/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 757 by woo409, Mon Jun 26 13:12:56 2006 UTC revision 1877 by ksteube, Tue Oct 14 02:58:39 2008 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) 2003-2008 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 "escript/blocktimer.h"
27    }
28    #include <vector>
29    
30    #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256
31    
32  using namespace std;  using namespace std;
33  using namespace escript;  using namespace escript;
# Line 29  MeshAdapter::FunctionSpaceNamesMapType M Line 40  MeshAdapter::FunctionSpaceNamesMapType M
40  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
41  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
42  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
43    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
44  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
45    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
46  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
47    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
48  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
49  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
50    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
51  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
52    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
53    
54  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
55  {  {
56    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
57    //     //
58    // 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
59    // for us.     // for us.
60    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
61  }  }
62    
63  //  //
# Line 49  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 65  MeshAdapter::MeshAdapter(Finley_Mesh* fi
65  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
66  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
67  {  {
68    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
69  }  }
70    
71  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
72  {  {
73    //     //
74    // 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.
75    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
76    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
77      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
78      Finley_Mesh_dealloc(m_finleyMesh.get());     }
     //   cout << "Finished dealloc." << endl;  
   }  
79  }  }
80    
81    int MeshAdapter::getMPISize() const
82    {
83       return m_finleyMesh.get()->MPIInfo->size;
84    }
85    int MeshAdapter::getMPIRank() const
86    {
87       return m_finleyMesh.get()->MPIInfo->rank;
88    }
89    void MeshAdapter::MPIBarrier() const
90    {
91    #ifdef PASO_MPI
92       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
93    #endif
94       return;
95    }
96    bool MeshAdapter::onMasterProcessor() const
97    {
98       return m_finleyMesh.get()->MPIInfo->rank == 0;
99    }
100    
101    
102  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
103     return m_finleyMesh.get();     return m_finleyMesh.get();
104  }  }
105    
106  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
107  {  {
108    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
109    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
110    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
111    checkFinleyError();     checkFinleyError();
112    TMPMEMFREE(fName);     TMPMEMFREE(fName);
113    }
114    
115    void MeshAdapter::Print_Mesh_Info(const bool full=false) const
116    {
117       Finley_PrintMesh_Info(m_finleyMesh.get(), full);
118    }
119    
120    void MeshAdapter::dump(const std::string& fileName) const
121    {
122    #ifdef USE_NETCDF
123       const NcDim* ncdims[12];
124       NcVar *ids;
125       int *int_ptr;
126       Finley_Mesh *mesh = m_finleyMesh.get();
127       Finley_TagMap* tag_map;
128       int num_Tags = 0;
129       int mpi_size             = mesh->MPIInfo->size;
130       int mpi_rank             = mesh->MPIInfo->rank;
131       int numDim               = mesh->Nodes->numDim;
132       int numNodes             = mesh->Nodes->numNodes;
133       int num_Elements         = mesh->Elements->numElements;
134       int num_FaceElements         = mesh->FaceElements->numElements;
135       int num_ContactElements      = mesh->ContactElements->numElements;
136       int num_Points           = mesh->Points->numElements;
137       int num_Elements_numNodes        = mesh->Elements->numNodes;
138       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
139       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
140    #ifdef PASO_MPI
141       MPI_Status status;
142    #endif
143    
144    /* Incoming token indicates it's my turn to write */
145    #ifdef PASO_MPI
146       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
147    #endif
148    
149       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
150                                                         mpi_size, mpi_rank);
151    
152       /* Figure out how much storage is required for tags */
153       tag_map = mesh->TagMap;
154       num_Tags = 0;
155       if (tag_map) {
156          while (tag_map) {
157             num_Tags++;
158             tag_map=tag_map->next;
159          }
160       }
161    
162       // NetCDF error handler
163       NcError err(NcError::verbose_nonfatal);
164       // Create the file.
165       NcFile dataFile(newFileName, NcFile::Replace);
166       // check if writing was successful
167       if (!dataFile.is_valid())
168          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
169    
170       // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
171       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
172          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
173       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
174          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
175       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
176          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
177       if (num_Elements>0)
178          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
179             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
180       if (num_FaceElements>0)
181          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
182             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
183       if (num_ContactElements>0)
184          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
185             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
186       if (num_Points>0)
187          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
188             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
189       if (num_Elements>0)
190          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
191             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
192       if (num_FaceElements>0)
193          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
194             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
195       if (num_ContactElements>0)
196          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
197             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
198       if (num_Tags>0)
199          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
200             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
201    
202       // Attributes: MPI size, MPI rank, Name, order, reduced_order
203       if (!dataFile.add_att("mpi_size", mpi_size) )
204          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
205       if (!dataFile.add_att("mpi_rank", mpi_rank) )
206          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
207       if (!dataFile.add_att("Name",mesh->Name) )
208          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
209       if (!dataFile.add_att("numDim",numDim) )
210          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
211       if (!dataFile.add_att("order",mesh->order) )
212          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
213       if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
214          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
215       if (!dataFile.add_att("numNodes",numNodes) )
216          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
217       if (!dataFile.add_att("num_Elements",num_Elements) )
218          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
219       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
220          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
221       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
222          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
223       if (!dataFile.add_att("num_Points",num_Points) )
224          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
225       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
226          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
227       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
228          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
229       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
230          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
231       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
232          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
233       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
234          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
235       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
236          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
237       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
238          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
239       if (!dataFile.add_att("num_Tags", num_Tags) )
240          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
241    
242       // // // // // Nodes // // // // //
243    
244       // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
245       if (numNodes>0) {
246    
247          // Nodes Id
248          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
249             throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
250          int_ptr = &mesh->Nodes->Id[0];
251          if (! (ids->put(int_ptr, numNodes)) )
252             throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
253    
254          // Nodes Tag
255          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
256             throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
257          int_ptr = &mesh->Nodes->Tag[0];
258          if (! (ids->put(int_ptr, numNodes)) )
259             throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
260    
261          // Nodes gDOF
262          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
263             throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
264          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
265          if (! (ids->put(int_ptr, numNodes)) )
266             throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
267    
268          // Nodes global node index
269          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
270             throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
271          int_ptr = &mesh->Nodes->globalNodesIndex[0];
272          if (! (ids->put(int_ptr, numNodes)) )
273             throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
274    
275          // Nodes grDof
276          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
277             throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
278          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
279          if (! (ids->put(int_ptr, numNodes)) )
280             throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
281    
282          // Nodes grNI
283          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
284             throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
285          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
286          if (! (ids->put(int_ptr, numNodes)) )
287             throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
288    
289          // Nodes Coordinates
290          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
291             throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
292          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
293             throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
294    
295          // Nodes degreesOfFreedomDistribution
296          if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
297             throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
298          int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
299          if (! (ids->put(int_ptr, mpi_size+1)) )
300             throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
301    
302          // Nodes nodeDistribution
303          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
