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

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revision 532 by gross, Wed Feb 15 09:45:53 2006 UTC revision 2518 by gross, Fri Jul 3 07:43:11 2009 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #include "MeshAdapter.h"  /*******************************************************
3    *
4    * Copyright (c) 2003-2008 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 "Data.h"  #include "MeshAdapter.h"
16  #include "DataFactory.h"  #include "escript/Data.h"
17    #include "escript/DataFactory.h"
18    #ifdef USE_NETCDF
19    #include <netcdfcpp.h>
20    #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25    extern "C" {
26    #include "esysUtils/blocktimer.h"
27    }
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
# Line 29  MeshAdapter::FunctionSpaceNamesMapType M Line 37  MeshAdapter::FunctionSpaceNamesMapType M
37  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
38  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
39  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
40    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
41  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
42    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
43  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
44    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
45  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
46  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
47    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
48  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52  {  {
53    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
54    //     //
55    // need to use a null_deleter as Finley_Mesh_dealloc deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
56    // for us.     // for us.
57    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
58  }  }
59    
60  //  //
# Line 49  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 62  MeshAdapter::MeshAdapter(Finley_Mesh* fi
62  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
63  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
64  {  {
65    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
66  }  }
67    
68  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
69  {  {
70    //     //
71    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
72    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
73    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
74      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
75      Finley_Mesh_dealloc(m_finleyMesh.get());     }
76      //   cout << "Finished dealloc." << endl;  }
77    }  
78    int MeshAdapter::getMPISize() const
79    {
80       return m_finleyMesh.get()->MPIInfo->size;
81    }
82    int MeshAdapter::getMPIRank() const
83    {
84       return m_finleyMesh.get()->MPIInfo->rank;
85    }
86    void MeshAdapter::MPIBarrier() const
87    {
88    #ifdef PASO_MPI
89       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
90    #endif
91       return;
92    }
93    bool MeshAdapter::onMasterProcessor() const
94    {
95       return m_finleyMesh.get()->MPIInfo->rank == 0;
96  }  }
97    
98    
99  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
100     return m_finleyMesh.get();     return m_finleyMesh.get();
101  }  }
102    
103  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
104  {  {
105    char fName[fileName.size()+1];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
106    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
107    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
108    checkFinleyError();     checkFinleyError();
109       TMPMEMFREE(fName);
110  }  }
111    
112  // void MeshAdapter::getTagList(int functionSpaceType,  void MeshAdapter::Print_Mesh_Info(const bool full=false) const
113  //                  int* numTags) const  {
114  // {     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
115  //   Finley_Mesh_tagList(m_finleyMesh.get(),functionSpaceType,tagList,numTags);  }
116  //   return;  
117  // }  void MeshAdapter::dump(const std::string& fileName) const
118    {
119    #ifdef USE_NETCDF
120       const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
121       NcVar *ids;
122       int *int_ptr;
123       Finley_Mesh *mesh = m_finleyMesh.get();
124       Finley_TagMap* tag_map;
125       int num_Tags = 0;
126       int mpi_size             = mesh->MPIInfo->size;
127       int mpi_rank             = mesh->MPIInfo->rank;
128       int numDim               = mesh->Nodes->numDim;
129       int numNodes             = mesh->Nodes->numNodes;
130       int num_Elements         = mesh->Elements->numElements;
131       int num_FaceElements         = mesh->FaceElements->numElements;
132       int num_ContactElements      = mesh->ContactElements->numElements;
133       int num_Points           = mesh->Points->numElements;
134       int num_Elements_numNodes        = mesh->Elements->numNodes;
135       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
136       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
137    #ifdef PASO_MPI
138       MPI_Status status;
139    #endif
140    
141    /* Incoming token indicates it's my turn to write */
142    #ifdef PASO_MPI
143       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
144    #endif
145    
146       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
147                                                         mpi_size, mpi_rank);
148    
149       /* Figure out how much storage is required for tags */
150       tag_map = mesh->TagMap;
151       num_Tags = 0;
152       if (tag_map) {
153          while (tag_map) {
154             num_Tags++;
155             tag_map=tag_map->next;
156          }
157       }
158    
159       // NetCDF error handler
160       NcError err(NcError::verbose_nonfatal);
161       // Create the file.
