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

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revision 682 by robwdcock, Mon Mar 27 02:43:09 2006 UTC revision 2641 by jfenwick, Mon Aug 31 07:41:49 2009 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #include "MeshAdapter.h"  /*******************************************************
3    *
4    * Copyright (c) 2003-2009 by University of Queensland
5    * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * Licensed under the Open Software License version 3.0
10    * http://www.opensource.org/licenses/osl-3.0.php
11    *
12    *******************************************************/
13    
14    
15    #include "MeshAdapter.h"
16  #include "escript/Data.h"  #include "escript/Data.h"
17  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
18    #ifdef USE_NETCDF
19    #include <netcdfcpp.h>
20    #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25    extern "C" {
26    #include "esysUtils/blocktimer.h"
27    }
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
# Line 29  MeshAdapter::FunctionSpaceNamesMapType M Line 37  MeshAdapter::FunctionSpaceNamesMapType M
37  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
38  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
39  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
40    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
41  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
42    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
43  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
44    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
45  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
46  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
47    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
48  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52  {  {
53    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
54    //     //
55    // need to use a null_deleter as Finley_Mesh_dealloc deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
56    // for us.     // for us.
57    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
58  }  }
59    
60  //  //
# Line 49  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 62  MeshAdapter::MeshAdapter(Finley_Mesh* fi
62  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
63  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
64  {  {
65    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
66  }  }
67    
68  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
69  {  {
70    //     //
71    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
72    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
73    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
74      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
75      Finley_Mesh_dealloc(m_finleyMesh.get());     }
76      //   cout << "Finished dealloc." << endl;  }
77    }  
78    int MeshAdapter::getMPISize() const
79    {
80       return m_finleyMesh.get()->MPIInfo->size;
81    }
82    int MeshAdapter::getMPIRank() const
83    {
84       return m_finleyMesh.get()->MPIInfo->rank;
85    }
86    void MeshAdapter::MPIBarrier() const
87    {
88    #ifdef PASO_MPI
89       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
90    #endif
91       return;
92    }
93    bool MeshAdapter::onMasterProcessor() const
94    {
95       return m_finleyMesh.get()->MPIInfo->rank == 0;
96  }  }
97    
98    
99    #ifdef PASO_MPI
100      MPI_Comm
101    #else
102      unsigned int
103    #endif
104    MeshAdapter::getMPIComm() const
105    {
106    #ifdef PASO_MPI
107        return m_finleyMesh->MPIInfo->comm;
108    #else
109        return 0;
110    #endif
111    }
112    
113    
114  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
115     return m_finleyMesh.get();     return m_finleyMesh.get();
116  }  }
117    
118  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
119  {  {
120    char fName[fileName.size()+1];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
121    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
122    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
123    checkFinleyError();     checkFinleyError();
124       TMPMEMFREE(fName);
125    }
126    
127    void MeshAdapter::Print_Mesh_Info(const bool full) const
128    {
129       Finley_PrintMesh_Info(m_finleyMesh.get(), full);
130    }
131    
132    void MeshAdapter::dump(const std::string& fileName) const
133    {
134    #ifdef USE_NETCDF
135       const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
136       NcVar *ids;
137       int *int_ptr;
138       Finley_Mesh *mesh = m_finleyMesh.get();
139       Finley_TagMap* tag_map;
140       int num_Tags = 0;
141       int mpi_size             = mesh->MPIInfo->size;
142       int mpi_rank             = mesh->MPIInfo->rank;
143       int numDim               = mesh->Nodes->numDim;
144       int numNodes             = mesh->Nodes->numNodes;
145       int num_Elements         = mesh->Elements->numElements;
146       int num_FaceElements         = mesh->FaceElements->numElements;
147       int num_ContactElements      = mesh->ContactElements->numElements;
148       int num_Points           = mesh->Points->numElements;
149       int num_Elements_numNodes        = mesh->Elements->numNodes;
150       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
151       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
152    #ifdef PASO_MPI
153       MPI_Status status;
154    #endif
155    
156    /* Incoming token indicates it's my turn to write */
157    #ifdef PASO_MPI
158       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
159    #endif
160    
161       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
162                                                         mpi_size, mpi_rank);
163    
164       /* Figure out how much storage is required for tags */
165       tag_map = mesh->TagMap;
166       num_Tags = 0;
167       if (tag_map) {
168          while (tag_map) {
169             num_Tags++;
170             tag_map=tag_map->next;
171          }
172       }
173    
174       // NetCDF error handler
175       NcError err(NcError::verbose_nonfatal);
176       // Create the file.
177       NcFile dataFile(newFileName, NcFile::Replace);
178       // check if writing was successful
179       if (!dataFile.is_valid())
180          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
181    
182       // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
183       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
184          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
185       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
186          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
187       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
188          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
189       if (num_Elements>0)
190          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
191             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
192       if (num_FaceElements>0)
193          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
194             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
195       if (num_ContactElements>0)
196          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
197             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
198       if (num_Points>0)
199          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
200             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
201       if (num_Elements>0)
202          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
203             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
204       if (num_FaceElements>0)
205          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
206             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
207       if (num_ContactElements>0)
208          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
209             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
210       if (num_Tags>0)
211          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
212             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
213    
214       // Attributes: MPI size, MPI rank, Name, order, reduced_order
215       if (!dataFile.add_att("mpi_size", mpi_size) )
216          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
217       if (!dataFile.add_att("mpi_rank", mpi_rank) )
218          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
219       if (!dataFile.add_att("Name",mesh->Name) )
220          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
221       if (!dataFile.add_att("numDim",numDim) )
222          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
223       if (!dataFile.add_att("order",mesh->order) )
224          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
225       if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
226          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
227       if (!dataFile.add_att("numNodes",numNodes) )
228          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
229       if (!dataFile.add_att("num_Elements",num_Elements) )
230          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
231       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
232          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
233       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
234          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
235       if (!dataFile.add_att("num_Points",num_Points) )
236          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
237       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
238          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
239       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
240          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
241       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
242          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
243       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
244          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
245       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
246          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
247       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
248          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
249       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
250          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
251       if (!dataFile.add_att("num_Tags", num_Tags) )
252          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
253    
254       // // // // // Nodes // // // // //
255    
256       // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
257       if (numNodes>0) {
258    
259          // Nodes Id
260          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
261             throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
262          int_ptr = &mesh->Nodes->Id[0];
263          if (! (ids->put(int_ptr, numNodes)) )
264             throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
265    
266          // Nodes Tag
267          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
268             throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
269          int_ptr = &mesh->Nodes->Tag[0];
270          if (! (ids->put(int_ptr, numNodes)) )
271             throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
272    
273          // Nodes gDOF
274          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
275             throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
276          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
277          if (! (ids->put(int_ptr, numNodes)) )
278             throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
279    
280          // Nodes global node index
281          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
282             throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
283          int_ptr = &mesh->Nodes->globalNodesIndex[0];
284          if (! (ids->put(int_ptr, numNodes)) )
285             throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
286    
287          // Nodes grDof
288          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
289             throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
290          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
291          if (! (ids->put(int_ptr, numNodes)) )
292             throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
293    
294          // Nodes grNI
295          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
296             throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
297          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
298          if (! (ids->put(int_ptr, numNodes)) )
299             throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
300    
301          // Nodes Coordinates
302          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
303             throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
304          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
305             throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
306    
307          // Nodes degreesOfFreedomDistribution
308          if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
309             throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
310          int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
311          if (! (ids->put(int_ptr, mpi_size+1)) )
312             throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
313    
314          // Nodes nodeDistribution
315          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
316             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
317          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
318          if (! (ids->put(int_ptr, mpi_size+1)) )
319             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
320    
321       }
322    
323       // // // // // Elements // // // // //
324    
325       if (num_Elements>0) {
326    
327          // Elements_Id
328          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
329             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
330          int_ptr = &mesh->Elements->Id[0];
331          if (! (ids->put(int_ptr, num_Elements)) )
332             throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
333    
334          // Elements_Tag
335          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
336             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
337          int_ptr = &mesh->Elements->Tag[0];
338          if (! (ids->put(int_ptr, num_Elements)) )
339             throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
340    
341          // Elements_Owner
342          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