304             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
305          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
306          if (! (ids->put(int_ptr, mpi_size+1)) )
307             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
308    
309       }
310    
311       // // // // // Elements // // // // //
312    
313       if (num_Elements>0) {
314    
315          // Elements_Id
316          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
317             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
318          int_ptr = &mesh->Elements->Id[0];
319          if (! (ids->put(int_ptr, num_Elements)) )
320             throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
321    
322          // Elements_Tag
323          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
324             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
325          int_ptr = &mesh->Elements->Tag[0];
326          if (! (ids->put(int_ptr, num_Elements)) )
327             throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
328    
329          // Elements_Owner
330          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
331             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
332          int_ptr = &mesh->Elements->Owner[0];
333          if (! (ids->put(int_ptr, num_Elements)) )
334             throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
335    
336          // Elements_Color
337          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
338             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
339          int_ptr = &mesh->Elements->Color[0];
340          if (! (ids->put(int_ptr, num_Elements)) )
341             throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
342    
343          // Elements_Nodes
344          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
345             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
346          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
347             throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
348    
349       }
350    
351       // // // // // Face_Elements // // // // //
352    
353       if (num_FaceElements>0) {
354    
355          // FaceElements_Id
356          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
357             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
358          int_ptr = &mesh->FaceElements->Id[0];
359          if (! (ids->put(int_ptr, num_FaceElements)) )
360             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
361    
362          // FaceElements_Tag
363          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
364             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
365          int_ptr = &mesh->FaceElements->Tag[0];
366          if (! (ids->put(int_ptr, num_FaceElements)) )
367             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
368    
369          // FaceElements_Owner
370          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
371             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
372          int_ptr = &mesh->FaceElements->Owner[0];
373          if (! (ids->put(int_ptr, num_FaceElements)) )
374             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
375    
376          // FaceElements_Color
377          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
378             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
379          int_ptr = &mesh->FaceElements->Color[0];
380          if (! (ids->put(int_ptr, num_FaceElements)) )
381             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
382    
383          // FaceElements_Nodes
384          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
385             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
386          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
387             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
388    
389       }
390    
391       // // // // // Contact_Elements // // // // //
392    
393       if (num_ContactElements>0) {
394    
395          // ContactElements_Id
396          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
397             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
398          int_ptr = &mesh->ContactElements->Id[0];
399          if (! (ids->put(int_ptr, num_ContactElements)) )
400             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
401    
402          // ContactElements_Tag
403          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
404             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
405          int_ptr = &mesh->ContactElements->Tag[0];
406          if (! (ids->put(int_ptr, num_ContactElements)) )
407             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
408    
409          // ContactElements_Owner
410          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
411             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
412          int_ptr = &mesh->ContactElements->Owner[0];
413          if (! (ids->put(int_ptr, num_ContactElements)) )
414             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
415    
416          // ContactElements_Color
417          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
418             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
419          int_ptr = &mesh->ContactElements->Color[0];
420          if (! (ids->put(int_ptr, num_ContactElements)) )
421             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
422    
423          // ContactElements_Nodes
424          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
425             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
426          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
427             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
428    
429       }
430    
431       // // // // // Points // // // // //
432    
433       if (num_Points>0) {
434    
435          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
436    
437          // Points_Id
438          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
439             throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
440          int_ptr = &mesh->Points->Id[0];
441          if (! (ids->put(int_ptr, num_Points)) )
442             throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
443    
444          // Points_Tag
445          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
446             throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
447          int_ptr = &mesh->Points->Tag[0];
448          if (! (ids->put(int_ptr, num_Points)) )
449             throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
450    
451          // Points_Owner
452          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
453             throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
454          int_ptr = &mesh->Points->Owner[0];
455          if (! (ids->put(int_ptr, num_Points)) )
456             throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
457    
458          // Points_Color
459          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
460             throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
461          int_ptr = &mesh->Points->Color[0];
462          if (! (ids->put(int_ptr, num_Points)) )
463             throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
464    
465          // Points_Nodes
466          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
467          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
468             throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
469          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
470             throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
471    
472       }
473    
474       // // // // // TagMap // // // // //
475    
476       if (num_Tags>0) {
477    
478          // Temp storage to gather node IDs
479          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
480          char name_temp[4096];
481    
482          /* Copy tag data into temp arrays */
483          tag_map = mesh->TagMap;
484          if (tag_map) {
485             int i = 0;
486             while (tag_map) {
487                Tags_keys[i++] = tag_map->tag_key;
488                tag_map=tag_map->next;
489             }
490          }
491    
492          // Tags_keys
493          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
494             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
495          int_ptr = &Tags_keys[0];
496          if (! (ids->put(int_ptr, num_Tags)) )
497             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
498    
499          // Tags_names_*
500          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
501          // because the NetCDF manual doesn't tell how to do an array of strings
502          tag_map = mesh->TagMap;
503          if (tag_map) {
504             int i = 0;
505             while (tag_map) {
506                sprintf(name_temp, "Tags_name_%d", i);
507                if (!dataFile.add_att(name_temp, tag_map->name) )
508                   throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
509                tag_map=tag_map->next;
510                i++;
511             }
512          }
513    
514          TMPMEMFREE(Tags_keys);
515    
516       }
517    
518    /* Send token to next MPI process so he can take his turn */
519    #ifdef PASO_MPI
520       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
521    #endif
522    
523       // NetCDF file is closed by destructor of NcFile object
524    
525    #else
526       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
527    #endif  /* USE_NETCDF */
528       checkFinleyError();
529  }  }
530    
531  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
532  {  {
533    return "FinleyMesh";     return "FinleyMesh";
534  }  }
535    
536  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
537  {  {
538    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
539    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
540    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
541      return "Invalid function space type code.";        return "Invalid function space type code.";
542    } else {     } else {
543      return loc->second;        return loc->second;
544    }     }
545  }  }
546    
547  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
548  {  {
549    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
550    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
551    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
552  }  }
553    
554  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
555  {  {
556    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
557      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
558    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
559      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
560    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
561      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
562    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
563      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
564    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
565      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
566    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
567      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
568    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
569      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
570    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
571      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
572       m_functionSpaceTypeNames.insert
573       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
574       m_functionSpaceTypeNames.insert
575       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
576       m_functionSpaceTypeNames.insert
577       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
578       m_functionSpaceTypeNames.insert
579       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
580       m_functionSpaceTypeNames.insert
581       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
582  }  }
583    
584  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
585  {  {
586    return Nodes;     return Nodes;
587    }
588    int MeshAdapter::getReducedContinuousFunctionCode() const
589    {
590       return ReducedNodes;
591  }  }
592    
593  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
594  {  {
595    return Elements;     return Elements;
596    }
597    int MeshAdapter::getReducedFunctionCode() const
598    {
599       return ReducedElements;
600  }  }
601    
602  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
603  {  {
604    return FaceElements;     return FaceElements;
605    }
606    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
607    {
608       return ReducedFaceElements;
609  }  }
610    
611  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
612  {  {
