReducedNodes):
2141       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2142       break;
2143       case(Elements):
2144       out=mesh->Elements->Tag[sampleNo];
2145       break;
2146       case(ReducedElements):
2147       out=mesh->Elements->Tag[sampleNo];
2148       break;
2149       case(FaceElements):
2150       out=mesh->FaceElements->Tag[sampleNo];
2151       break;
2152       case(ReducedFaceElements):
2153       out=mesh->FaceElements->Tag[sampleNo];
2154       break;
2155       case(Points):
2156       out=mesh->Points->Tag[sampleNo];
2157       break;
2158       case(ContactElementsZero):
2159       out=mesh->ContactElements->Tag[sampleNo];
2160       break;
2161       case(ReducedContactElementsZero):
2162       out=mesh->ContactElements->Tag[sampleNo];
2163       break;
2164       case(ContactElementsOne):
2165       out=mesh->ContactElements->Tag[sampleNo];
2166       break;
2167       case(ReducedContactElementsOne):
2168       out=mesh->ContactElements->Tag[sampleNo];
2169       break;
2170       case(DegreesOfFreedom):
2171       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2172       break;
2173       case(ReducedDegreesOfFreedom):
2174       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2175       break;
2176       default:
2177          stringstream temp;
2178          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2179          throw FinleyAdapterException(temp.str());
2180          break;
2181       }
2182       return out;
2183    }
2184    
2185    
2186    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
2187    {
2188       Finley_Mesh* mesh=m_finleyMesh.get();
2189       escriptDataC tmp=mask.getDataC();
2190       switch(functionSpaceType) {
2191       case(Nodes):
2192       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2193       break;
2194       case(ReducedNodes):
2195       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2196       break;
2197       case(DegreesOfFreedom):
2198       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2199       break;
2200       case(ReducedDegreesOfFreedom):
2201       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2202       break;
2203       case(Elements):
2204       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2205       break;
2206       case(ReducedElements):
2207       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2208       break;
2209       case(FaceElements):
2210       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2211       break;
2212       case(ReducedFaceElements):
2213       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2214       break;
2215       case(Points):
2216       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2217       break;
2218       case(ContactElementsZero):
2219       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2220       break;
2221       case(ReducedContactElementsZero):
2222       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2223       break;
2224       case(ContactElementsOne):
2225       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2226       break;
2227       case(ReducedContactElementsOne):
2228       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2229       break;
2230       default:
2231          stringstream temp;
2232          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2233          throw FinleyAdapterException(temp.str());
2234       }
2235       checkFinleyError();
2236       return;
2237    }
2238    
2239    void MeshAdapter::setTagMap(const string& name,  int tag)
2240    {
2241       Finley_Mesh* mesh=m_finleyMesh.get();
2242       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2243       checkPasoError();
2244       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2245    }
2246    
2247    int MeshAdapter::getTag(const string& name) const
2248    {
2249       Finley_Mesh* mesh=m_finleyMesh.get();
2250       int tag=0;
2251       tag=Finley_Mesh_getTag(mesh, name.c_str());
2252       checkPasoError();
2253       // throwStandardException("MeshAdapter::getTag is not implemented.");
2254       return tag;
2255    }
2256    
2257    bool MeshAdapter::isValidTagName(const string& name) const
2258    {
2259       Finley_Mesh* mesh=m_finleyMesh.get();
2260       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2261    }
2262    
2263    string MeshAdapter::showTagNames() const
2264    {
2265       stringstream temp;
2266       Finley_Mesh* mesh=m_finleyMesh.get();
2267       Finley_TagMap* tag_map=mesh->TagMap;
2268       while (tag_map) {
2269          temp << tag_map->name;
2270          tag_map=tag_map->next;
2271          if (tag_map) temp << ", ";
2272       }
2273       return temp.str();
2274    }
2275    
2276    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2277    {
2278      Finley_Mesh* mesh=m_finleyMesh.get();
2279      dim_t numTags=0;
2280      switch(functionSpaceCode) {
2281       case(Nodes):
2282              numTags=mesh->Nodes->numTagsInUse;
2283            break;            break;
2284         case(Elements):     case(ReducedNodes):
2285         case(FaceElements):            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
        case(Points):  
        case(ContactElementsZero):  
        case(ContactElementsOne):  
           return true;  
2286            break;            break;
2287         default:     case(DegreesOfFreedom):