343             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
344          int_ptr = &mesh->Elements->Owner[0];
345          if (! (ids->put(int_ptr, num_Elements)) )
346             throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
347    
348          // Elements_Color
349          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
350             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
351          int_ptr = &mesh->Elements->Color[0];
352          if (! (ids->put(int_ptr, num_Elements)) )
353             throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
354    
355          // Elements_Nodes
356          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
357             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
358          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
359             throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
360    
361       }
362    
363       // // // // // Face_Elements // // // // //
364    
365       if (num_FaceElements>0) {
366    
367          // FaceElements_Id
368          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
369             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
370          int_ptr = &mesh->FaceElements->Id[0];
371          if (! (ids->put(int_ptr, num_FaceElements)) )
372             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
373    
374          // FaceElements_Tag
375          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
376             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
377          int_ptr = &mesh->FaceElements->Tag[0];
378          if (! (ids->put(int_ptr, num_FaceElements)) )
379             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
380    
381          // FaceElements_Owner
382          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
383             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
384          int_ptr = &mesh->FaceElements->Owner[0];
385          if (! (ids->put(int_ptr, num_FaceElements)) )
386             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
387    
388          // FaceElements_Color
389          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
390             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
391          int_ptr = &mesh->FaceElements->Color[0];
392          if (! (ids->put(int_ptr, num_FaceElements)) )
393             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
394    
395          // FaceElements_Nodes
396          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
397             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
398          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
399             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
400    
401       }
402    
403       // // // // // Contact_Elements // // // // //
404    
405       if (num_ContactElements>0) {
406    
407          // ContactElements_Id
408          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
409             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
410          int_ptr = &mesh->ContactElements->Id[0];
411          if (! (ids->put(int_ptr, num_ContactElements)) )
412             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
413    
414          // ContactElements_Tag
415          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
416             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
417          int_ptr = &mesh->ContactElements->Tag[0];
418          if (! (ids->put(int_ptr, num_ContactElements)) )
419             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
420    
421          // ContactElements_Owner
422          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
423             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
424          int_ptr = &mesh->ContactElements->Owner[0];
425          if (! (ids->put(int_ptr, num_ContactElements)) )
426             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
427    
428          // ContactElements_Color
429          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
430             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
431          int_ptr = &mesh->ContactElements->Color[0];
432          if (! (ids->put(int_ptr, num_ContactElements)) )
433             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
434    
435          // ContactElements_Nodes
436          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
437             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
438          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
439             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
440    
441       }
442    
443       // // // // // Points // // // // //
444    
445       if (num_Points>0) {
446    
447          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
448    
449          // Points_Id
450          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
451             throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
452          int_ptr = &mesh->Points->Id[0];
453          if (! (ids->put(int_ptr, num_Points)) )
454             throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
455    
456          // Points_Tag
457          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
458             throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
459          int_ptr = &mesh->Points->Tag[0];
460          if (! (ids->put(int_ptr, num_Points)) )
461             throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
462    
463          // Points_Owner
464          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
465             throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
466          int_ptr = &mesh->Points->Owner[0];
467          if (! (ids->put(int_ptr, num_Points)) )
468             throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
469    
470          // Points_Color
471          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
472             throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
473          int_ptr = &mesh->Points->Color[0];
474          if (! (ids->put(int_ptr, num_Points)) )
475             throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
476    
477          // Points_Nodes
478          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
479          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
480             throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
481          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
482             throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
483    
484       }
485    
486       // // // // // TagMap // // // // //
487    
488       if (num_Tags>0) {
489    
490          // Temp storage to gather node IDs
491          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
492          char name_temp[4096];
493    
494          /* Copy tag data into temp arrays */
495          tag_map = mesh->TagMap;
496          if (tag_map) {
497             int i = 0;
498             while (tag_map) {
499                Tags_keys[i++] = tag_map->tag_key;
500                tag_map=tag_map->next;
501             }
502          }
503    
504          // Tags_keys
505          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
506             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
507          int_ptr = &Tags_keys[0];
508          if (! (ids->put(int_ptr, num_Tags)) )
509             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
510    
511          // Tags_names_*
512          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
513          // because the NetCDF 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("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
521                tag_map=tag_map->next;
522                i++;
523             }
524          }
525    
526          TMPMEMFREE(Tags_keys);
527    
528       }
529    
530    /* Send token to next MPI process so he can take his turn */
531    #ifdef PASO_MPI
532       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
533    #endif
534    
535       // NetCDF file is closed by destructor of NcFile object
536    
537    #else
538       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
539    #endif  /* USE_NETCDF */
540       checkFinleyError();
541  }  }
542    
543  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
544  {  {
545    return "FinleyMesh";     return "FinleyMesh";
546  }  }
547    
548  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
549  {  {
550    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
551    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
552    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
553      return "Invalid function space type code.";        return "Invalid function space type code.";
554    } else {     } else {
555      return loc->second;        return loc->second;
556    }     }
557  }  }
558    
559  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
560  {  {
561    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
562    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
563    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
564  }  }
565    
566  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
567  {  {
568    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
569      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
570    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
571      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
572    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
573      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
574    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
575      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
576    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
577      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
578    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
579      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
580    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
581      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
582    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
583      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
584       m_functionSpaceTypeNames.insert
585       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
586       m_functionSpaceTypeNames.insert
587       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
588       m_functionSpaceTypeNames.insert
589       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
590       m_functionSpaceTypeNames.insert
591       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
592       m_functionSpaceTypeNames.insert
593       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
594  }  }
595    
596  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
597  {  {
598    return Nodes;     return Nodes;
599    }
600    int MeshAdapter::getReducedContinuousFunctionCode() const
601    {
602       return ReducedNodes;
603  }  }
604    
605  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
606  {  {
607    return Elements;     return Elements;
608    }
609    int MeshAdapter::getReducedFunctionCode() const
610    {
611       return ReducedElements;
612  }  }
613    
614  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
615  {  {
616    return FaceElements;     return FaceElements;
617    }
618    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
619    {
620       return ReducedFaceElements;
621  }  }
622    
623  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
624  {  {
625    return ContactElementsZero;     return ContactElementsZero;
626    }
627    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
628    {
629       return ReducedContactElementsZero;
630  }  }
631    
632  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
633  {  {
634    return ContactElementsOne;     return ContactElementsOne;
635    }
636    int MeshAdapter::getReducedFunctionOnContactOneCode() const
637    {
638       return ReducedContactElementsOne;
639  }  }
640    
641  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
642  {  {
643    return DegreesOfFreedom;     return DegreesOfFreedom;
644  }  }
645    
646  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
647  {  {
648    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
649  }  }
650    
651  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
652  {  {
653    return Points;     return Points;
654  }  }
655    
656  //  //
# Line 164  int MeshAdapter::getDiracDeltaFunctionCo Line 658  int MeshAdapter::getDiracDeltaFunctionCo
658  //  //
659  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
660  {  {
661    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     Finley_Mesh* mesh=m_finleyMesh.get();
662    checkFinleyError();     int numDim=Finley_Mesh_getDim(mesh);
663    return numDim;     checkFinleyError();
664       return numDim;
665    }
666    
667    //
668    // Return the number of data points summed across all MPI processes
669    //
670    int MeshAdapter::getNumDataPointsGlobal() const
671    {
672       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
673  }  }
674    
675  //  //
# Line 179  pair<int,int> MeshAdapter::getDataShape( Line 682  pair<int,int> MeshAdapter::getDataShape(
682     int numSamples=0;     int numSamples=0;
683     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
684     switch (functionSpaceCode) {     switch (functionSpaceCode) {
685        case(Nodes):     case(Nodes):
686             numDataPointsPerSample=1;     numDataPointsPerSample=1;
687             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
688             break;     break;
689        case(Elements):     case(ReducedNodes):
690             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
691               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
692               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
693             }     case(Elements):
694             break;     if (mesh->Elements!=NULL) {
695        case(FaceElements):        numSamples=mesh->Elements->numElements;
696             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
697                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
698                  numSamples=mesh->FaceElements->numElements;     break;
699             }     case(ReducedElements):
700             break;     if (mesh->Elements!=NULL) {
701        case(Points):        numSamples=mesh->Elements->numElements;
702             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
703               numDataPointsPerSample=1;     }
704               numSamples=mesh->Points->numElements;     break;
705             }     case(FaceElements):
706             break;     if (mesh->FaceElements!=NULL) {
707        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
708             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