613    return ContactElementsZero;     return ContactElementsZero;
614    }
615    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
616    {
617       return ReducedContactElementsZero;
618  }  }
619    
620  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
621  {  {
622    return ContactElementsOne;     return ContactElementsOne;
623    }
624    int MeshAdapter::getReducedFunctionOnContactOneCode() const
625    {
626       return ReducedContactElementsOne;
627  }  }
628    
629  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
630  {  {
631    return DegreesOfFreedom;     return DegreesOfFreedom;
632  }  }
633    
634  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
635  {  {
636    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
637  }  }
638    
639  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
640  {  {
641    return Points;     return Points;
642  }  }
643    
644  //  //
# Line 165  int MeshAdapter::getDiracDeltaFunctionCo Line 646  int MeshAdapter::getDiracDeltaFunctionCo
646  //  //
647  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
648  {  {
649    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
650    checkFinleyError();     checkFinleyError();
651    return numDim;     return numDim;
652    }
653    
654    //
655    // Return the number of data points summed across all MPI processes
656    //
657    int MeshAdapter::getNumDataPointsGlobal() const
658    {
659       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
660  }  }
661    
662  //  //
# Line 180  pair<int,int> MeshAdapter::getDataShape( Line 669  pair<int,int> MeshAdapter::getDataShape(
669     int numSamples=0;     int numSamples=0;
670     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
671     switch (functionSpaceCode) {     switch (functionSpaceCode) {
672        case(Nodes):     case(Nodes):
673             numDataPointsPerSample=1;     numDataPointsPerSample=1;
674             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
675             break;     break;
676        case(Elements):     case(ReducedNodes):
677             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
678               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
679               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
680             }     case(Elements):
681             break;     if (mesh->Elements!=NULL) {
682        case(FaceElements):        numSamples=mesh->Elements->numElements;
683             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
684                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
685                  numSamples=mesh->FaceElements->numElements;     break;
686             }     case(ReducedElements):
687             break;     if (mesh->Elements!=NULL) {
688        case(Points):        numSamples=mesh->Elements->numElements;
689             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
690               numDataPointsPerSample=1;     }
691               numSamples=mesh->Points->numElements;     break;
692             }     case(FaceElements):
693             break;     if (mesh->FaceElements!=NULL) {
694        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
695             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
696               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
697               numSamples=mesh->ContactElements->numElements;     break;
698             }     case(ReducedFaceElements):
699             break;     if (mesh->FaceElements!=NULL) {
700        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
701             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
702               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
703               numSamples=mesh->ContactElements->numElements;     break;
704             }     case(Points):
705             break;     if (mesh->Points!=NULL) {
706        case(DegreesOfFreedom):        numDataPointsPerSample=1;
707             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
708               numDataPointsPerSample=1;     }
709  #ifndef PASO_MPI     break;
710               numSamples=mesh->Nodes->numDegreesOfFreedom;     case(ContactElementsZero):
711  #else     if (mesh->ContactElements!=NULL) {
712               numSamples=mesh->Nodes->degreeOfFreedomDistribution->numLocal;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
713  #endif        numSamples=mesh->ContactElements->numElements;
714             }     }
715             break;     break;
716        case(ReducedDegreesOfFreedom):     case(ReducedContactElementsZero):
717             if (mesh->Nodes!=NULL) {     if (mesh->ContactElements!=NULL) {
718               numDataPointsPerSample=1;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
719  #ifndef PASO_MPI        numSamples=mesh->ContactElements->numElements;
720               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     }
721  #else     break;
722               numSamples=mesh->Nodes->reducedDegreeOfFreedomDistribution->numLocal;     case(ContactElementsOne):
723  #endif     if (mesh->ContactElements!=NULL) {
724             }        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
725             break;        numSamples=mesh->ContactElements->numElements;
726        default:     }
727          stringstream temp;     break;
728          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     case(ReducedContactElementsOne):
729          throw FinleyAdapterException(temp.str());     if (mesh->ContactElements!=NULL) {
730          break;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
731        }        numSamples=mesh->ContactElements->numElements;
732        return pair<int,int>(numDataPointsPerSample,numSamples);     }
733       break;
734       case(DegreesOfFreedom):
735       if (mesh->Nodes!=NULL) {
736          numDataPointsPerSample=1;
737          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
738       }
739       break;
740       case(ReducedDegreesOfFreedom):
741       if (mesh->Nodes!=NULL) {
742          numDataPointsPerSample=1;
743          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
744       }
745       break;
746       default:
747          stringstream temp;
748          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
749          throw FinleyAdapterException(temp.str());
750          break;
751       }
752       return pair<int,int>(numDataPointsPerSample,numSamples);
753  }  }
754    
755  //  //
756  // 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:
757  //  //
758  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
759                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
760                       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,
761                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
762                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
763  {  {
764    escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
765    escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
766    escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
767    escriptDataC _C=C.getDataC();     escriptDataC _C=C.getDataC();
768    escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
769    escriptDataC _X=X.getDataC();     escriptDataC _X=X.getDataC();
770    escriptDataC _Y=Y.getDataC();     escriptDataC _Y=Y.getDataC();
771    escriptDataC _d=d.getDataC();     escriptDataC _d=d.getDataC();
772    escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
773    escriptDataC _d_contact=d_contact.getDataC();     escriptDataC _d_contact=d_contact.getDataC();
774    escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
775    
776     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
777    
778     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
779       checkFinleyError();
780    
781       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
782     checkFinleyError();     checkFinleyError();
783    
784     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, &_d, &_y, Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
785     checkFinleyError();     checkFinleyError();
786    }
787    
788    void  MeshAdapter::addPDEToLumpedSystem(
789                                            escript::Data& mat,
790                                            const escript::Data& D,
791                                            const escript::Data& d) const
792    {
793       escriptDataC _mat=mat.getDataC();
794       escriptDataC _D=D.getDataC();
795       escriptDataC _d=d.getDataC();
796    
797       Finley_Mesh* mesh=m_finleyMesh.get();
798    
799       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
800       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
801    
    Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , &_d_contact, &_y_contact ,             Finley_Assemble_handelShapeMissMatch_Step_out);  
802     checkFinleyError();     checkFinleyError();
803  }  }
804    
805    
806  //  //
807  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
808  //  //
# Line 283  void MeshAdapter::addPDEToRHS( escript:: Line 810  void MeshAdapter::addPDEToRHS( escript::
810  {  {
811     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
812    
813     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
814     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
815       escriptDataC _Y=Y.getDataC();
816       escriptDataC _y=y.getDataC();
817       escriptDataC _y_contact=y_contact.getDataC();
818    
819       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
820     checkFinleyError();     checkFinleyError();
821    
822     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->FaceElements,&(rhs.getDataC()),&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
823     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
824    
825       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
826     checkFinleyError();     checkFinleyError();
827     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  }
828     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->ContactElements,&(rhs.getDataC()),&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  //
829    // adds PDE of second order into a transport problem
830    //
831    void MeshAdapter::addPDEToTransportProblem(
832                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
833                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
834                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
835                                               const escript::Data& d, const escript::Data& y,
836                                               const escript::Data& d_contact,const escript::Data& y_contact) const
837    {
838       DataTypes::ShapeType shape;
839       source.expand();
840       escriptDataC _source=source.getDataC();
841       escriptDataC _M=M.getDataC();
842       escriptDataC _A=A.getDataC();
843       escriptDataC _B=B.getDataC();
844       escriptDataC _C=C.getDataC();
845       escriptDataC _D=D.getDataC();
846       escriptDataC _X=X.getDataC();
847       escriptDataC _Y=Y.getDataC();
848       escriptDataC _d=d.getDataC();
849       escriptDataC _y=y.getDataC();
850       escriptDataC _d_contact=d_contact.getDataC();
851       escriptDataC _y_contact=y_contact.getDataC();
852    
853       Finley_Mesh* mesh=m_finleyMesh.get();
854       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
855    
856       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
857       checkFinleyError();
858    
859       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
860       checkFinleyError();
861    
862       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
863       checkFinleyError();
864    
865       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
866     checkFinleyError();     checkFinleyError();
867  }  }
868    
# Line 301  void MeshAdapter::addPDEToRHS( escript:: Line 871  void MeshAdapter::addPDEToRHS( escript::
871  //  //
872  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
873  {  {
874    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
875    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
876    if (inDomain!=*this)       if (inDomain!=*this)  
877      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
878    if (targetDomain!=*this)     if (targetDomain!=*this)
879      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
880    
881    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
882    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
883       case(Nodes):     escriptDataC _in=in.getDataC();
884          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
885             case(Nodes):     case(Nodes):
886             case(ReducedDegreesOfFreedom):     switch(target.getFunctionSpace().getTypeCode()) {
887             case(DegreesOfFreedom):     case(Nodes):
888                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));     case(ReducedNodes):
889                 break;     case(DegreesOfFreedom):
890             case(Elements):     case(ReducedDegreesOfFreedom):