162       NcFile dataFile(newFileName, NcFile::Replace);
163       // check if writing was successful
164       if (!dataFile.is_valid())
165          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
166    
167       // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
168       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
169          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
170       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
171          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
172       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
173          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
174       if (num_Elements>0)
175          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
176             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
177       if (num_FaceElements>0)
178          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
179             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
180       if (num_ContactElements>0)
181          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
182             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
183       if (num_Points>0)
184          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
185             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
186       if (num_Elements>0)
187          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
188             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
189       if (num_FaceElements>0)
190          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
191             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
192       if (num_ContactElements>0)
193          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
194             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
195       if (num_Tags>0)
196          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
197             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
198    
199       // Attributes: MPI size, MPI rank, Name, order, reduced_order
200       if (!dataFile.add_att("mpi_size", mpi_size) )
201          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
202       if (!dataFile.add_att("mpi_rank", mpi_rank) )
203          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
204       if (!dataFile.add_att("Name",mesh->Name) )
205          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
206       if (!dataFile.add_att("numDim",numDim) )
207          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
208       if (!dataFile.add_att("order",mesh->order) )
209          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
210       if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
211          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
212       if (!dataFile.add_att("numNodes",numNodes) )
213          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
214       if (!dataFile.add_att("num_Elements",num_Elements) )
215          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
216       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
217          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
218       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
219          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
220       if (!dataFile.add_att("num_Points",num_Points) )
221          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
222       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
223          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
224       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
225          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
226       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
227          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
228       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
229          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
230       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
231          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
232       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
233          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
234       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
235          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
236       if (!dataFile.add_att("num_Tags", num_Tags) )
237          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
238    
239       // // // // // Nodes // // // // //
240    
241       // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
242       if (numNodes>0) {
243    
244          // Nodes Id
245          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
246             throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
247          int_ptr = &mesh->Nodes->Id[0];
248          if (! (ids->put(int_ptr, numNodes)) )
249             throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
250    
251          // Nodes Tag
252          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
253             throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
254          int_ptr = &mesh->Nodes->Tag[0];
255          if (! (ids->put(int_ptr, numNodes)) )
256             throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
257    
258          // Nodes gDOF
259          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
260             throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
261          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
262          if (! (ids->put(int_ptr, numNodes)) )
263             throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
264    
265          // Nodes global node index
266          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
267             throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
268          int_ptr = &mesh->Nodes->globalNodesIndex[0];
269          if (! (ids->put(int_ptr, numNodes)) )
270             throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
271    
272          // Nodes grDof
273          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
274             throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
275          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
276          if (! (ids->put(int_ptr, numNodes)) )
277             throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
278    
279          // Nodes grNI
280          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
281             throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
282          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
283          if (! (ids->put(int_ptr, numNodes)) )
284             throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
285    
286          // Nodes Coordinates
287          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
288             throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
289          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
290             throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
291    
292          // Nodes degreesOfFreedomDistribution
293          if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
294             throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
295          int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
296          if (! (ids->put(int_ptr, mpi_size+1)) )