709               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
710               numSamples=mesh->ContactElements->numElements;     break;
711             }     case(ReducedFaceElements):
712             break;     if (mesh->FaceElements!=NULL) {
713        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
714             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
715               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
716               numSamples=mesh->ContactElements->numElements;     break;
717             }     case(Points):
718             break;     if (mesh->Points!=NULL) {
719        case(DegreesOfFreedom):        numDataPointsPerSample=1;
720             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
721               numDataPointsPerSample=1;     }
722               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
723             }     case(ContactElementsZero):
724             break;     if (mesh->ContactElements!=NULL) {
725        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
726             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
727               numDataPointsPerSample=1;     }
728               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
729             }     case(ReducedContactElementsZero):
730             break;     if (mesh->ContactElements!=NULL) {
731        default:        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
732          stringstream temp;        numSamples=mesh->ContactElements->numElements;
733          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     }
734          throw FinleyAdapterException(temp.str());     break;
735          break;     case(ContactElementsOne):
736        }     if (mesh->ContactElements!=NULL) {
737        return pair<int,int>(numDataPointsPerSample,numSamples);        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
738          numSamples=mesh->ContactElements->numElements;
739       }
740       break;
741       case(ReducedContactElementsOne):
742       if (mesh->ContactElements!=NULL) {
743          numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
744          numSamples=mesh->ContactElements->numElements;
745       }
746       break;
747       case(DegreesOfFreedom):
748       if (mesh->Nodes!=NULL) {
749          numDataPointsPerSample=1;
750          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
751       }
752       break;
753       case(ReducedDegreesOfFreedom):
754       if (mesh->Nodes!=NULL) {
755          numDataPointsPerSample=1;
756          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
757       }
758       break;
759       default:
760          stringstream temp;
761          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
762          throw FinleyAdapterException(temp.str());
763          break;
764       }
765       return pair<int,int>(numDataPointsPerSample,numSamples);
766  }  }
767    
768  //  //
769  // 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:
770  //  //
771  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
772                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
773                       const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
774                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
775                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
776  {  {
777     Finley_Mesh* mesh=m_finleyMesh.get();     escriptDataC _rhs=rhs.getDataC();
778     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(),&(rhs.getDataC()),     escriptDataC _A  =A.getDataC();
779                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _B=B.getDataC();
780     checkFinleyError();     escriptDataC _C=C.getDataC();
781     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     escriptDataC _D=D.getDataC();
782                    mat.getPaso_SystemMatrix(),     escriptDataC _X=X.getDataC();
783                    &(rhs.getDataC()),     escriptDataC _Y=Y.getDataC();
784                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _d=d.getDataC();
785                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _y=y.getDataC();
786     checkFinleyError();     escriptDataC _d_contact=d_contact.getDataC();
787     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,     escriptDataC _y_contact=y_contact.getDataC();
788                    mat.getPaso_SystemMatrix(),  
789                    &(rhs.getDataC()),     Finley_Mesh* mesh=m_finleyMesh.get();
790                                    &(d_contact.getDataC()),  
791                    &(y_contact.getDataC()),     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
792                                    Finley_Assemble_handelShapeMissMatch_Step_out);     checkFinleyError();
793    
794       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
795       checkFinleyError();
796    
797       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
798       checkFinleyError();
799    }
800    
801    void  MeshAdapter::addPDEToLumpedSystem(
802                                            escript::Data& mat,
803                                            const escript::Data& D,
804                                            const escript::Data& d) const
805    {
806       escriptDataC _mat=mat.getDataC();
807       escriptDataC _D=D.getDataC();
808       escriptDataC _d=d.getDataC();
809    
810       Finley_Mesh* mesh=m_finleyMesh.get();
811    
812       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
813       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
814    
815     checkFinleyError();     checkFinleyError();
816  }  }
817    
818    
819  //  //
820  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
821  //  //
822  void MeshAdapter::addPDEToRHS( escript::Data& rhs,  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const
                      const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  
823  {  {
824     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
825    
826     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
827     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
828       escriptDataC _Y=Y.getDataC();
829       escriptDataC _y=y.getDataC();
830       escriptDataC _y_contact=y_contact.getDataC();
831    
832       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
833       checkFinleyError();
834    
835       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
836       checkFinleyError();
837    
838       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
839       checkFinleyError();
840    }
841    //
842    // adds PDE of second order into a transport problem
843    //
844    void MeshAdapter::addPDEToTransportProblem(
845                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
846                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
847                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
848                                               const escript::Data& d, const escript::Data& y,
849                                               const escript::Data& d_contact,const escript::Data& y_contact) const
850    {
851       DataTypes::ShapeType shape;
852       source.expand();
853       escriptDataC _source=source.getDataC();
854       escriptDataC _M=M.getDataC();
855       escriptDataC _A=A.getDataC();
856       escriptDataC _B=B.getDataC();
857       escriptDataC _C=C.getDataC();
858       escriptDataC _D=D.getDataC();
859       escriptDataC _X=X.getDataC();
860       escriptDataC _Y=Y.getDataC();
861       escriptDataC _d=d.getDataC();
862       escriptDataC _y=y.getDataC();
863       escriptDataC _d_contact=d_contact.getDataC();
864       escriptDataC _y_contact=y_contact.getDataC();
865    
866       Finley_Mesh* mesh=m_finleyMesh.get();
867       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
868    
869       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
870     checkFinleyError();     checkFinleyError();
871    
872     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->FaceElements,&(rhs.getDataC()),&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
873     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
874    
875       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
876     checkFinleyError();     checkFinleyError();
877     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  
878     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->ContactElements,&(rhs.getDataC()),&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
879     checkFinleyError();     checkFinleyError();
880  }  }
881    
# Line 288  void MeshAdapter::addPDEToRHS( escript:: Line 884  void MeshAdapter::addPDEToRHS( escript::
884  //  //
885  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
886  {  {
887    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
888    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
889    if (inDomain!=*this)     if (inDomain!=*this)  
890       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
891    if (targetDomain!=*this)     if (targetDomain!=*this)
892       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
893    
894    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
895    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
896       case(Nodes):     escriptDataC _in=in.getDataC();
897          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
898             case(Nodes):     case(Nodes):
899             case(ReducedDegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
900             case(DegreesOfFreedom):        case(Nodes):
901                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        case(ReducedNodes):
902                 break;        case(DegreesOfFreedom):
903             case(Elements):        case(ReducedDegreesOfFreedom):
904                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
905                 break;        break;
906             case(FaceElements):        case(Elements):
907                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        case(ReducedElements):
908                 break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
909             case(Points):        break;
910                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        case(FaceElements):
911                 break;        case(ReducedFaceElements):
912             case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
913                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
914                 break;        case(Points):
915             case(ContactElementsOne):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
916                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
917                 break;        case(ContactElementsZero):
918             default:        case(ReducedContactElementsZero):
919                 stringstream temp;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
920                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
921                 throw FinleyAdapterException(temp.str());        case(ContactElementsOne):
922                 break;        case(ReducedContactElementsOne):
923          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
924          break;        break;
925       case(Elements):        default:
926          if (target.getFunctionSpace().getTypeCode()==Elements) {           stringstream temp;
927             Finley_Assemble_CopyElementData(mesh->Elements,&(target.getDataC()),&(in.getDataC()));           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
928          } else {           throw FinleyAdapterException(temp.str());
929             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");           break;
930          }        }
931          break;        break;
932       case(FaceElements):     case(ReducedNodes):
933          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        switch(target.getFunctionSpace().getTypeCode()) {
934             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));        case(Nodes):
935          } else {        case(ReducedNodes):
936             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        case(DegreesOfFreedom):
937             break;        case(ReducedDegreesOfFreedom):
938         }        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
939       case(Points):        break;
940          if (target.getFunctionSpace().getTypeCode()==Points) {        case(Elements):
941             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        case(ReducedElements):
942          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
943             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        break;
944             break;        case(FaceElements):
945          }        case(ReducedFaceElements):
946          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
947       case(ContactElementsZero):        break;
948       case(ContactElementsOne):        case(Points):
949          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
950             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        break;
951          } else {        case(ContactElementsZero):
952             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        case(ReducedContactElementsZero):
953             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
954          }        break;
955          break;        case(ContactElementsOne):
956       case(DegreesOfFreedom):        case(ReducedContactElementsOne):
957          switch(target.getFunctionSpace().getTypeCode()) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
958             case(ReducedDegreesOfFreedom):        break;
959             case(DegreesOfFreedom):        default:
960             case(Nodes):           stringstream temp;
961                Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
962                break;           throw FinleyAdapterException(temp.str());
963             case(Elements):           break;
964                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        }
965                break;        break;
966             case(FaceElements):     case(Elements):
967                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Elements) {
968                break;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
969             case(Points):        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
970                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
971                break;        } else {
972             case(ContactElementsZero):           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
973             case(ContactElementsOne):        }
974                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
975               break;     case(ReducedElements):
976             default:        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
977               stringstream temp;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