891                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
892                 break;     break;
893             case(FaceElements):     case(Elements):
894                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     case(ReducedElements):
895                 break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
896             case(Points):     break;
897                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     case(FaceElements):
898                 break;     case(ReducedFaceElements):
899             case(ContactElementsZero):     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
900                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
901                 break;     case(Points):
902             case(ContactElementsOne):     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
903                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
904                 break;     case(ContactElementsZero):
905             default:     case(ReducedContactElementsZero):
906                 stringstream temp;     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
907                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     break;
908                 throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
909                 break;     case(ReducedContactElementsOne):
910          }     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
911          break;     break;
912       case(Elements):     default:
913          if (target.getFunctionSpace().getTypeCode()==Elements) {        stringstream temp;
914             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();
915          } else {        throw FinleyAdapterException(temp.str());
916             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        break;
917          }     }
918          break;     break;
919       case(FaceElements):     case(ReducedNodes):
920          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     switch(target.getFunctionSpace().getTypeCode()) {
921             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));     case(Nodes):
922          } else {     case(ReducedNodes):
923             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");     case(DegreesOfFreedom):
924             break;     case(ReducedDegreesOfFreedom):
925         }     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
926       case(Points):     break;
927          if (target.getFunctionSpace().getTypeCode()==Points) {     case(Elements):
928             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));     case(ReducedElements):
929          } else {     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
930             throw FinleyAdapterException("Error - No interpolation with data on points possible.");     break;
931             break;     case(FaceElements):
932          }     case(ReducedFaceElements):
933          break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
934       case(ContactElementsZero):     break;
935       case(ContactElementsOne):     case(Points):
936          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
937             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));     break;
938          } else {     case(ContactElementsZero):
939             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");     case(ReducedContactElementsZero):
940             break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
941          }     break;
942          break;     case(ContactElementsOne):
943       case(DegreesOfFreedom):           case(ReducedContactElementsOne):
944          switch(target.getFunctionSpace().getTypeCode()) {     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
945             case(ReducedDegreesOfFreedom):     break;
946             case(DegreesOfFreedom):     default:
947             case(Nodes):        stringstream temp;
948                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();
949                break;        throw FinleyAdapterException(temp.str());
950  #ifndef PASO_MPI        break;
951             case(Elements):     }
952                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     break;
953                break;     case(Elements):
954             case(FaceElements):     if (target.getFunctionSpace().getTypeCode()==Elements) {
955                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
956                break;     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
957             case(Points):        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
958                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     } else {
959                break;        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
960             case(ContactElementsZero):     }
961             case(ContactElementsOne):     break;
962                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     case(ReducedElements):
963               break;     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
964  #else        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
965             /* need to copy Degrees of freedom data to nodal data so that the external values are available */     } else {
966             case(Elements):        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
967             {     }
968                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );     break;
969                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(nodeTemp.getDataC()),&(target.getDataC()));     case(FaceElements):
970                break;     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
971             }        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
972             case(FaceElements):     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
973             {        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
974                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );     } else {
975                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(nodeTemp.getDataC()),&(target.getDataC()));        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
976                break;     }
977             }     break;
978             case(Points):     case(ReducedFaceElements):
979             {     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
980                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
981                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(nodeTemp.getDataC()),&(target.getDataC()));     } else {
982                break;        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
983             }     }
984             case(ContactElementsZero):     break;
985             case(ContactElementsOne):     case(Points):
986             {     if (target.getFunctionSpace().getTypeCode()==Points) {
987                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
988                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(nodeTemp.getDataC()),&(target.getDataC()));     } else {
989               break;        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
990             }     }
991  #endif     break;
992             default:     case(ContactElementsZero):
993               stringstream temp;     case(ContactElementsOne):
994               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
995               throw FinleyAdapterException(temp.str());        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
996               break;     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
997          }        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
998          break;     } else {
999       case(ReducedDegreesOfFreedom):        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1000         switch(target.getFunctionSpace().getTypeCode()) {     }
1001            case(ReducedDegreesOfFreedom):     break;
1002               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));     case(ReducedContactElementsZero):
1003               break;     case(ReducedContactElementsOne):
1004            case(Elements):     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1005               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1006               break;     } else {
1007            case(FaceElements):        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1008               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     }
1009               break;     break;
1010            case(Points):     case(DegreesOfFreedom):      
1011               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     switch(target.getFunctionSpace().getTypeCode()) {
1012               break;     case(ReducedDegreesOfFreedom):
1013            case(ContactElementsZero):     case(DegreesOfFreedom):
1014            case(ContactElementsOne):     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1015               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
1016               break;  
1017            case(Nodes):     case(Nodes):
1018               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");     case(ReducedNodes):
1019               break;     if (getMPISize()>1) {
1020            case(DegreesOfFreedom):        escript::Data temp=escript::Data(in);
1021               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        temp.expand();
1022               break;        escriptDataC _in2 = temp.getDataC();
1023            default:        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1024               stringstream temp;     } else {
1025               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1026               throw FinleyAdapterException(temp.str());     }
1027               break;     break;
1028         }     case(Elements):
1029         break;     case(ReducedElements):
1030       default:     if (getMPISize()>1) {
1031          stringstream temp;        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1032          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        escriptDataC _in2 = temp.getDataC();
1033          throw FinleyAdapterException(temp.str());        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1034          break;     } else {
1035    }        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1036    checkFinleyError();     }
1037       break;
1038       case(FaceElements):
1039       case(ReducedFaceElements):
1040       if (getMPISize()>1) {
1041          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1042          escriptDataC _in2 = temp.getDataC();
1043          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1044    
1045       } else {
1046          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1047       }
1048       break;
1049       case(Points):
1050       if (getMPISize()>1) {
1051          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1052          escriptDataC _in2 = temp.getDataC();
1053       } else {
1054          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1055       }
1056       break;
1057       case(ContactElementsZero):
1058       case(ContactElementsOne):
1059       case(ReducedContactElementsZero):
1060       case(ReducedContactElementsOne):
1061       if (getMPISize()>1) {
1062          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1063          escriptDataC _in2 = temp.getDataC();
1064          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1065       } else {
1066          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1067       }
1068       break;
1069       default:
1070          stringstream temp;
1071          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1072          throw FinleyAdapterException(temp.str());
1073          break;
1074       }
1075       break;
1076       case(ReducedDegreesOfFreedom):
1077       switch(target.getFunctionSpace().getTypeCode()) {
1078       case(Nodes):
1079       throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1080       break;
1081       case(ReducedNodes):
1082       if (getMPISize()>1) {
1083          escript::Data temp=escript::Data(in);
1084          temp.expand();
1085          escriptDataC _in2 = temp.getDataC();
1086          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1087       } else {
1088          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1089       }
1090       break;
1091       case(DegreesOfFreedom):
1092       throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1093       break;
1094       case(ReducedDegreesOfFreedom):
1095       Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1096       break;
1097       case(Elements):
1098       case(ReducedElements):
1099       if (getMPISize()>1) {
1100          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1101          escriptDataC _in2 = temp.getDataC();
1102          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1103       } else {
1104          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1105       }