297             throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
298    
299          // Nodes nodeDistribution
300          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
301             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
302          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
303          if (! (ids->put(int_ptr, mpi_size+1)) )
304             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
305    
306       }
307    
308       // // // // // Elements // // // // //
309    
310       if (num_Elements>0) {
311    
312          // Elements_Id
313          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
314             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
315          int_ptr = &mesh->Elements->Id[0];
316          if (! (ids->put(int_ptr, num_Elements)) )
317             throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
318    
319          // Elements_Tag
320          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
321             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
322          int_ptr = &mesh->Elements->Tag[0];
323          if (! (ids->put(int_ptr, num_Elements)) )
324             throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
325    
326          // Elements_Owner
327          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
328             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
329          int_ptr = &mesh->Elements->Owner[0];
330          if (! (ids->put(int_ptr, num_Elements)) )
331             throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
332    
333          // Elements_Color
334          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
335             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
336          int_ptr = &mesh->Elements->Color[0];
337          if (! (ids->put(int_ptr, num_Elements)) )
338             throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
339    
340          // Elements_Nodes
341          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
342             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
343          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
344             throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
345    
346       }
347    
348       // // // // // Face_Elements // // // // //
349    
350       if (num_FaceElements>0) {
351    
352          // FaceElements_Id
353          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
354             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
355          int_ptr = &mesh->FaceElements->Id[0];
356          if (! (ids->put(int_ptr, num_FaceElements)) )
357             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
358    
359          // FaceElements_Tag
360          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
361             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
362          int_ptr = &mesh->FaceElements->Tag[0];
363          if (! (ids->put(int_ptr, num_FaceElements)) )
364             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
365    
366          // FaceElements_Owner
367          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
368             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
369          int_ptr = &mesh->FaceElements->Owner[0];
370          if (! (ids->put(int_ptr, num_FaceElements)) )
371             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
372    
373          // FaceElements_Color
374          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
375             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
376          int_ptr = &mesh->FaceElements->Color[0];
377          if (! (ids->put(int_ptr, num_FaceElements)) )
378             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
379    
380          // FaceElements_Nodes
381          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
382             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
383          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
384             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
385    
386       }
387    
388       // // // // // Contact_Elements // // // // //
389    
390       if (num_ContactElements>0) {
391    
392          // ContactElements_Id
393          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
394             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
395          int_ptr = &mesh->ContactElements->Id[0];
396          if (! (ids->put(int_ptr, num_ContactElements)) )
397             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
398    
399          // ContactElements_Tag
400          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
401             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
402          int_ptr = &mesh->ContactElements->Tag[0];
403          if (! (ids->put(int_ptr, num_ContactElements)) )
404             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
405    
406          // ContactElements_Owner
407          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
408             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
409          int_ptr = &mesh->ContactElements->Owner[0];
410          if (! (ids->put(int_ptr, num_ContactElements)) )
411             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
412    
413          // ContactElements_Color
414          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
415             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
416          int_ptr = &mesh->ContactElements->Color[0];
417          if (! (ids->put(int_ptr, num_ContactElements)) )
418             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
419    
420          // ContactElements_Nodes
421          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
422             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
423          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
424             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
425    
426       }
427    
428       // // // // // Points // // // // //
429    
430       if (num_Points>0) {
431    
432          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
433    
434          // Points_Id
435          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
436             throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
437          int_ptr = &mesh->Points->Id[0];
438          if (! (ids->put(int_ptr, num_Points)) )
439             throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
440    
441          // Points_Tag
442          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
443             throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
444          int_ptr = &mesh->Points->Tag[0];
445          if (! (ids->put(int_ptr, num_Points)) )
446             throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
447    
448          // Points_Owner
449          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
450             throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
451          int_ptr = &mesh->Points->Owner[0];
452          if (! (ids->put(int_ptr, num_Points)) )
453             throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
454    
455          // Points_Color
456          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