978               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        } else {
979               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
980               break;        }
981          }        break;
982          break;     case(FaceElements):
983       case(ReducedDegreesOfFreedom):        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
984         switch(target.getFunctionSpace().getTypeCode()) {           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
985            case(ReducedDegreesOfFreedom):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
986               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
987               break;        } else {
988            case(Elements):           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
989               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        }
990               break;        break;
991            case(FaceElements):     case(ReducedFaceElements):
992               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
993               break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
994            case(Points):        } else {
995               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
996               break;        }
997            case(ContactElementsZero):        break;
998            case(ContactElementsOne):     case(Points):
999               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Points) {
1000               break;           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1001            case(Nodes):        } else {
1002               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1003               break;        }
1004            case(DegreesOfFreedom):        break;
1005               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsZero):
1006               break;     case(ContactElementsOne):
1007            default:        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1008               stringstream temp;           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1009               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1010               throw FinleyAdapterException(temp.str());           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1011               break;        } else {
1012         }           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1013         break;        }
1014       default:        break;
1015          stringstream temp;     case(ReducedContactElementsZero):
1016          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();     case(ReducedContactElementsOne):
1017          throw FinleyAdapterException(temp.str());        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1018          break;           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1019    }        } else {
1020    checkFinleyError();           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1021          }
1022          break;
1023       case(DegreesOfFreedom):      
1024          switch(target.getFunctionSpace().getTypeCode()) {
1025          case(ReducedDegreesOfFreedom):
1026          case(DegreesOfFreedom):
1027          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1028          break;
1029      
1030          case(Nodes):
1031          case(ReducedNodes):
1032          if (getMPISize()>1) {
1033             escript::Data temp=escript::Data(in);
1034             temp.expand();
1035             escriptDataC _in2 = temp.getDataC();
1036             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1037          } else {
1038             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1039          }
1040          break;
1041          case(Elements):
1042          case(ReducedElements):
1043          if (getMPISize()>1) {
1044             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1045             escriptDataC _in2 = temp.getDataC();
1046             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1047          } else {
1048             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1049          }
1050          break;
1051          case(FaceElements):
1052          case(ReducedFaceElements):
1053          if (getMPISize()>1) {
1054             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1055             escriptDataC _in2 = temp.getDataC();
1056             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1057      
1058          } else {
1059             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1060          }
1061          break;
1062          case(Points):
1063          if (getMPISize()>1) {
1064             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1065             escriptDataC _in2 = temp.getDataC();
1066          } else {
1067             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1068          }
1069          break;
1070          case(ContactElementsZero):
1071          case(ContactElementsOne):
1072          case(ReducedContactElementsZero):
1073          case(ReducedContactElementsOne):
1074          if (getMPISize()>1) {
1075             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1076             escriptDataC _in2 = temp.getDataC();
1077             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1078          } else {
1079             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1080          }
1081          break;
1082          default:
1083             stringstream temp;
1084             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1085             throw FinleyAdapterException(temp.str());
1086             break;
1087          }
1088          break;
1089       case(ReducedDegreesOfFreedom):
1090          switch(target.getFunctionSpace().getTypeCode()) {
1091          case(Nodes):
1092          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1093          break;
1094          case(ReducedNodes):
1095          if (getMPISize()>1) {
1096             escript::Data temp=escript::Data(in);
1097             temp.expand();
1098             escriptDataC _in2 = temp.getDataC();
1099             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1100          } else {
1101             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1102          }
1103          break;
1104          case(DegreesOfFreedom):
1105          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1106          break;
1107          case(ReducedDegreesOfFreedom):
1108          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1109          break;
1110          case(Elements):
1111          case(ReducedElements):
1112          if (getMPISize()>1) {
1113             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1114             escriptDataC _in2 = temp.getDataC();
1115             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1116          } else {
1117             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1118          }
1119          break;
1120          case(FaceElements):
1121          case(ReducedFaceElements):
1122          if (getMPISize()>1) {
1123             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1124             escriptDataC _in2 = temp.getDataC();
1125             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1126          } else {
1127             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1128          }
1129          break;
1130          case(Points):
1131          if (getMPISize()>1) {
1132             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1133             escriptDataC _in2 = temp.getDataC();
1134             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1135          } else {
1136             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1137          }
1138          break;
1139          case(ContactElementsZero):
1140          case(ContactElementsOne):
1141          case(ReducedContactElementsZero):
1142          case(ReducedContactElementsOne):
1143          if (getMPISize()>1) {
1144             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1145             escriptDataC _in2 = temp.getDataC();
1146             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1147          } else {
1148             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1149          }
1150          break;
1151          default:
1152             stringstream temp;
1153             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1154             throw FinleyAdapterException(temp.str());
1155             break;
1156          }
1157          break;
1158       default:
1159          stringstream temp;
1160          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1161          throw FinleyAdapterException(temp.str());
1162          break;
1163       }
1164       checkFinleyError();
1165  }  }
1166    
1167  //  //
# Line 429  void MeshAdapter::interpolateOnDomain(es Line 1169  void MeshAdapter::interpolateOnDomain(es
1169  //  //
1170  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1171  {  {
1172    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1173    if (argDomain!=*this)     if (argDomain!=*this)
1174       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1175    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1176    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1177    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1178       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1179    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1180       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1181       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1182       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1183       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1184    }        // this is then interpolated onto arg:
1185    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1186       }
1187       checkFinleyError();
1188  }  }
1189    
1190  //  //
# Line 450  void MeshAdapter::setToX(escript::Data& Line 1192  void MeshAdapter::setToX(escript::Data&
1192  //  //
1193  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1194  {  {
1195    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1196    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1197       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1198    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1199    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1200      case(Nodes):     escriptDataC _normal=normal.getDataC();
1201        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     switch(normal.getFunctionSpace().getTypeCode()) {
1202        break;     case(Nodes):
1203      case(Elements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1204        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     break;
1205        break;     case(ReducedNodes):
1206      case (FaceElements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1207        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     break;
1208        break;     case(Elements):
1209      case(Points):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1210        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     break;
1211        break;     case(ReducedElements):
1212      case (ContactElementsOne):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1213      case (ContactElementsZero):     break;
1214        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (FaceElements):
1215        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1216      case(DegreesOfFreedom):     break;
1217        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case (ReducedFaceElements):
1218        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1219      case(ReducedDegreesOfFreedom):     break;
1220        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(Points):
1221        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1222      default:     break;
1223       case (ContactElementsOne):
1224       case (ContactElementsZero):
1225       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1226       break;
1227       case (ReducedContactElementsOne):
1228       case (ReducedContactElementsZero):
1229       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1230       break;
1231       case(DegreesOfFreedom):
1232       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1233       break;
1234       case(ReducedDegreesOfFreedom):
1235       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1236       break;
1237       default:
1238        stringstream temp;        stringstream temp;
1239        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1240        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1241        break;        break;
1242    }     }
1243    checkFinleyError();     checkFinleyError();
1244  }  }
1245    
1246  //  //
# Line 491  void MeshAdapter::setToNormal(escript::D Line 1248  void MeshAdapter::setToNormal(escript::D
1248  //  //
1249  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1250  {  {
1251    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1252    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1253       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1254          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1255    
1256    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1257  }  }
1258    
1259  //  //
# Line 503  void MeshAdapter::interpolateACross(escr Line 1261  void MeshAdapter::interpolateACross(escr
1261  //  //
1262  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1263  {  {
1264    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1265    if (argDomain!=*this)     if (argDomain!=*this)
1266       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1267    
1268    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1269    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1270       case(Nodes):     escriptDataC _temp;
1271          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1272          break;     escriptDataC _arg=arg.getDataC();
1273       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1274          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1275          break;     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1276       case(FaceElements):     _temp=temp.getDataC();
1277          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1278          break;     break;
1279       case(Points):     case(ReducedNodes):
1280          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1281          break;     _temp=temp.getDataC();
1282       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1283          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1284          break;     case(Elements):
1285       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1286          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1287          break;     case(ReducedElements):