1106       break;
1107       case(FaceElements):
1108       case(ReducedFaceElements):
1109       if (getMPISize()>1) {
1110          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1111          escriptDataC _in2 = temp.getDataC();
1112          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1113       } else {
1114          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1115       }
1116       break;
1117       case(Points):
1118       if (getMPISize()>1) {
1119          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1120          escriptDataC _in2 = temp.getDataC();
1121          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1122       } else {
1123          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1124       }
1125       break;
1126       case(ContactElementsZero):
1127       case(ContactElementsOne):
1128       case(ReducedContactElementsZero):
1129       case(ReducedContactElementsOne):
1130       if (getMPISize()>1) {
1131          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1132          escriptDataC _in2 = temp.getDataC();
1133          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1134       } else {
1135          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1136       }
1137       break;
1138       default:
1139          stringstream temp;
1140          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1141          throw FinleyAdapterException(temp.str());
1142          break;
1143       }
1144       break;
1145       default:
1146          stringstream temp;
1147          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1148          throw FinleyAdapterException(temp.str());
1149          break;
1150       }
1151       checkFinleyError();
1152  }  }
1153    
1154  //  //
# Line 471  void MeshAdapter::interpolateOnDomain(es Line 1156  void MeshAdapter::interpolateOnDomain(es
1156  //  //
1157  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1158  {  {
1159    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1160    if (argDomain!=*this)     if (argDomain!=*this)
1161       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1162    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1163    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1164    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1165       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1166    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1167       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1168       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1169       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1170       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1171    }        // this is then interpolated onto arg:
1172    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1173       }
1174       checkFinleyError();
1175  }  }
1176    
1177  //  //
# Line 492  void MeshAdapter::setToX(escript::Data& Line 1179  void MeshAdapter::setToX(escript::Data&
1179  //  //
1180  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1181  {  {
1182    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1183    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1184       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1185    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1186    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1187      case(Nodes):     escriptDataC _normal=normal.getDataC();
1188        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     switch(normal.getFunctionSpace().getTypeCode()) {
1189        break;     case(Nodes):
1190      case(Elements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1191        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     break;
1192        break;     case(ReducedNodes):
1193      case (FaceElements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1194        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     break;
1195        break;     case(Elements):
1196      case(Points):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1197        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     break;
1198        break;     case(ReducedElements):
1199      case (ContactElementsOne):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1200      case (ContactElementsZero):     break;
1201        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (FaceElements):
1202        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1203      case(DegreesOfFreedom):     break;
1204        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case (ReducedFaceElements):
1205        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1206      case(ReducedDegreesOfFreedom):     break;
1207        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(Points):
1208        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1209      default:     break;
1210       case (ContactElementsOne):
1211       case (ContactElementsZero):
1212       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1213       break;
1214       case (ReducedContactElementsOne):
1215       case (ReducedContactElementsZero):
1216       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1217       break;
1218       case(DegreesOfFreedom):
1219       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1220       break;
1221       case(ReducedDegreesOfFreedom):
1222       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1223       break;
1224       default:
1225        stringstream temp;        stringstream temp;
1226        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();
1227        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1228        break;        break;
1229    }     }
1230    checkFinleyError();     checkFinleyError();
1231  }  }
1232    
1233  //  //
# Line 533  void MeshAdapter::setToNormal(escript::D Line 1235  void MeshAdapter::setToNormal(escript::D
1235  //  //
1236  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1237  {  {
1238    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
1239    if (targetDomain!=*this)     if (targetDomain!=*this)
1240       throw FinleyAdapterException("Error - Illegal domain of interpolation target");        throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1241    
1242    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1243  }  }
1244    
1245  //  //
# Line 545  void MeshAdapter::interpolateACross(escr Line 1247  void MeshAdapter::interpolateACross(escr
1247  //  //
1248  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1249  {  {
1250    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1251    if (argDomain!=*this)     if (argDomain!=*this)
1252       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1253    
1254    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1255    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1256       case(Nodes):     escriptDataC _temp;
1257          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1258          break;     escriptDataC _arg=arg.getDataC();
1259       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1260          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1261          break;     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1262       case(FaceElements):     _temp=temp.getDataC();
1263          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1264          break;     break;
1265       case(Points):     case(ReducedNodes):
1266          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1267          break;     _temp=temp.getDataC();
1268       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1269          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1270          break;     case(Elements):
1271       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1272          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1273          break;     case(ReducedElements):
1274       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1275          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1276          break;     case(FaceElements):
1277       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1278          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1279          break;     case(ReducedFaceElements):
1280       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1281          stringstream temp;     break;
1282          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1283          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1284          break;     break;
1285    }     case(ContactElementsZero):
1286    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287       break;
1288       case(ReducedContactElementsZero):
1289       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1290       break;
1291       case(ContactElementsOne):
1292       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1293       break;
1294       case(ReducedContactElementsOne):
1295       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1296       break;
1297       case(DegreesOfFreedom):
1298       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1299       _temp=temp.getDataC();
1300       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1301       break;
1302       case(ReducedDegreesOfFreedom):
1303       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1304       _temp=temp.getDataC();
1305       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1306       break;
1307       default:
1308          stringstream temp;
1309          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1310          throw FinleyAdapterException(temp.str());
1311          break;
1312       }
1313       checkFinleyError();
1314       blocktimer_increment("integrate()", blocktimer_start);
1315  }  }
1316    
1317  //  //
# Line 589  void MeshAdapter::setToIntegrals(std::ve Line 1319  void MeshAdapter::setToIntegrals(std::ve
1319  //  //
1320  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1321  {  {
1322    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1323    if (argDomain!=*this)     if (argDomain!=*this)
1324      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1325    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1326    if (gradDomain!=*this)     if (gradDomain!=*this)
1327       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1328    
1329    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1330    escriptDataC nodeDataC;     escriptDataC _grad=grad.getDataC();
1331  #ifdef PASO_MPI     escriptDataC nodeDataC;
1332    escript::Data nodeTemp( arg, continuousFunction(asAbstractContinuousDomain()) );     escript::Data temp;
1333    if( arg.getFunctionSpace().getTypeCode() != Nodes )     if (getMPISize()>1) {
1334    {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1335      Finley_Assemble_CopyNodalData(mesh->Nodes,&(nodeTemp.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1336      nodeDataC = nodeTemp.getDataC();           nodeDataC = temp.getDataC();
1337    }        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1338    else           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1339      nodeDataC = arg.getDataC();           nodeDataC = temp.getDataC();
1340  #else        } else {
1341    nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1342  #endif        }
1343    switch(grad.getFunctionSpace().getTypeCode()) {     } else {
1344         case(Nodes):        nodeDataC = arg.getDataC();
1345            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     }
1346            break;     switch(grad.getFunctionSpace().getTypeCode()) {
1347         case(Elements):     case(Nodes):
1348            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&nodeDataC);     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1349            break;     break;
1350         case(FaceElements):     case(ReducedNodes):
1351            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&nodeDataC);     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1352            break;     break;
1353         case(Points):     case(Elements):
1354            throw FinleyAdapterException("Error - Gradient at points is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1355            break;     break;
1356         case(ContactElementsZero):     case(ReducedElements):
1357            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1358            break;     break;
1359         case(ContactElementsOne):     case(FaceElements):
1360            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1361            break;     break;
1362         case(DegreesOfFreedom):     case(ReducedFaceElements):
1363            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1364            break;     break;
1365         case(ReducedDegreesOfFreedom):     case(Points):
1366            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1367            break;     break;
1368         default:     case(ContactElementsZero):
1369            stringstream temp;     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     break;