457             throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
458          int_ptr = &mesh->Points->Color[0];
459          if (! (ids->put(int_ptr, num_Points)) )
460             throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
461    
462          // Points_Nodes
463          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
464          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
465             throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
466          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
467             throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
468    
469       }
470    
471       // // // // // TagMap // // // // //
472    
473       if (num_Tags>0) {
474    
475          // Temp storage to gather node IDs
476          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
477          char name_temp[4096];
478    
479          /* Copy tag data into temp arrays */
480          tag_map = mesh->TagMap;
481          if (tag_map) {
482             int i = 0;
483             while (tag_map) {
484                Tags_keys[i++] = tag_map->tag_key;
485                tag_map=tag_map->next;
486             }
487          }
488    
489          // Tags_keys
490          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
491             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
492          int_ptr = &Tags_keys[0];
493          if (! (ids->put(int_ptr, num_Tags)) )
494             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
495    
496          // Tags_names_*
497          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
498          // because the NetCDF manual doesn't tell how to do an array of strings
499          tag_map = mesh->TagMap;
500          if (tag_map) {
501             int i = 0;
502             while (tag_map) {
503                sprintf(name_temp, "Tags_name_%d", i);
504                if (!dataFile.add_att(name_temp, tag_map->name) )
505                   throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
506                tag_map=tag_map->next;
507                i++;
508             }
509          }
510    
511          TMPMEMFREE(Tags_keys);
512    
513       }
514    
515    /* Send token to next MPI process so he can take his turn */
516    #ifdef PASO_MPI
517       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
518    #endif
519    
520       // NetCDF file is closed by destructor of NcFile object
521    
522    #else
523       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
524    #endif  /* USE_NETCDF */
525       checkFinleyError();
526    }
527    
528  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
529  {  {
530    return "FinleyMesh";     return "FinleyMesh";
531  }  }
532    
533  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
534  {  {
535    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
536    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
537    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
538      return "Invalid function space type code.";        return "Invalid function space type code.";
539    } else {     } else {
540      return loc->second;        return loc->second;
541    }     }
542  }  }
543    
544  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
545  {  {
546    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
547    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
548    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
549  }  }
550    
551  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
552  {  {
553    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
554      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
555    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
556      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
557    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
558      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
559    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
560      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
561    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
562      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
563    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
564      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
565    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
566      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
567    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
568      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
569       m_functionSpaceTypeNames.insert
570       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
571       m_functionSpaceTypeNames.insert
572       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
573       m_functionSpaceTypeNames.insert
574       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
575       m_functionSpaceTypeNames.insert
576       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
577       m_functionSpaceTypeNames.insert
578       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
579  }  }
580    
581  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
582  {  {
583    return Nodes;     return Nodes;
584    }
585    int MeshAdapter::getReducedContinuousFunctionCode() const
586    {
587       return ReducedNodes;
588  }  }
589    
590  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
591  {  {
592    return Elements;     return Elements;
593    }
594    int MeshAdapter::getReducedFunctionCode() const
595    {
596       return ReducedElements;
597  }  }
598    
599  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
600  {  {
601    return FaceElements;     return FaceElements;
602    }
603    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
604    {
605       return ReducedFaceElements;
606  }  }
607    
608  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
609  {  {
610    return ContactElementsZero;     return ContactElementsZero;
611    }
612    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
613    {
614       return ReducedContactElementsZero;
615  }  }
616    
617  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
618  {  {
619    return ContactElementsOne;     return ContactElementsOne;
620    }
621    int MeshAdapter::getReducedFunctionOnContactOneCode() const
622    {
623       return ReducedContactElementsOne;
624  }  }
625    
626  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
627  {  {
628    return DegreesOfFreedom;     return DegreesOfFreedom;
629  }  }
630    
631  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
632  {  {
633    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
634  }  }
635    
636  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
637  {  {
638    return Points;     return Points;
639  }  }
640    
641  //  //
642  // returns a pointer to the tag list of samples of functionSpaceType  // return the spatial dimension of the Mesh:
 //  
 void MeshAdapter::getTagList(int functionSpaceType, int** tagList,  
                  int* numTags) const  
 {  
   *tagList=NULL;  
   *numTags=0;  
   Finley_Mesh* mesh=m_finleyMesh.get();  
   switch (functionSpaceType) {  
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *tagList=mesh->Nodes->Tag;  
       *numTags=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *tagList=mesh->Elements->Tag;  
       *numTags=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *tagList=mesh->FaceElements->Tag;  