1288       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1289          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1290          break;     case(FaceElements):
1291       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1292          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1293          break;     case(ReducedFaceElements):
1294       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1295          stringstream temp;     break;
1296          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1297          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1298          break;     break;
1299    }     case(ContactElementsZero):
1300    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1301       break;
1302       case(ReducedContactElementsZero):
1303       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1304       break;
1305       case(ContactElementsOne):
1306       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1307       break;
1308       case(ReducedContactElementsOne):
1309       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1310       break;
1311       case(DegreesOfFreedom):
1312       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1313       _temp=temp.getDataC();
1314       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1315       break;
1316       case(ReducedDegreesOfFreedom):
1317       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1318       _temp=temp.getDataC();
1319       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1320       break;
1321       default:
1322          stringstream temp;
1323          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1324          throw FinleyAdapterException(temp.str());
1325          break;
1326       }
1327       checkFinleyError();
1328       blocktimer_increment("integrate()", blocktimer_start);
1329  }  }
1330    
1331  //  //
# Line 547  void MeshAdapter::setToIntegrals(std::ve Line 1333  void MeshAdapter::setToIntegrals(std::ve
1333  //  //
1334  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1335  {  {
1336    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1337    if (argDomain!=*this)     if (argDomain!=*this)
1338      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1339    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1340    if (gradDomain!=*this)     if (gradDomain!=*this)
1341       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1342    
1343    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1344    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1345         case(Nodes):     escriptDataC nodeDataC;
1346            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     escript::Data temp;
1347            break;     if (getMPISize()>1) {
1348         case(Elements):        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1349            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1350            break;           nodeDataC = temp.getDataC();
1351         case(FaceElements):        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1352            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1353            break;           nodeDataC = temp.getDataC();
1354         case(Points):        } else {
1355            throw FinleyAdapterException("Error - Gradient at points is not supported.");           nodeDataC = arg.getDataC();
1356            break;        }
1357         case(ContactElementsZero):     } else {
1358            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));        nodeDataC = arg.getDataC();
1359            break;     }
1360         case(ContactElementsOne):     switch(grad.getFunctionSpace().getTypeCode()) {
1361            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     case(Nodes):
1362            break;     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1363         case(DegreesOfFreedom):     break;
1364            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     case(ReducedNodes):
1365            break;     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1366         case(ReducedDegreesOfFreedom):     break;
1367            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     case(Elements):
1368            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1369         default:     break;
1370            stringstream temp;     case(ReducedElements):
1371            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1372            throw FinleyAdapterException(temp.str());     break;
1373            break;     case(FaceElements):
1374    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1375    checkFinleyError();     break;
1376       case(ReducedFaceElements):
1377       Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1378       break;
1379       case(Points):
1380       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1381       break;
1382       case(ContactElementsZero):
1383       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1384       break;
1385       case(ReducedContactElementsZero):
1386       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1387       break;
1388       case(ContactElementsOne):
1389       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1390       break;
1391       case(ReducedContactElementsOne):
1392       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1393       break;
1394       case(DegreesOfFreedom):
1395       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1396       break;
1397       case(ReducedDegreesOfFreedom):
1398       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1399       break;
1400       default:
1401          stringstream temp;
1402          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1403          throw FinleyAdapterException(temp.str());
1404          break;
1405       }
1406       checkFinleyError();
1407  }  }
1408    
1409  //  //
# Line 594  void MeshAdapter::setToGradient(escript: Line 1411  void MeshAdapter::setToGradient(escript:
1411  //  //
1412  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1413  {  {
1414    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1415    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1416    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1417         case(Nodes):     case(Nodes):
1418            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1419            break;     break;
1420         case(Elements):     case(ReducedNodes):
1421            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1422            break;     break;
1423         case(FaceElements):     case(Elements):
1424            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1425            break;     break;
1426         case(Points):     case(ReducedElements):
1427            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1428            break;     break;
1429         case(ContactElementsZero):     case(FaceElements):
1430         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1431            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1432            break;     case(ReducedFaceElements):
1433         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1434            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1435            break;     case(Points):
1436         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1437            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1438            break;     case(ContactElementsZero):
1439         default:     case(ContactElementsOne):
1440            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1441            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1442            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1443            break;     case(ReducedContactElementsOne):
1444    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1445    checkFinleyError();     break;
1446       case(DegreesOfFreedom):
1447       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1448       break;
1449       case(ReducedDegreesOfFreedom):
1450       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1451       break;
1452       default:
1453          stringstream temp;
1454          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1455          throw FinleyAdapterException(temp.str());
1456          break;
1457       }
1458       checkFinleyError();
1459  }  }
1460    
1461  // sets the location of nodes:  //
1462    // sets the location of nodes
1463    //
1464  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1465  {  {
1466    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1467    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1468    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1469       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1470    Finley_Mesh_setCoordinates(mesh,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1471    checkFinleyError();     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {
1472           tmp = new_x.getDataC();
1473           Finley_Mesh_setCoordinates(mesh,&tmp);
1474       } else {
1475           escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );
1476           tmp = new_x_inter.getDataC();
1477           Finley_Mesh_setCoordinates(mesh,&tmp);
1478       }
1479       checkFinleyError();
1480    }
1481    
1482    //
1483    // Helper for the save* methods. Extracts optional data variable names and the
1484    // corresponding pointers from python dictionary. Caller must free arrays.
1485    //
1486    void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1487    {
1488       numData = boost::python::extract<int>(arg.attr("__len__")());
1489       /* win32 refactor */
1490       names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1491       data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1492       dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1493    
1494       boost::python::list keys=arg.keys();
1495       for (int i=0; i<numData; ++i) {
1496          std::string n=boost::python::extract<std::string>(keys[i]);
1497          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1498          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1499             throw FinleyAdapterException("Error: Data must be defined on same Domain");
1500          data[i] = d.getDataC();
1501          dataPtr[i] = &(data[i]);
1502          names[i] = TMPMEMALLOC(n.length()+1, char);
1503          strcpy(names[i], n.c_str());
1504       }
1505  }  }
1506    
1507  // saves a data array in openDX format:  //
1508    // saves mesh and optionally data arrays in openDX format
1509    //
1510  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1511  {  {
1512      int MAX_namelength=256;     int num_data;
1513      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1514      char names[num_data][MAX_namelength];     escriptDataC *data;
1515      char* c_names[num_data];     escriptDataC **ptr_data;
1516      escriptDataC data[num_data];  
1517      escriptDataC* ptr_data[num_data];     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1518       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1519      boost::python::list keys=arg.keys();     checkFinleyError();
1520      for (int i=0;i<num_data;++i) {  
1521           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     /* win32 refactor */
1522           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     TMPMEMFREE(data);
1523               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     TMPMEMFREE(ptr_data);
1524           data[i]=d.getDataC();     for(int i=0; i<num_data; i++)
1525           ptr_data[i]=&(data[i]);     {
1526           std::string n=boost::python::extract<std::string>(keys[i]);        TMPMEMFREE(names[i]);
1527           c_names[i]=&(names[i][0]);     }
1528           if (n.length()>MAX_namelength-1) {     TMPMEMFREE(names);
1529              strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
1530              c_names[i][MAX_namelength-1]='\0';     return;
1531           } else {  }
1532              strcpy(c_names[i],n.c_str());  
1533           }  //
1534      }  // saves mesh and optionally data arrays in VTK format
1535      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  //
1536      checkFinleyError();  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg,  const std::string& metadata, const std::string& metadata_schema) const
1537      return;  {
1538  }     int num_data;
1539       char **names;
1540  // saves a data array in openVTK format:     escriptDataC *data;
1541  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const     escriptDataC **ptr_data;
1542  {  
1543      int MAX_namelength=256;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1544      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());
1545      char names[num_data][MAX_namelength];     checkFinleyError();
1546      char* c_names[num_data];  
1547      escriptDataC data[num_data];     /* win32 refactor */
1548      escriptDataC* ptr_data[num_data];     TMPMEMFREE(data);
1549       TMPMEMFREE(ptr_data);
1550      boost::python::list keys=arg.keys();     for(int i=0; i<num_data; i++)
1551      for (int i=0;i<num_data;++i) {     {
1552           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);        TMPMEMFREE(names[i]);
1553           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     }
1554               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     TMPMEMFREE(names);
1555           data[i]=d.getDataC();  }
1556           ptr_data[i]=&(data[i]);  
1557           std::string n=boost::python::extract<std::string>(keys[i]);  //
1558           c_names[i]=&(names[i][0]);  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1559           if (n.length()>MAX_namelength-1) {  //
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
     return;  
 }  
                                                                                                                                                                           
                                                                                                                                                                           
 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  
1560  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1561                        const int row_blocksize,                                                   const int row_blocksize,
1562                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1563                        const int column_blocksize,                                                   const int column_blocksize,
1564                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1565                        const int type) const                                                   const int type) const
1566  {  {
1567      int reduceRowOrder=0;     int reduceRowOrder=0;
1568      int reduceColOrder=0;     int reduceColOrder=0;
1569      // is the domain right?     // is the domain right?