1371            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1372            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1373    }     break;
1374    checkFinleyError();     case(ContactElementsOne):
1375       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1376       break;
1377       case(ReducedContactElementsOne):
1378       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1379       break;
1380       case(DegreesOfFreedom):
1381       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1382       break;
1383       case(ReducedDegreesOfFreedom):
1384       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1385       break;
1386       default:
1387          stringstream temp;
1388          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1389          throw FinleyAdapterException(temp.str());
1390          break;
1391       }
1392       checkFinleyError();
1393  }  }
1394    
1395  //  //
# Line 649  void MeshAdapter::setToGradient(escript: Line 1397  void MeshAdapter::setToGradient(escript:
1397  //  //
1398  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1399  {  {
1400    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1401    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1402    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1403         case(Nodes):     case(Nodes):
1404            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1405            break;     break;
1406         case(Elements):     case(ReducedNodes):
1407            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1408            break;     break;
1409         case(FaceElements):     case(Elements):
1410            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1411            break;     break;
1412         case(Points):     case(ReducedElements):
1413            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1414            break;     break;
1415         case(ContactElementsZero):     case(FaceElements):
1416         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1417            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1418            break;     case(ReducedFaceElements):
1419         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1420            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1421            break;     case(Points):
1422         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1423            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1424            break;     case(ContactElementsZero):
1425         default:     case(ContactElementsOne):
1426            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1427            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1428            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1429            break;     case(ReducedContactElementsOne):
1430    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1431    checkFinleyError();     break;
1432       case(DegreesOfFreedom):
1433       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1434       break;
1435       case(ReducedDegreesOfFreedom):
1436       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1437       break;
1438       default:
1439          stringstream temp;
1440          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1441          throw FinleyAdapterException(temp.str());
1442          break;
1443       }
1444       checkFinleyError();
1445  }  }
1446    
1447  // sets the location of nodes:  // sets the location of nodes:
1448  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1449  {  {
1450    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1451    escriptDataC tmp;     escriptDataC tmp;
1452    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1453    if (newDomain!=*this)     if (newDomain!=*this)
1454       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1455    tmp = new_x.getDataC();     tmp = new_x.getDataC();
1456    Finley_Mesh_setCoordinates(mesh,&tmp);     Finley_Mesh_setCoordinates(mesh,&tmp);
1457    checkFinleyError();     checkFinleyError();
1458  }  }
1459    
1460  // saves a data array in openDX format:  // saves a data array in openDX format:
1461  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
1462  {  {
1463      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1464      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1465    /* win32 refactor */     /* win32 refactor */
1466    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1467    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1468    {     {
1469      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1470    }     }
1471    
1472    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1473    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1474    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
1475       boost::python::list keys=arg.keys();
1476      boost::python::list keys=arg.keys();     for (int i=0;i<num_data;++i) {
1477      for (int i=0;i<num_data;++i) {        std::string n=boost::python::extract<std::string>(keys[i]);
1478           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1479           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1480               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1481           data[i]=d.getDataC();        data[i]=d.getDataC();
1482           ptr_data[i]=&(data[i]);        ptr_data[i]= &(data[i]);
1483           std::string n=boost::python::extract<std::string>(keys[i]);        if (n.length()>MAX_namelength-1) {
1484           c_names[i]=&(names[i][0]);           strncpy(names[i],n.c_str(),MAX_namelength-1);
1485           if (n.length()>MAX_namelength-1) {           names[i][MAX_namelength-1]='\0';
1486              strncpy(c_names[i],n.c_str(),MAX_namelength-1);        } else {
1487              c_names[i][MAX_namelength-1]='\0';           strcpy(names[i],n.c_str());
1488           } else {        }
1489              strcpy(c_names[i],n.c_str());     }
1490           }     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1491      }     checkFinleyError();
1492      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
1493      checkFinleyError();     /* win32 refactor */
1494           TMPMEMFREE(data);
1495        /* win32 refactor */     TMPMEMFREE(ptr_data);
1496    TMPMEMFREE(c_names);     for(int i=0;i<num_data;i++)
1497    TMPMEMFREE(data);     {
1498    TMPMEMFREE(ptr_data);        TMPMEMFREE(names[i]);
1499    for(int i=0;i<num_data;i++)     }
1500    {     TMPMEMFREE(names);
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1501    
1502      return;     return;
1503  }  }
1504    
1505  // saves a data array in openVTK format:  // saves a data array in openVTK format:
1506  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1507  {  {
1508      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1509      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1510    /* win32 refactor */     /* win32 refactor */
1511    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1512    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1513    {     {
1514      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1515    }     }
1516    
1517       escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1518       escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1519    
1520       boost::python::list keys=arg.keys();
1521       for (int i=0;i<num_data;++i) {
1522          std::string n=boost::python::extract<std::string>(keys[i]);
1523          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1524          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1525             throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1526          data[i]=d.getDataC();
1527          ptr_data[i]=&(data[i]);
1528          if (n.length()>MAX_namelength-1) {
1529             strncpy(names[i],n.c_str(),MAX_namelength-1);
1530             names[i][MAX_namelength-1]='\0';
1531          } else {
1532             strcpy(names[i],n.c_str());
1533          }
1534       }
1535       Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1536    
1537    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     checkFinleyError();
1538    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     /* win32 refactor */
1539    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;     TMPMEMFREE(data);
1540       TMPMEMFREE(ptr_data);
1541      boost::python::list keys=arg.keys();     for(int i=0;i<num_data;i++)
1542      for (int i=0;i<num_data;++i) {     {
1543           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);        TMPMEMFREE(names[i]);
1544           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     }
1545               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     TMPMEMFREE(names);
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          c_names[i]=&(names[i][0]);  
          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();  
   /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1546    
1547      return;     return;
1548  }  }
1549                                                                                                                                                                                                                                                                                                                                                
1550                                                                                                                                                                                                                                                                                                                                                
1551  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1552  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1553                        const int row_blocksize,                                                   const int row_blocksize,
1554                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1555                        const int column_blocksize,                                                   const int column_blocksize,
1556                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1557                        const int type) const                                                   const int type) const
1558  {  {
1559      int reduceRowOrder=0;     int reduceRowOrder=0;
1560      int reduceColOrder=0;     int reduceColOrder=0;
1561      // is the domain right?     // is the domain right?
1562      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1563      if (row_domain!=*this)     if (row_domain!=*this)
1564            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.");
1565      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1566      if (col_domain!=*this)     if (col_domain!=*this)
1567            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.");
1568      // is the function space type right     // is the function space type right
1569      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1570          reduceRowOrder=0;        reduceRowOrder=0;
1571      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1572          reduceRowOrder=1;        reduceRowOrder=1;
1573      } else {     } else {
1574          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1575      }     }
1576      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1577          reduceColOrder=0;        reduceColOrder=0;
1578      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1579          reduceColOrder=1;        reduceColOrder=1;
1580      } else {     } else {
1581          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1582      }     }
1583      // generate matrix:     // generate matrix:
1584        
1585      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1586      checkFinleyError();     checkFinleyError();
1587      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1588      checkPasoError();     int trilinos = 0;
1589      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1590      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1591          /* Allocation Epetra_VrbMatrix here */
1592    #endif
1593       }
1594       else {
1595          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1596       }
1597       checkPasoError();
1598       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1599       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1600    }
1601    // creates a TransportProblemAdapter
1602    TransportProblemAdapter MeshAdapter::newTransportProblem(
1603                                                             const double theta,
1604                                                             const int blocksize,
1605                                                             const escript::FunctionSpace& functionspace,
1606                                                             const int type) const
1607    {
1608       int reduceOrder=0;
1609       // is the domain right?