       *numTags=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *tagList=mesh->Points->Tag;  
       *numTags=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   if (*tagList==NULL) {  
     stringstream temp;  
     temp << "Error - no tags available for " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
   }  
   return;  
 }  
   
 //  
 // returns a pointer to the reference no list of samples of functionSpaceType  
643  //  //
644  void MeshAdapter::getReferenceNoList(int functionSpaceType, int** referenceNoList,  int MeshAdapter::getDim() const
                  int* numReferenceNo) const  
645  {  {
646    *referenceNoList=NULL;     Finley_Mesh* mesh=m_finleyMesh.get();
647    *numReferenceNo=0;     int numDim=Finley_Mesh_getDim(mesh);
648    Finley_Mesh* mesh=m_finleyMesh.get();     checkFinleyError();
649    switch (functionSpaceType) {     return numDim;
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=mesh->Nodes->Id;  
       *numReferenceNo=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *referenceNoList=mesh->Elements->Id;  
       *numReferenceNo=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *referenceNoList=mesh->FaceElements->Id;  
       *numReferenceNo=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *referenceNoList=mesh->Points->Id;  
       *numReferenceNo=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *referenceNoList=mesh->ContactElements->Id;  
       *numReferenceNo=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *referenceNoList=mesh->ContactElements->Id;  
       *numReferenceNo=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=NULL;  
       *numReferenceNo=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=NULL;  
       *numReferenceNo=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   if (*referenceNoList==NULL) {  
     stringstream temp;  
     temp << "Error - reference number list available for " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
   }  
   return;  
650  }  }
651    
652  //  //
653  // return the spatial dimension of the Mesh:  // Return the number of data points summed across all MPI processes
654  //  //
655  int MeshAdapter::getDim() const  int MeshAdapter::getNumDataPointsGlobal() const
656  {  {
657    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
   checkFinleyError();  
   return numDim;  
658  }  }
659    
660  //  //
# Line 330  pair<int,int> MeshAdapter::getDataShape( Line 667  pair<int,int> MeshAdapter::getDataShape(
667     int numSamples=0;     int numSamples=0;
668     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
669     switch (functionSpaceCode) {     switch (functionSpaceCode) {
670        case(Nodes):     case(Nodes):
671             numDataPointsPerSample=1;     numDataPointsPerSample=1;
672             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
673             break;     break;
674        case(Elements):     case(ReducedNodes):
675             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
676               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
677               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
678             }     case(Elements):
679             break;     if (mesh->Elements!=NULL) {
680        case(FaceElements):        numSamples=mesh->Elements->numElements;
681             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
682                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
683                  numSamples=mesh->FaceElements->numElements;     break;
684             }     case(ReducedElements):
685             break;     if (mesh->Elements!=NULL) {
686        case(Points):        numSamples=mesh->Elements->numElements;
687             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
688               numDataPointsPerSample=1;     }
689               numSamples=mesh->Points->numElements;     break;
690             }     case(FaceElements):
691             break;     if (mesh->FaceElements!=NULL) {
692        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
693             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
694               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
695               numSamples=mesh->ContactElements->numElements;     break;
696             }     case(ReducedFaceElements):
697             break;     if (mesh->FaceElements!=NULL) {
698        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
699             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
700               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
701               numSamples=mesh->ContactElements->numElements;     break;
702             }     case(Points):
703             break;     if (mesh->Points!=NULL) {
704        case(DegreesOfFreedom):        numDataPointsPerSample=1;
705             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
706               numDataPointsPerSample=1;     }
707               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
708             }     case(ContactElementsZero):
709             break;     if (mesh->ContactElements!=NULL) {
710        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
711             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
712               numDataPointsPerSample=1;     }
713               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
714             }     case(ReducedContactElementsZero):
715             break;     if (mesh->ContactElements!=NULL) {
716        default:        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
717          stringstream temp;        numSamples=mesh->ContactElements->numElements;
718          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     }
719          throw FinleyAdapterException(temp.str());     break;
720          break;     case(ContactElementsOne):
721        }     if (mesh->ContactElements!=NULL) {
722        return pair<int,int>(numDataPointsPerSample,numSamples);        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
723          numSamples=mesh->ContactElements->numElements;
724       }
725       break;
726       case(ReducedContactElementsOne):
727       if (mesh->ContactElements!=NULL) {
728          numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
729          numSamples=mesh->ContactElements->numElements;
730       }
731       break;
732       case(DegreesOfFreedom):
733       if (mesh->Nodes!=NULL) {
734          numDataPointsPerSample=1;
735          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
736       }
737       break;
738       case(ReducedDegreesOfFreedom):
739       if (mesh->Nodes!=NULL) {
740          numDataPointsPerSample=1;
741          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
742       }
743       break;
744       default:
745          stringstream temp;
746          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
747          throw FinleyAdapterException(temp.str());
748          break;
749       }
750       return pair<int,int>(numDataPointsPerSample,numSamples);
751  }  }
752    
753  //  //
754  // 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:
755  //  //
756  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
757                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
758                       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,
759                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