1570      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1571      if (row_domain!=*this)     if (row_domain!=*this)
1572            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1573      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1574      if (col_domain!=*this)     if (col_domain!=*this)
1575            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1576      // is the function space type right     // is the function space type right
1577      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1578          reduceRowOrder=0;        reduceRowOrder=0;
1579      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1580          reduceRowOrder=1;        reduceRowOrder=1;
1581      } else {     } else {
1582          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1583      }     }
1584      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1585          reduceColOrder=0;        reduceColOrder=0;
1586      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1587          reduceColOrder=1;        reduceColOrder=1;
1588      } else {     } else {
1589          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1590      }     }
1591      // generate matrix:     // generate matrix:
1592        
1593      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1594      checkFinleyError();     checkFinleyError();
1595      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1596      checkPasoError();     int trilinos = 0;
1597      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1598      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1599          /* Allocation Epetra_VrbMatrix here */
1600    #endif
1601       }
1602       else {
1603          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1604       }
1605       checkPasoError();
1606       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1607       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1608    }
1609    
1610    //
1611    // creates a TransportProblemAdapter
1612    //
1613    TransportProblemAdapter MeshAdapter::newTransportProblem(
1614                                                             const double theta,
1615                                                             const int blocksize,
1616                                                             const escript::FunctionSpace& functionspace,
1617                                                             const int type) const
1618    {
1619       int reduceOrder=0;
1620       // is the domain right?
1621       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1622       if (domain!=*this)
1623          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1624       // is the function space type right
1625       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1626          reduceOrder=0;
1627       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1628          reduceOrder=1;
1629       } else {
1630          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1631       }
1632       // generate matrix:
1633    
1634       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1635       checkFinleyError();
1636       Paso_FCTransportProblem* transportProblem;
1637       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1638       checkPasoError();
1639       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1640       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1641  }  }
1642    
1643  //  //
# Line 753  SystemMatrixAdapter MeshAdapter::newSyst Line 1649  SystemMatrixAdapter MeshAdapter::newSyst
1649  // 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:
1650  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1651  {  {
1652    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1653         case(Nodes):     case(Nodes):
1654         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1655         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1656            return false;     return false;
1657            break;     break;
1658         case(Elements):     case(Elements):
1659         case(FaceElements):     case(FaceElements):
1660         case(Points):     case(Points):
1661         case(ContactElementsZero):     case(ContactElementsZero):
1662         case(ContactElementsOne):     case(ContactElementsOne):
1663            return true;     case(ReducedElements):
1664            break;     case(ReducedFaceElements):
1665         default:     case(ReducedContactElementsZero):
1666            stringstream temp;     case(ReducedContactElementsOne):
1667            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1668            throw FinleyAdapterException(temp.str());     break;
1669            break;     default:
1670    }        stringstream temp;
1671    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1672    return false;        throw FinleyAdapterException(temp.str());
1673          break;
1674       }
1675       checkFinleyError();
1676       return false;
1677    }
1678    
1679    bool
1680    MeshAdapter::commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const
1681    {
1682       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1683        class 1: DOF <-> Nodes
1684        class 2: ReducedDOF <-> ReducedNodes
1685        class 3: Points
1686        class 4: Elements
1687        class 5: ReducedElements
1688        class 6: FaceElements
1689        class 7: ReducedFaceElements
1690        class 8: ContactElementZero <-> ContactElementOne
1691        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1692    
1693       There is also a set of lines. Interpolation is possible down a line but not between lines.
1694       class 1 and 2 belong to all lines so aren't considered.
1695        line 0: class 3
1696        line 1: class 4,5
1697        line 2: class 6,7
1698        line 3: class 8,9
1699    
1700       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1701       eg hasnodes is true if we have at least one instance of Nodes.
1702       */
1703        if (fs.size()==0)
1704        {
1705        return false;
1706        }
1707        std::vector<int> hasclass(10);
1708        std::vector<int> hasline(4);    
1709        bool hasnodes=false;
1710        bool hasrednodes=false;
1711        bool hascez=false;
1712        bool hasrcez=false;
1713        for (int i=0;i<fs.size();++i)
1714        {
1715        switch(fs[i])
1716        {
1717        case(Nodes):   hasnodes=true;   // no break is deliberate
1718        case(DegreesOfFreedom):
1719            hasclass[1]=1;
1720            break;
1721        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1722        case(ReducedDegreesOfFreedom):
1723            hasclass[2]=1;
1724            break;
1725        case(Points):
1726            hasline[0]=1;
1727            hasclass[3]=1;
1728            break;
1729        case(Elements):
1730            hasclass[4]=1;
1731            hasline[1]=1;
1732            break;
1733        case(ReducedElements):
1734            hasclass[5]=1;
1735            hasline[1]=1;
1736            break;
1737        case(FaceElements):
1738            hasclass[6]=1;
1739            hasline[2]=1;
1740            break;
1741        case(ReducedFaceElements):
1742            hasclass[7]=1;
1743            hasline[2]=1;
1744            break;
1745        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1746        case(ContactElementsOne):
1747            hasclass[8]=1;
1748            hasline[3]=1;
1749            break;
1750        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1751        case(ReducedContactElementsOne):
1752            hasclass[9]=1;
1753            hasline[3]=1;
1754            break;
1755        default:
1756            return false;
1757        }
1758        }
1759        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1760        // fail if we have more than one leaf group
1761    
1762        if (totlines>1)
1763        {
1764        return false;   // there are at least two branches we can't interpolate between
1765        }
1766        else if (totlines==1)
1767        {
1768        if (hasline[0]==1)      // we have points
1769        {
1770            resultcode=Points;
1771        }
1772        else if (hasline[1]==1)
1773        {
1774            if (hasclass[5]==1)
1775            {
1776            resultcode=ReducedElements;
1777            }
1778            else
1779            {
1780            resultcode=Elements;
1781            }
1782        }
1783        else if (hasline[2]==1)
1784        {
1785            if (hasclass[7]==ReducedFaceElements)
1786            {
1787            resultcode=ReducedFaceElements;
1788            }
1789            else
1790            {
1791            resultcode=FaceElements;
1792            }
1793        }
1794        else    // so we must be in line3
1795        {
1796            if (hasclass[9]==1)
1797            {
1798            // need something from class 9
1799            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1800            }
1801            else
1802            {
1803            // something from class 8
1804            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1805            }
1806        }
1807        }
1808        else    // totlines==0
1809        {
1810        if (hasclass[2]==1)
1811        {
1812            // something from class 2
1813            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1814        }
1815        else
1816        {   // something from class 1
1817            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1818        }
1819        }
1820        return true;
1821  }  }
1822    
1823  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1824  {  {
1825    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1826       case(Nodes):     case(Nodes):
1827          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1828             case(Nodes):      case(Nodes):
1829             case(ReducedDegreesOfFreedom):      case(ReducedNodes):
1830             case(DegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1831             case(Elements):      case(DegreesOfFreedom):
1832             case(FaceElements):      case(Elements):
1833             case(Points):      case(ReducedElements):
1834             case(ContactElementsZero):      case(FaceElements):
1835             case(ContactElementsOne):      case(ReducedFaceElements):
1836                 return true;      case(Points):
1837             default:      case(ContactElementsZero):
1838                 stringstream temp;      case(ReducedContactElementsZero):