1610       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1611       if (domain!=*this)
1612          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1613       // is the function space type right
1614       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1615          reduceOrder=0;
1616       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1617          reduceOrder=1;
1618       } else {
1619          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1620       }
1621       // generate matrix:
1622    
1623       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1624       checkFinleyError();
1625       Paso_FCTransportProblem* transportProblem;
1626       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1627       checkPasoError();
1628       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1629       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1630  }  }
1631    
1632  //  //
# Line 843  SystemMatrixAdapter MeshAdapter::newSyst Line 1638  SystemMatrixAdapter MeshAdapter::newSyst
1638  // 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:
1639  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1640  {  {
1641    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1642         case(Nodes):     case(Nodes):
1643         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1644         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1645            return false;     return false;
1646            break;     break;
1647         case(Elements):     case(Elements):
1648         case(FaceElements):     case(FaceElements):
1649         case(Points):     case(Points):
1650         case(ContactElementsZero):     case(ContactElementsZero):
1651         case(ContactElementsOne):     case(ContactElementsOne):
1652            return true;     case(ReducedElements):
1653            break;     case(ReducedFaceElements):
1654         default:     case(ReducedContactElementsZero):
1655            stringstream temp;     case(ReducedContactElementsOne):
1656            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1657            throw FinleyAdapterException(temp.str());     break;
1658            break;     default:
1659    }        stringstream temp;
1660    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1661    return false;        throw FinleyAdapterException(temp.str());
1662          break;
1663       }
1664       checkFinleyError();
1665       return false;
1666  }  }
1667    
1668  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1669  {  {
1670    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1671       case(Nodes):     case(Nodes):
1672          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1673             case(Nodes):     case(Nodes):
1674             case(ReducedDegreesOfFreedom):     case(ReducedNodes):
1675             case(DegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1676             case(Elements):     case(DegreesOfFreedom):
1677             case(FaceElements):     case(Elements):
1678             case(Points):     case(ReducedElements):
1679             case(ContactElementsZero):     case(FaceElements):
1680             case(ContactElementsOne):     case(ReducedFaceElements):
1681                 return true;     case(Points):
1682             default:     case(ContactElementsZero):
1683                 stringstream temp;     case(ReducedContactElementsZero):
1684                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(ContactElementsOne):
1685                 throw FinleyAdapterException(temp.str());     case(ReducedContactElementsOne):
1686          }     return true;
1687          break;     default:
1688       case(Elements):        stringstream temp;
1689          if (functionSpaceType_target==Elements) {        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1690             return true;        throw FinleyAdapterException(temp.str());
1691          } else {     }
1692             return false;     break;
1693          }     case(ReducedNodes):
1694       case(FaceElements):     switch(functionSpaceType_target) {
1695          if (functionSpaceType_target==FaceElements) {     case(ReducedNodes):
1696             return true;     case(ReducedDegreesOfFreedom):
1697          } else {     case(Elements):
1698             return false;     case(ReducedElements):
1699          }     case(FaceElements):
1700       case(Points):     case(ReducedFaceElements):
1701          if (functionSpaceType_target==Points) {     case(Points):
1702             return true;     case(ContactElementsZero):
1703          } else {     case(ReducedContactElementsZero):
1704             return false;     case(ContactElementsOne):
1705          }     case(ReducedContactElementsOne):
1706       case(ContactElementsZero):     return true;
1707       case(ContactElementsOne):     case(Nodes):
1708          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     case(DegreesOfFreedom):
1709             return true;     return false;
1710          } else {     default:
1711             return false;        stringstream temp;
1712          }        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1713       case(DegreesOfFreedom):        throw FinleyAdapterException(temp.str());
1714          switch(functionSpaceType_target) {     }
1715             case(ReducedDegreesOfFreedom):     break;
1716             case(DegreesOfFreedom):     case(Elements):
1717             case(Nodes):     if (functionSpaceType_target==Elements) {
1718             case(Elements):        return true;
1719             case(FaceElements):     } else if (functionSpaceType_target==ReducedElements) {
1720             case(Points):        return true;
1721             case(ContactElementsZero):     } else {
1722             case(ContactElementsOne):        return false;
1723                return true;     }
1724             default:     case(ReducedElements):
1725               stringstream temp;     if (functionSpaceType_target==ReducedElements) {
1726               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;        return true;
1727               throw FinleyAdapterException(temp.str());     } else {
1728          }        return false;
1729          break;     }
1730       case(ReducedDegreesOfFreedom):     case(FaceElements):
1731         switch(functionSpaceType_target) {     if (functionSpaceType_target==FaceElements) {
1732            case(ReducedDegreesOfFreedom):        return true;
1733            case(Elements):     } else if (functionSpaceType_target==ReducedFaceElements) {
1734            case(FaceElements):        return true;
1735            case(Points):     } else {
1736            case(ContactElementsZero):        return false;
1737            case(ContactElementsOne):     }
1738                return true;     case(ReducedFaceElements):
1739            case(Nodes):     if (functionSpaceType_target==ReducedFaceElements) {
1740            case(DegreesOfFreedom):        return true;
1741               return false;     } else {
1742            default:        return false;
1743               stringstream temp;     }
1744               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1745               throw FinleyAdapterException(temp.str());     if (functionSpaceType_target==Points) {
1746         }        return true;
1747         break;     } else {
1748       default:        return false;
1749          stringstream temp;     }
1750          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1751          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1752          break;     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1753    }        return true;
1754    checkFinleyError();     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1755    return false;        return true;
1756       } else {
1757          return false;
1758       }
1759       case(ReducedContactElementsZero):
1760       case(ReducedContactElementsOne):
1761       if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1762          return true;
1763       } else {
1764          return false;
1765       }
1766       case(DegreesOfFreedom):
1767       switch(functionSpaceType_target) {
1768       case(ReducedDegreesOfFreedom):
1769       case(DegreesOfFreedom):
1770       case(Nodes):
1771       case(ReducedNodes):
1772       case(Elements):
1773       case(ReducedElements):
1774       case(Points):
1775       case(FaceElements):
1776       case(ReducedFaceElements):
1777       case(ContactElementsZero):
1778       case(ReducedContactElementsZero):
1779       case(ContactElementsOne):
1780       case(ReducedContactElementsOne):
1781       return true;
1782       default:
1783          stringstream temp;
1784          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1785          throw FinleyAdapterException(temp.str());
1786       }
1787       break;
1788       case(ReducedDegreesOfFreedom):
1789       switch(functionSpaceType_target) {
1790       case(ReducedDegreesOfFreedom):
1791       case(ReducedNodes):
1792       case(Elements):
1793       case(ReducedElements):
1794       case(FaceElements):
1795       case(ReducedFaceElements):
1796       case(Points):
1797       case(ContactElementsZero):
1798       case(ReducedContactElementsZero):
1799       case(ContactElementsOne):
1800       case(ReducedContactElementsOne):
1801       return true;
1802       case(Nodes):
1803       case(DegreesOfFreedom):
1804       return false;
1805       default:
1806          stringstream temp;
1807          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1808          throw FinleyAdapterException(temp.str());
1809       }
1810       break;
1811       default:
1812          stringstream temp;
1813          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1814          throw FinleyAdapterException(temp.str());
1815          break;
1816       }
1817       checkFinleyError();
1818       return false;
1819  }  }
1820    
1821  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
1822  {  {
1823      return false;     return false;
1824  }  }
1825    
1826  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1827  {  {
1828    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1829    if (temp!=0) {     if (temp!=0) {
1830      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1831    } else {     } else {
1832      return false;        return false;
1833    }     }
1834  }  }
1835    
1836  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1837  {  {
1838    return !(operator==(other));     return !(operator==(other));
1839  }  }
1840    
1841  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
1842  {  {
1843     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1844       checkPasoError();
1845       return out;
1846    }
1847    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1848    {
1849       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1850     checkPasoError();     checkPasoError();
1851     return out;     return out;
1852  }  }
1853    
1854  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1855  {  {
1856    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1857  }  }
1858    
1859  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1860  {  {
1861    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1862  }  }
1863    
1864  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1865  {  {
1866    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1867  }  }
1868    
1869    int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1870    {
1871       int *out = NULL;
1872       Finley_Mesh* mesh=m_finleyMesh.get();
1873       switch (functionSpaceType) {
1874       case(Nodes):
1875       out=mesh->Nodes->Id;
1876       break;