760                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
761  {  {
762     Finley_Mesh* mesh=m_finleyMesh.get();     escriptDataC _rhs=rhs.getDataC();
763     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(),&(rhs.getDataC()),     escriptDataC _A  =A.getDataC();
764                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _B=B.getDataC();
765     checkFinleyError();     escriptDataC _C=C.getDataC();
766     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     escriptDataC _D=D.getDataC();
767                    mat.getPaso_SystemMatrix(),     escriptDataC _X=X.getDataC();
768                    &(rhs.getDataC()),     escriptDataC _Y=Y.getDataC();
769                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _d=d.getDataC();
770                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _y=y.getDataC();
771     checkFinleyError();     escriptDataC _d_contact=d_contact.getDataC();
772     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,     escriptDataC _y_contact=y_contact.getDataC();
773                    mat.getPaso_SystemMatrix(),  
774                    &(rhs.getDataC()),     Finley_Mesh* mesh=m_finleyMesh.get();
775                                    &(d_contact.getDataC()),  
776                    &(y_contact.getDataC()),     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
777                                    Finley_Assemble_handelShapeMissMatch_Step_out);     checkFinleyError();
778    
779       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
780       checkFinleyError();
781    
782       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
783     checkFinleyError();     checkFinleyError();
784  }  }
785    
786    void  MeshAdapter::addPDEToLumpedSystem(
787                                            escript::Data& mat,
788                                            const escript::Data& D,
789                                            const escript::Data& d) const
790    {
791       escriptDataC _mat=mat.getDataC();
792       escriptDataC _D=D.getDataC();
793       escriptDataC _d=d.getDataC();
794    
795       Finley_Mesh* mesh=m_finleyMesh.get();
796    
797       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
798       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
799    
800       checkFinleyError();
801    }
802    
803    
804  //  //
805  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
806  //  //
807  void MeshAdapter::addPDEToRHS( escript::Data& rhs,  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const
                      const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  
808  {  {
809     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
810    
811     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
812     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
813       escriptDataC _Y=Y.getDataC();
814       escriptDataC _y=y.getDataC();
815       escriptDataC _y_contact=y_contact.getDataC();
816    
817       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
818       checkFinleyError();
819    
820       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
821     checkFinleyError();     checkFinleyError();
822    
823     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->FaceElements,&(rhs.getDataC()),&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
824     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
825    }
826    //
827    // adds PDE of second order into a transport problem
828    //
829    void MeshAdapter::addPDEToTransportProblem(
830                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
831                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
832                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
833                                               const escript::Data& d, const escript::Data& y,
834                                               const escript::Data& d_contact,const escript::Data& y_contact) const
835    {
836       DataTypes::ShapeType shape;
837       source.expand();
838       escriptDataC _source=source.getDataC();
839       escriptDataC _M=M.getDataC();
840       escriptDataC _A=A.getDataC();
841       escriptDataC _B=B.getDataC();
842       escriptDataC _C=C.getDataC();
843       escriptDataC _D=D.getDataC();
844       escriptDataC _X=X.getDataC();
845       escriptDataC _Y=Y.getDataC();
846       escriptDataC _d=d.getDataC();
847       escriptDataC _y=y.getDataC();
848       escriptDataC _d_contact=d_contact.getDataC();
849       escriptDataC _y_contact=y_contact.getDataC();
850    
851       Finley_Mesh* mesh=m_finleyMesh.get();
852       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
853    
854       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
855       checkFinleyError();
856    
857       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
858     checkFinleyError();     checkFinleyError();
859     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  
860     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->ContactElements,&(rhs.getDataC()),&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
861       checkFinleyError();
862    
863       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
864     checkFinleyError();     checkFinleyError();
865  }  }
866    
# Line 439  void MeshAdapter::addPDEToRHS( escript:: Line 869  void MeshAdapter::addPDEToRHS( escript::
869  //  //
870  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
871  {  {
872    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
873    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
874    if (inDomain!=*this)     if (inDomain!=*this)  
875       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
876    if (targetDomain!=*this)     if (targetDomain!=*this)
877       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
878    
879    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
880    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
881       case(Nodes):     escriptDataC _in=in.getDataC();
882          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
883             case(Nodes):     case(Nodes):
884             case(ReducedDegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
885             case(DegreesOfFreedom):        case(Nodes):
886                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        case(ReducedNodes):
887                 break;        case(DegreesOfFreedom):
888             case(Elements):        case(ReducedDegreesOfFreedom):
889                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
890                 break;        break;
891             case(FaceElements):        case(Elements):
892                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        case(ReducedElements):
893                 break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
894             case(Points):        break;
895                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        case(FaceElements):
896                 break;        case(ReducedFaceElements):
897             case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
898                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
899                 break;        case(Points):
900             case(ContactElementsOne):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
901                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