1839                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      case(ContactElementsOne):
1840                 throw FinleyAdapterException(temp.str());      case(ReducedContactElementsOne):
1841          }      return true;
1842          break;      default:
1843       case(Elements):            stringstream temp;
1844          if (functionSpaceType_target==Elements) {            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1845             return true;            throw FinleyAdapterException(temp.str());
1846       }
1847       break;
1848       case(ReducedNodes):
1849        switch(functionSpaceType_target) {
1850        case(ReducedNodes):
1851        case(ReducedDegreesOfFreedom):
1852        case(Elements):
1853        case(ReducedElements):
1854        case(FaceElements):
1855        case(ReducedFaceElements):
1856        case(Points):
1857        case(ContactElementsZero):
1858        case(ReducedContactElementsZero):
1859        case(ContactElementsOne):
1860        case(ReducedContactElementsOne):
1861        return true;
1862        case(Nodes):
1863        case(DegreesOfFreedom):
1864        return false;
1865        default:
1866            stringstream temp;
1867            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1868            throw FinleyAdapterException(temp.str());
1869       }
1870       break;
1871       case(Elements):
1872        if (functionSpaceType_target==Elements) {
1873          return true;
1874        } else if (functionSpaceType_target==ReducedElements) {
1875          return true;
1876          } else {          } else {
1877             return false;            return false;
         }  
      case(FaceElements):  
         if (functionSpaceType_target==FaceElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(Points):  
         if (functionSpaceType_target==Points) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ContactElementsZero):  
      case(ContactElementsOne):  
         if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {  
            return true;  
         } else {  
            return false;  
         }  
      case(DegreesOfFreedom):  
         switch(functionSpaceType_target) {  
            case(ReducedDegreesOfFreedom):  
            case(DegreesOfFreedom):  
            case(Nodes):  
            case(Elements):  
            case(FaceElements):  
            case(Points):  
            case(ContactElementsZero):  
            case(ContactElementsOne):  
               return true;  
            default:  
              stringstream temp;  
              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;  
              throw FinleyAdapterException(temp.str());  
1878          }          }
1879          break;     case(ReducedElements):
1880       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1881         switch(functionSpaceType_target) {        return true;
1882            case(ReducedDegreesOfFreedom):      } else {
1883            case(Elements):            return false;
1884            case(FaceElements):      }
1885            case(Points):     case(FaceElements):
1886            case(ContactElementsZero):      if (functionSpaceType_target==FaceElements) {
1887            case(ContactElementsOne):              return true;
1888                return true;      } else if (functionSpaceType_target==ReducedFaceElements) {
1889            case(Nodes):              return true;
1890            case(DegreesOfFreedom):      } else {
1891               return false;              return false;
1892            default:      }
1893               stringstream temp;     case(ReducedFaceElements):
1894               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      if (functionSpaceType_target==ReducedFaceElements) {
1895               throw FinleyAdapterException(temp.str());              return true;
1896         }      } else {
1897         break;          return false;
1898       default:      }
1899          stringstream temp;     case(Points):
1900          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;      if (functionSpaceType_target==Points) {
1901          throw FinleyAdapterException(temp.str());              return true;
1902          break;      } else {
1903    }              return false;
1904    checkFinleyError();      }
1905    return false;     case(ContactElementsZero):
1906       case(ContactElementsOne):
1907        if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1908                return true;
1909        } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1910                return true;
1911        } else {
1912                return false;
1913        }
1914       case(ReducedContactElementsZero):
1915       case(ReducedContactElementsOne):
1916        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1917                return true;
1918        } else {
1919                return false;
1920        }
1921       case(DegreesOfFreedom):
1922        switch(functionSpaceType_target) {
1923        case(ReducedDegreesOfFreedom):
1924        case(DegreesOfFreedom):
1925        case(Nodes):
1926        case(ReducedNodes):
1927        case(Elements):
1928        case(ReducedElements):
1929        case(Points):
1930        case(FaceElements):
1931        case(ReducedFaceElements):
1932        case(ContactElementsZero):
1933        case(ReducedContactElementsZero):
1934        case(ContactElementsOne):
1935        case(ReducedContactElementsOne):
1936        return true;
1937        default:
1938            stringstream temp;
1939            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1940            throw FinleyAdapterException(temp.str());
1941        }
1942        break;
1943       case(ReducedDegreesOfFreedom):
1944       switch(functionSpaceType_target) {
1945        case(ReducedDegreesOfFreedom):
1946        case(ReducedNodes):
1947        case(Elements):
1948        case(ReducedElements):
1949        case(FaceElements):
1950        case(ReducedFaceElements):
1951        case(Points):
1952        case(ContactElementsZero):
1953        case(ReducedContactElementsZero):
1954        case(ContactElementsOne):
1955        case(ReducedContactElementsOne):
1956        return true;
1957        case(Nodes):
1958        case(DegreesOfFreedom):
1959        return false;
1960        default:
1961            stringstream temp;
1962            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1963            throw FinleyAdapterException(temp.str());
1964        }
1965        break;
1966       default:
1967          stringstream temp;
1968          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1969          throw FinleyAdapterException(temp.str());
1970          break;
1971       }
1972       checkFinleyError();
1973       return false;
1974  }  }
1975    
1976  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
1977  {  {
1978      return false;     return false;
1979  }  }
1980    
1981  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1982  {  {
1983    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1984    if (temp!=0) {     if (temp!=0) {
1985      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1986    } else {     } else {
1987      return false;        return false;
1988    }     }
1989  }  }
1990    
1991  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1992  {  {
1993    return !(operator==(other));     return !(operator==(other));
1994  }  }
1995    
1996  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1997  {  {
1998     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
1999       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2000       checkPasoError();
2001       return out;
2002    }
2003    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2004    {
2005       Finley_Mesh* mesh=m_finleyMesh.get();
2006       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2007     checkPasoError();     checkPasoError();
2008     return out;     return out;
2009  }  }
2010    
2011  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2012  {  {
2013    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
2014  }  }
2015    
2016  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2017  {  {
2018    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
2019  }  }
2020    
2021  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2022  {  {
2023    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
2024  }  }
2025    
2026    const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2027    {
2028       int *out = NULL;
2029       Finley_Mesh* mesh=m_finleyMesh.get();
2030       switch (functionSpaceType) {
2031       case(Nodes):
2032       out=mesh->Nodes->Id;
2033       break;
2034       case(ReducedNodes):
2035       out=mesh->Nodes->reducedNodesId;
2036       break;
2037       case(Elements):
2038       out=mesh->Elements->Id;
2039       break;
2040       case(ReducedElements):
2041       out=mesh->Elements->Id;
2042       break;
2043       case(FaceElements):
2044       out=mesh->FaceElements->Id;
2045       break;
2046       case(ReducedFaceElements):
2047       out=mesh->FaceElements->Id;
2048       break;
2049       case(Points):
2050       out=mesh->Points->Id;
2051       break;
2052       case(ContactElementsZero):
2053       out=mesh->ContactElements->Id;
2054       break;
2055       case(ReducedContactElementsZero):
2056       out=mesh->ContactElements->Id;
2057       break;
2058       case(ContactElementsOne):
2059       out=mesh->ContactElements->Id;
2060       break;
2061       case(ReducedContactElementsOne):
2062       out=mesh->ContactElements->Id;
2063       break;
2064       case(DegreesOfFreedom):
2065       out=mesh->Nodes->degreesOfFreedomId;
2066       break;
2067       case(ReducedDegreesOfFreedom):
2068       out=mesh->Nodes->reducedDegreesOfFreedomId;
2069       break;
2070       default:
2071          stringstream temp;
2072          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2073          throw FinleyAdapterException(temp.str());
2074          break;
2075       }
2076       return out;
2077    }
2078  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2079  {  {
2080    int out=0;     int out=0;
2081       Finley_Mesh* mesh=m_finleyMesh.get();
2082       switch (functionSpaceType) {
2083       case(Nodes):
2084       out=mesh->Nodes->Tag[sampleNo];
2085       break;
2086       case(ReducedNodes):
2087       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2088       break;
2089       case(Elements):