1877       case(ReducedNodes):
1878       out=mesh->Nodes->reducedNodesId;
1879       break;
1880       case(Elements):
1881       out=mesh->Elements->Id;
1882       break;
1883       case(ReducedElements):
1884       out=mesh->Elements->Id;
1885       break;
1886       case(FaceElements):
1887       out=mesh->FaceElements->Id;
1888       break;
1889       case(ReducedFaceElements):
1890       out=mesh->FaceElements->Id;
1891       break;
1892       case(Points):
1893       out=mesh->Points->Id;
1894       break;
1895       case(ContactElementsZero):
1896       out=mesh->ContactElements->Id;
1897       break;
1898       case(ReducedContactElementsZero):
1899       out=mesh->ContactElements->Id;
1900       break;
1901       case(ContactElementsOne):
1902       out=mesh->ContactElements->Id;
1903       break;
1904       case(ReducedContactElementsOne):
1905       out=mesh->ContactElements->Id;
1906       break;
1907       case(DegreesOfFreedom):
1908       out=mesh->Nodes->degreesOfFreedomId;
1909       break;
1910       case(ReducedDegreesOfFreedom):
1911       out=mesh->Nodes->reducedDegreesOfFreedomId;
1912       break;
1913       default:
1914          stringstream temp;
1915          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1916          throw FinleyAdapterException(temp.str());
1917          break;
1918       }
1919       return out;
1920    }
1921  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1922  {  {
1923    int out=0;     int out=0;
1924       Finley_Mesh* mesh=m_finleyMesh.get();
1925       switch (functionSpaceType) {
1926       case(Nodes):
1927       out=mesh->Nodes->Tag[sampleNo];
1928       break;
1929       case(ReducedNodes):
1930       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1931       break;
1932       case(Elements):
1933       out=mesh->Elements->Tag[sampleNo];
1934       break;
1935       case(ReducedElements):
1936       out=mesh->Elements->Tag[sampleNo];
1937       break;
1938       case(FaceElements):
1939       out=mesh->FaceElements->Tag[sampleNo];
1940       break;
1941       case(ReducedFaceElements):
1942       out=mesh->FaceElements->Tag[sampleNo];
1943       break;
1944       case(Points):
1945       out=mesh->Points->Tag[sampleNo];
1946       break;
1947       case(ContactElementsZero):
1948       out=mesh->ContactElements->Tag[sampleNo];
1949       break;
1950       case(ReducedContactElementsZero):
1951       out=mesh->ContactElements->Tag[sampleNo];
1952       break;
1953       case(ContactElementsOne):
1954       out=mesh->ContactElements->Tag[sampleNo];
1955       break;
1956       case(ReducedContactElementsOne):
1957       out=mesh->ContactElements->Tag[sampleNo];
1958       break;
1959       case(DegreesOfFreedom):
1960       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1961       break;
1962       case(ReducedDegreesOfFreedom):
1963       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1964       break;
1965       default:
1966          stringstream temp;
1967          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1968          throw FinleyAdapterException(temp.str());
1969          break;
1970       }
1971       return out;
1972    }
1973    
1974    
1975    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1976    {
1977       Finley_Mesh* mesh=m_finleyMesh.get();
1978       escriptDataC tmp=mask.getDataC();
1979       switch(functionSpaceType) {
1980       case(Nodes):
1981       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1982       break;
1983       case(ReducedNodes):
1984       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1985       break;
1986       case(DegreesOfFreedom):
1987       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1988       break;
1989       case(ReducedDegreesOfFreedom):
1990       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1991       break;
1992       case(Elements):
1993       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1994       break;
1995       case(ReducedElements):
1996       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1997       break;
1998       case(FaceElements):
1999       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2000       break;
2001       case(ReducedFaceElements):
2002       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2003       break;
2004       case(Points):
2005       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2006       break;
2007       case(ContactElementsZero):
2008       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2009       break;
2010       case(ReducedContactElementsZero):
2011       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2012       break;
2013       case(ContactElementsOne):
2014       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2015       break;
2016       case(ReducedContactElementsOne):
2017       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2018       break;
2019       default:
2020          stringstream temp;
2021          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2022          throw FinleyAdapterException(temp.str());
2023       }
2024       checkFinleyError();
2025       return;
2026    }
2027    
2028    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2029    {
2030       Finley_Mesh* mesh=m_finleyMesh.get();
2031       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2032       checkPasoError();
2033       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2034    }
2035    
2036    int MeshAdapter::getTag(const std::string& name) const
2037    {
2038       Finley_Mesh* mesh=m_finleyMesh.get();
2039       int tag=0;
2040       tag=Finley_Mesh_getTag(mesh, name.c_str());
2041       checkPasoError();
2042       // throwStandardException("MeshAdapter::getTag is not implemented.");
2043       return tag;
2044    }
2045    
2046    bool MeshAdapter::isValidTagName(const std::string& name) const
2047    {
2048       Finley_Mesh* mesh=m_finleyMesh.get();
2049       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2050    }
2051    
2052    std::string MeshAdapter::showTagNames() const
2053    {
2054       stringstream temp;
2055       Finley_Mesh* mesh=m_finleyMesh.get();
2056       Finley_TagMap* tag_map=mesh->TagMap;
2057       while (tag_map) {
2058          temp << tag_map->name;
2059          tag_map=tag_map->next;
2060          if (tag_map) temp << ", ";
2061       }
2062       return temp.str();
2063    }
2064    
2065    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2066    {
2067    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2068    switch (functionSpaceType) {    dim_t numTags=0;
2069    case(Nodes):    switch(functionSpaceCode) {
2070      out=mesh->Nodes->Tag[sampleNo];     case(Nodes):
2071      break;            numTags=mesh->Nodes->numTagsInUse;
2072    case(Elements):            break;
2073      out=mesh->Elements->Tag[sampleNo];     case(ReducedNodes):
2074      break;            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2075    case(FaceElements):            break;
2076      out=mesh->FaceElements->Tag[sampleNo];     case(DegreesOfFreedom):
2077      break;            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2078    case(Points):            break;
2079      out=mesh->Points->Tag[sampleNo];     case(ReducedDegreesOfFreedom):
2080      break;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2081    case(ContactElementsZero):            break;
2082      out=mesh->ContactElements->Tag[sampleNo];     case(Elements):
2083      break;     case(ReducedElements):
2084    case(ContactElementsOne):            numTags=mesh->Elements->numTagsInUse;
2085      out=mesh->ContactElements->Tag[sampleNo];            break;
2086      break;     case(FaceElements):
2087    case(DegreesOfFreedom):     case(ReducedFaceElements):
2088      break;            numTags=mesh->FaceElements->numTagsInUse;
2089    case(ReducedDegreesOfFreedom):            break;
2090      break;     case(Points):
2091    default:            numTags=mesh->Points->numTagsInUse;
2092      stringstream temp;            break;
2093      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();     case(ContactElementsZero):
2094      throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
2095      break;     case(ContactElementsOne):
2096       case(ReducedContactElementsOne):
2097              numTags=mesh->ContactElements->numTagsInUse;
2098              break;
2099       default:
2100          stringstream temp;
2101          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2102          throw FinleyAdapterException(temp.str());
2103    }    }
2104    return out;    return numTags;
2105  }  }
2106  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2107  {  {
   int out=0,i;  
2108    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2109    switch (functionSpaceType) {    index_t* tags=NULL;
2110    case(Nodes):    switch(functionSpaceCode) {
2111      if (mesh->Nodes!=NULL) {     case(Nodes):
2112        out=mesh->Nodes->Id[sampleNo];            tags=mesh->Nodes->tagsInUse;
2113        break;            break;
2114      }     case(ReducedNodes):
2115    case(Elements):            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2116      out=mesh->Elements->Id[sampleNo];            break;
2117      break;     case(DegreesOfFreedom):
2118    case(FaceElements):            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2119      out=mesh->FaceElements->Id[sampleNo];            break;
2120      break;     case(ReducedDegreesOfFreedom):
2121    case(Points):            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
     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];  
2122            break;            break;
2123         }     case(Elements):
2124      }     case(ReducedElements):
2125      break;            tags=mesh->Elements->tagsInUse;
   case(ReducedDegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->reducedDegreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
2126            break;            break;
2127         }     case(FaceElements):
2128      }     case(ReducedFaceElements):
2129      break;            tags=mesh->FaceElements->tagsInUse;
2130    default:            break;
2131      stringstream temp;     case(Points):
2132      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();            tags=mesh->Points->tagsInUse;
2133      throw FinleyAdapterException(temp.str());            break;
2134      break;     case(ContactElementsZero):
2135       case(ReducedContactElementsZero):
2136       case(ContactElementsOne):
2137       case(ReducedContactElementsOne):
2138              tags=mesh->ContactElements->tagsInUse;
2139              break;
2140       default:
2141          stringstream temp;
2142          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2143          throw FinleyAdapterException(temp.str());
2144    }    }
2145    return out;    return tags;
2146  }  }
2147    
2148    
2149    bool MeshAdapter::canTag(int functionSpaceCode) const
2150    {
2151      switch(functionSpaceCode) {
2152       case(Nodes):
2153       case(Elements):
2154       case(ReducedElements):
2155       case(FaceElements):
2156       case(ReducedFaceElements):
2157       case(Points):
2158       case(ContactElementsZero):
2159       case(ReducedContactElementsZero):
2160       case(ContactElementsOne):
2161       case(ReducedContactElementsOne):
2162              return true;
2163       case(ReducedNodes):
2164       case(DegreesOfFreedom):
2165       case(ReducedDegreesOfFreedom):
2166          return false;
2167       default:
2168        return false;
2169      }
2170    }
2171    
2172    
2173  }  // end of namespace  }  // end of namespace

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