902                 break;        case(ContactElementsZero):
903             default:        case(ReducedContactElementsZero):
904                 stringstream temp;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
905                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
906                 throw FinleyAdapterException(temp.str());        case(ContactElementsOne):
907                 break;        case(ReducedContactElementsOne):
908          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
909          break;        break;
910       case(Elements):        default:
911          if (target.getFunctionSpace().getTypeCode()==Elements) {           stringstream temp;
912             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();
913          } else {           throw FinleyAdapterException(temp.str());
914             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");           break;
915          }        }
916          break;        break;
917       case(FaceElements):     case(ReducedNodes):
918          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        switch(target.getFunctionSpace().getTypeCode()) {
919             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));        case(Nodes):
920          } else {        case(ReducedNodes):
921             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        case(DegreesOfFreedom):
922             break;        case(ReducedDegreesOfFreedom):
923         }        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
924       case(Points):        break;
925          if (target.getFunctionSpace().getTypeCode()==Points) {        case(Elements):
926             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        case(ReducedElements):
927          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
928             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        break;
929             break;        case(FaceElements):
930          }        case(ReducedFaceElements):
931          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
932       case(ContactElementsZero):        break;
933       case(ContactElementsOne):        case(Points):
934          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
935             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        break;
936          } else {        case(ContactElementsZero):
937             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        case(ReducedContactElementsZero):
938             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
939          }        break;
940          break;        case(ContactElementsOne):
941       case(DegreesOfFreedom):        case(ReducedContactElementsOne):
942          switch(target.getFunctionSpace().getTypeCode()) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
943             case(ReducedDegreesOfFreedom):        break;
944             case(DegreesOfFreedom):        default:
945             case(Nodes):           stringstream temp;
946                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();
947                break;           throw FinleyAdapterException(temp.str());
948             case(Elements):           break;
949                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        }
950                break;        break;
951             case(FaceElements):     case(Elements):
952                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Elements) {
953                break;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
954             case(Points):        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
955                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
956                break;        } else {
957             case(ContactElementsZero):           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
958             case(ContactElementsOne):        }
959                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
960               break;     case(ReducedElements):
961             default:        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
962               stringstream temp;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
963               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        } else {
964               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
965               break;        }
966          }        break;
967          break;     case(FaceElements):
968       case(ReducedDegreesOfFreedom):        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
969         switch(target.getFunctionSpace().getTypeCode()) {           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
970            case(ReducedDegreesOfFreedom):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
971               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
972               break;        } else {
973            case(Elements):           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
974               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        }
975               break;        break;
976            case(FaceElements):     case(ReducedFaceElements):
977               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
978               break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
979            case(Points):        } else {
980               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
981               break;        }
982            case(ContactElementsZero):        break;
983            case(ContactElementsOne):     case(Points):
984               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Points) {
985               break;           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
986            case(Nodes):        } else {
987               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
988               break;        }
989            case(DegreesOfFreedom):        break;
990               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsZero):
991               break;     case(ContactElementsOne):
992            default:        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
993               stringstream temp;           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
994               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
995               throw FinleyAdapterException(temp.str());           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
996               break;        } else {
997         }           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
998         break;        }
999       default:        break;
1000          stringstream temp;     case(ReducedContactElementsZero):
1001          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();     case(ReducedContactElementsOne):
1002          throw FinleyAdapterException(temp.str());        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1003          break;           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1004    }        } else {
1005    checkFinleyError();           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1006          }
1007          break;
1008       case(DegreesOfFreedom):      
1009          switch(target.getFunctionSpace().getTypeCode()) {
1010          case(ReducedDegreesOfFreedom):
1011          case(DegreesOfFreedom):