2288            Finley_ErrorCode=TYPE_ERROR;            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
           sprintf(Finley_ErrorMsg,"Cell: Finley does not know anything about function space type %d",functionSpaceCode);  
2289            break;            break;
2290       case(ReducedDegreesOfFreedom):
2291              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2292              break;
2293       case(Elements):
2294       case(ReducedElements):
2295              numTags=mesh->Elements->numTagsInUse;
2296              break;
2297       case(FaceElements):
2298       case(ReducedFaceElements):
2299              numTags=mesh->FaceElements->numTagsInUse;
2300              break;
2301       case(Points):
2302              numTags=mesh->Points->numTagsInUse;
2303              break;
2304       case(ContactElementsZero):
2305       case(ReducedContactElementsZero):
2306       case(ContactElementsOne):
2307       case(ReducedContactElementsOne):
2308              numTags=mesh->ContactElements->numTagsInUse;
2309              break;
2310       default:
2311          stringstream temp;
2312          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2313          throw FinleyAdapterException(temp.str());
2314    }    }
2315    checkFinleyError();    return numTags;
   return false;  
2316  }  }
2317  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  
2318    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2319  {  {
2320    switch(functionSpaceType_source) {    Finley_Mesh* mesh=m_finleyMesh.get();
2321       case(Nodes):    index_t* tags=NULL;
2322          switch(functionSpaceType_target) {    switch(functionSpaceCode) {
2323             case(Nodes):     case(Nodes):
2324             case(ReducedDegreesOfFreedom):            tags=mesh->Nodes->tagsInUse;
2325             case(DegreesOfFreedom):            break;
2326             case(Elements):     case(ReducedNodes):
2327             case(FaceElements):            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2328             case(Points):            break;
2329             case(ContactElementsZero):     case(DegreesOfFreedom):
2330             case(ContactElementsOne):            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2331                 return true;            break;
2332             default:     case(ReducedDegreesOfFreedom):
2333                 Finley_ErrorCode=TYPE_ERROR;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2334                 sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_target);            break;
2335          }     case(Elements):
2336          break;     case(ReducedElements):
2337       case(Elements):            tags=mesh->Elements->tagsInUse;
2338          if (functionSpaceType_target==Elements) {            break;
2339             return true;     case(FaceElements):
2340          } else {     case(ReducedFaceElements):
2341             return false;            tags=mesh->FaceElements->tagsInUse;
2342          }            break;
2343       case(FaceElements):     case(Points):
2344          if (functionSpaceType_target==FaceElements) {            tags=mesh->Points->tagsInUse;
2345             return true;            break;
2346          } else {     case(ContactElementsZero):
2347             return false;     case(ReducedContactElementsZero):
2348          }     case(ContactElementsOne):
2349       case(Points):     case(ReducedContactElementsOne):
2350          if (functionSpaceType_target==Points) {            tags=mesh->ContactElements->tagsInUse;
2351             return true;            break;
2352          } else {     default:
2353             return false;        stringstream temp;
2354          }        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2355       case(ContactElementsZero):        throw FinleyAdapterException(temp.str());
      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);  
         }  
         break;  
      case(ReducedDegreesOfFreedom):  
        switch(functionSpaceType_target) {  
           case(ReducedDegreesOfFreedom):  
           case(Nodes):  
           case(Elements):  
           case(FaceElements):  
           case(Points):  
           case(ContactElementsZero):  
           case(ContactElementsOne):  
               return true;  
           case(DegreesOfFreedom):  
              return false;  
           default:  
              Finley_ErrorCode=TYPE_ERROR;  
              sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_target);  
        }  
        break;  
      default:  
         Finley_ErrorCode=TYPE_ERROR;  
         sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_source);  
         break;  
2356    }    }
2357    checkFinleyError();    return tags;
   return false;  
2358  }  }
2359  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  
2360    
2361    bool MeshAdapter::canTag(int functionSpaceCode) const
2362  {  {
2363      return false;    switch(functionSpaceCode) {
2364       case(Nodes):
2365       case(Elements):
2366       case(ReducedElements):
2367       case(FaceElements):
2368       case(ReducedFaceElements):
2369       case(Points):
2370       case(ContactElementsZero):
2371       case(ReducedContactElementsZero):
2372       case(ContactElementsOne):
2373       case(ReducedContactElementsOne):
2374              return true;
2375       case(ReducedNodes):
2376       case(DegreesOfFreedom):