2090       out=mesh->Elements->Tag[sampleNo];
2091       break;
2092       case(ReducedElements):
2093       out=mesh->Elements->Tag[sampleNo];
2094       break;
2095       case(FaceElements):
2096       out=mesh->FaceElements->Tag[sampleNo];
2097       break;
2098       case(ReducedFaceElements):
2099       out=mesh->FaceElements->Tag[sampleNo];
2100       break;
2101       case(Points):
2102       out=mesh->Points->Tag[sampleNo];
2103       break;
2104       case(ContactElementsZero):
2105       out=mesh->ContactElements->Tag[sampleNo];
2106       break;
2107       case(ReducedContactElementsZero):
2108       out=mesh->ContactElements->Tag[sampleNo];
2109       break;
2110       case(ContactElementsOne):
2111       out=mesh->ContactElements->Tag[sampleNo];
2112       break;
2113       case(ReducedContactElementsOne):
2114       out=mesh->ContactElements->Tag[sampleNo];
2115       break;
2116       case(DegreesOfFreedom):
2117       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2118       break;
2119       case(ReducedDegreesOfFreedom):
2120       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2121       break;
2122       default:
2123          stringstream temp;
2124          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2125          throw FinleyAdapterException(temp.str());
2126          break;
2127       }
2128       return out;
2129    }
2130    
2131    
2132    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
2133    {
2134       Finley_Mesh* mesh=m_finleyMesh.get();
2135       escriptDataC tmp=mask.getDataC();
2136       switch(functionSpaceType) {
2137       case(Nodes):
2138       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2139       break;
2140       case(ReducedNodes):
2141       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2142       break;
2143       case(DegreesOfFreedom):
2144       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2145       break;
2146       case(ReducedDegreesOfFreedom):
2147       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2148       break;
2149       case(Elements):
2150       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2151       break;
2152       case(ReducedElements):
2153       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2154       break;
2155       case(FaceElements):
2156       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2157       break;
2158       case(ReducedFaceElements):
2159       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2160       break;
2161       case(Points):
2162       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2163       break;
2164       case(ContactElementsZero):
2165       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2166       break;
2167       case(ReducedContactElementsZero):
2168       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2169       break;
2170       case(ContactElementsOne):
2171       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2172       break;
2173       case(ReducedContactElementsOne):
2174       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2175       break;
2176       default:
2177          stringstream temp;
2178          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2179          throw FinleyAdapterException(temp.str());
2180       }
2181       checkFinleyError();
2182       return;
2183    }
2184    
2185    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2186    {
2187       Finley_Mesh* mesh=m_finleyMesh.get();
2188       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2189       checkPasoError();
2190       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2191    }
2192    
2193    int MeshAdapter::getTag(const std::string& name) const
2194    {
2195       Finley_Mesh* mesh=m_finleyMesh.get();
2196       int tag=0;
2197       tag=Finley_Mesh_getTag(mesh, name.c_str());
2198       checkPasoError();
2199       // throwStandardException("MeshAdapter::getTag is not implemented.");
2200       return tag;
2201    }
2202    
2203    bool MeshAdapter::isValidTagName(const std::string& name) const
2204    {
2205       Finley_Mesh* mesh=m_finleyMesh.get();
2206       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2207    }
2208    
2209    std::string MeshAdapter::showTagNames() const
2210    {
2211       stringstream temp;
2212       Finley_Mesh* mesh=m_finleyMesh.get();
2213       Finley_TagMap* tag_map=mesh->TagMap;
2214       while (tag_map) {
2215          temp << tag_map->name;
2216          tag_map=tag_map->next;
2217          if (tag_map) temp << ", ";
2218       }
2219       return temp.str();
2220    }
2221    
2222    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2223    {
2224    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2225    switch (functionSpaceType) {    dim_t numTags=0;
2226    case(Nodes):    switch(functionSpaceCode) {
2227      out=mesh->Nodes->Tag[sampleNo];     case(Nodes):
2228      break;            numTags=mesh->Nodes->numTagsInUse;
2229    case(Elements):            break;
2230      out=mesh->Elements->Tag[sampleNo];     case(ReducedNodes):
2231      break;            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2232    case(FaceElements):            break;
2233      out=mesh->FaceElements->Tag[sampleNo];     case(DegreesOfFreedom):
2234      break;            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2235    case(Points):            break;
2236      out=mesh->Points->Tag[sampleNo];     case(ReducedDegreesOfFreedom):
2237      break;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2238    case(ContactElementsZero):            break;
2239      out=mesh->ContactElements->Tag[sampleNo];     case(Elements):
2240      break;     case(ReducedElements):
2241    case(ContactElementsOne):            numTags=mesh->Elements->numTagsInUse;
2242      out=mesh->ContactElements->Tag[sampleNo];            break;
2243      break;     case(FaceElements):
2244    case(DegreesOfFreedom):     case(ReducedFaceElements):
2245      break;            numTags=mesh->FaceElements->numTagsInUse;
2246    case(ReducedDegreesOfFreedom):            break;
2247      break;     case(Points):
2248    default:            numTags=mesh->Points->numTagsInUse;
2249      stringstream temp;            break;
2250      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();     case(ContactElementsZero):
2251      throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
2252      break;     case(ContactElementsOne):
2253       case(ReducedContactElementsOne):
2254              numTags=mesh->ContactElements->numTagsInUse;
2255              break;
2256       default:
2257          stringstream temp;
2258          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2259          throw FinleyAdapterException(temp.str());
2260    }    }
2261    return out;    return numTags;
2262  }  }
2263  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  
2264    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2265  {  {
   int out=0,i;  
2266    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2267    switch (functionSpaceType) {    index_t* tags=NULL;
2268    case(Nodes):    switch(functionSpaceCode) {
2269      if (mesh->Nodes!=NULL) {     case(Nodes):
2270        out=mesh->Nodes->Id[sampleNo];            tags=mesh->Nodes->tagsInUse;
       break;  
     }  
   case(Elements):  
     out=mesh->Elements->Id[sampleNo];  
     break;  
   case(FaceElements):  
     out=mesh->FaceElements->Id[sampleNo];  
     break;  
   case(Points):  
     out=mesh->Points->Id[sampleNo];  
     break;  
   case(ContactElementsZero):  
     out=mesh->ContactElements->Id[sampleNo];  
     break;  
   case(ContactElementsOne):  
     out=mesh->ContactElements->Id[sampleNo];  
     break;  
   case(DegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->degreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
2271            break;            break;
2272         }     case(ReducedNodes):
2273      }            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
     break;  
   case(ReducedDegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->reducedDegreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
2274            break;            break;
2275         }     case(DegreesOfFreedom):
2276      }            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2277      break;            break;
2278    default:     case(ReducedDegreesOfFreedom):
2279      stringstream temp;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2280      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();            break;
2281      throw FinleyAdapterException(temp.str());     case(Elements):
2282      break;     case(ReducedElements):
2283              tags=mesh->Elements->tagsInUse;
2284              break;
2285       case(FaceElements):
2286       case(ReducedFaceElements):
2287              tags=mesh->FaceElements->tagsInUse;
2288              break;
2289       case(Points):
2290              tags=mesh->Points->tagsInUse;
2291              break;
2292       case(ContactElementsZero):
2293       case(ReducedContactElementsZero):
2294       case(ContactElementsOne):
2295       case(ReducedContactElementsOne):
2296              tags=mesh->ContactElements->tagsInUse;
2297              break;
2298       default:
2299          stringstream temp;
2300          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2301          throw FinleyAdapterException(temp.str());
2302    }    }
2303    return out;    return tags;
2304  }  }
2305    
2306    
2307    bool MeshAdapter::canTag(int functionSpaceCode) const
2308    {
2309      switch(functionSpaceCode) {
2310       case(Nodes):
2311       case(Elements):
2312       case(ReducedElements):
2313       case(FaceElements):
2314       case(ReducedFaceElements):
2315       case(Points):
2316       case(ContactElementsZero):
2317       case(ReducedContactElementsZero):
2318       case(ContactElementsOne):
2319       case(ReducedContactElementsOne):
2320              return true;
2321       case(ReducedNodes):
2322       case(DegreesOfFreedom):
2323       case(ReducedDegreesOfFreedom):
2324          return false;
2325       default:
2326        return false;
2327      }
2328    }
2329    
2330    AbstractDomain::StatusType MeshAdapter::getStatus() const
2331    {
2332      Finley_Mesh* mesh=m_finleyMesh.get();
2333      return Finley_Mesh_getStatus(mesh);
2334    }
2335    
2336    
2337    
2338  }  // end of namespace  }  // end of namespace

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