2377       case(ReducedDegreesOfFreedom):
2378          return false;
2379       default:
2380        return false;
2381      }
2382  }  }
2383  bool MeshAdapter::operator==(const MeshAdapter& other) const  
2384    AbstractDomain::StatusType MeshAdapter::getStatus() const
2385  {  {
2386    return (m_finleyMesh==other.m_finleyMesh);    Finley_Mesh* mesh=m_finleyMesh.get();
2387      return Finley_Mesh_getStatus(mesh);
2388  }  }
2389    
2390  bool MeshAdapter::operator!=(const MeshAdapter& other) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2391  {  {
2392    return !operator==(other);    
2393      Finley_Mesh* mesh=m_finleyMesh.get();
2394      int order =-1;
2395      switch(functionSpaceCode) {
2396       case(Nodes):
2397       case(DegreesOfFreedom):
2398              order=mesh->approximationOrder;
2399              break;
2400       case(ReducedNodes):
2401       case(ReducedDegreesOfFreedom):
2402              order=mesh->reducedApproximationOrder;
2403              break;
2404       case(Elements):
2405       case(FaceElements):
2406       case(Points):
2407       case(ContactElementsZero):
2408       case(ContactElementsOne):
2409              order=mesh->integrationOrder;
2410              break;
2411       case(ReducedElements):
2412       case(ReducedFaceElements):
2413       case(ReducedContactElementsZero):
2414       case(ReducedContactElementsOne):
2415              order=mesh->reducedIntegrationOrder;
2416              break;
2417       default:
2418          stringstream temp;
2419          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2420          throw FinleyAdapterException(temp.str());
2421      }
2422      return order;
2423    }
2424    
2425    bool MeshAdapter::supportsContactElements() const
2426    {
2427      return true;
2428  }  }
2429  // bool MeshAdapter::operator==(const AbstractDomain& other) const  
2430  // {  ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2431    // try {  {
2432      // const MeshAdapter& ref = dynamic_cast<const MeshAdapter&>(other);    m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2433      // return (operator==(ref));  }
2434    // }  
2435    // catch (bad_cast) {  ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2436      // return false;  {
2437    // }    Finley_ReferenceElementSet_dealloc(m_refSet);
2438  // }  }
2439    
2440    void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2441    {
2442          const int dim = getDim();
2443          int numPoints=boost::python::extract<int>(points.attr("__len__")());
2444          int numTags=boost::python::extract<int>(tags.attr("__len__")());
2445          Finley_Mesh* mesh=m_finleyMesh.get();
2446          
2447          if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2448         throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2449          
2450          double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2451          int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2452          
2453          for (int i=0;i<numPoints;++i) {
2454           int tag_id=-1;
2455           int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2456           if  ( numComps !=   dim ) {
2457                   stringstream temp;          
2458                   temp << "Error - illegal number of components " << numComps << " for point " << i;              
2459                   throw FinleyAdapterException(temp.str());
2460           }
2461           points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2462           if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2463           if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2464          
2465           if ( numTags > 0) {
2466                  boost::python::extract<string> ex_str(tags[i]);
2467              if  ( ex_str.check() ) {
2468                  tag_id=getTag( ex_str());
2469              } else {
2470                   boost::python::extract<int> ex_int(tags[i]);
2471                   if ( ex_int.check() ) {
2472                       tag_id=ex_int();
2473                   } else {
2474                    stringstream temp;          
2475                        temp << "Error - unable to extract tag for point " << i;
2476                    throw FinleyAdapterException(temp.str());
2477                  }
2478              }
2479           }      
2480               tags_ptr[i]=tag_id;
2481          }
2482          
2483          Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2484          checkPasoError();
2485          
2486          TMPMEMFREE(points_ptr);
2487          TMPMEMFREE(tags_ptr);
2488    }
2489    
2490    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2491    {  
2492        boost::python::list points =  boost::python::list();
2493        boost::python::list tags =  boost::python::list();
2494        points.append(point);
2495        tags.append(tag);
2496        addDiracPoints(points, tags);
2497    }
2498    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const
2499    {
2500            boost::python::list points =   boost::python::list();
2501            boost::python::list tags =   boost::python::list();
2502            points.append(point);
2503            tags.append(tag);
2504            addDiracPoints(points, tags);
2505    }  
2506  }  // end of namespace  }  // end of namespace

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