1012          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1013          break;
1014      
1015          case(Nodes):
1016          case(ReducedNodes):
1017          if (getMPISize()>1) {
1018             escript::Data temp=escript::Data(in);
1019             temp.expand();
1020             escriptDataC _in2 = temp.getDataC();
1021             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1022          } else {
1023             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1024          }
1025          break;
1026          case(Elements):
1027          case(ReducedElements):
1028          if (getMPISize()>1) {
1029             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1030             escriptDataC _in2 = temp.getDataC();
1031             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1032          } else {
1033             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1034          }
1035          break;
1036          case(FaceElements):
1037          case(ReducedFaceElements):
1038          if (getMPISize()>1) {
1039             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1040             escriptDataC _in2 = temp.getDataC();
1041             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1042      
1043          } else {
1044             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1045          }
1046          break;
1047          case(Points):
1048          if (getMPISize()>1) {
1049             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1050             escriptDataC _in2 = temp.getDataC();
1051          } else {
1052             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1053          }
1054          break;
1055          case(ContactElementsZero):
1056          case(ContactElementsOne):
1057          case(ReducedContactElementsZero):
1058          case(ReducedContactElementsOne):
1059          if (getMPISize()>1) {
1060             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1061             escriptDataC _in2 = temp.getDataC();
1062             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1063          } else {
1064             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1065          }
1066          break;
1067          default:
1068             stringstream temp;
1069             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1070             throw FinleyAdapterException(temp.str());
1071             break;
1072          }
1073          break;
1074       case(ReducedDegreesOfFreedom):
1075          switch(target.getFunctionSpace().getTypeCode()) {
1076          case(Nodes):
1077          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1078          break;
1079          case(ReducedNodes):
1080          if (getMPISize()>1) {
1081             escript::Data temp=escript::Data(in);
1082             temp.expand();
1083             escriptDataC _in2 = temp.getDataC();
1084             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1085          } else {
1086             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1087          }
1088          break;
1089          case(DegreesOfFreedom):
1090          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1091          break;
1092          case(ReducedDegreesOfFreedom):
1093          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1094          break;
1095          case(Elements):
1096          case(ReducedElements):
1097          if (getMPISize()>1) {
1098             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1099             escriptDataC _in2 = temp.getDataC();
1100             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1101          } else {
1102             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1103          }
1104          break;
1105          case(FaceElements):
1106          case(ReducedFaceElements):
1107          if (getMPISize()>1) {
1108             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1109             escriptDataC _in2 = temp.getDataC();
1110             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1111          } else {
1112             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1113          }
1114          break;
1115          case(Points):
1116          if (getMPISize()>1) {
1117             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1118             escriptDataC _in2 = temp.getDataC();
1119             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1120          } else {
1121             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1122          }
1123          break;
1124          case(ContactElementsZero):
1125          case(ContactElementsOne):
1126          case(ReducedContactElementsZero):
1127          case(ReducedContactElementsOne):
1128          if (getMPISize()>1) {
1129             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1130             escriptDataC _in2 = temp.getDataC();
1131             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1132          } else {
1133             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1134          }
1135          break;
1136          default:
1137             stringstream temp;
1138             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1139             throw FinleyAdapterException(temp.str());
1140             break;
1141          }
1142          break;
1143       default:
1144          stringstream temp;
1145          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1146          throw FinleyAdapterException(temp.str());
1147          break;
1148       }
1149       checkFinleyError();
1150  }  }
1151    
1152  //  //
# Line 580  void MeshAdapter::interpolateOnDomain(es Line 1154  void MeshAdapter::interpolateOnDomain(es
1154  //  //
1155  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1156  {  {
1157    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1158    if (argDomain!=*this)     if (argDomain!=*this)
1159       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1160    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1161    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1162    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1163       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1164    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1165       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1166       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1167       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1168       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1169    }        // this is then interpolated onto arg:
1170    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1171       }
1172       checkFinleyError();
1173  }  }
1174    
1175  //  //
# Line 601  void MeshAdapter::setToX(escript::Data& Line 1177  void MeshAdapter::setToX(escript::Data&
1177  //  //
1178  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1179  {  {
1180    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1181    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1182       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1183    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1184    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1185      case(Nodes):     escriptDataC _normal=normal.getDataC();
1186        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     switch(normal.getFunctionSpace().getTypeCode()) {
1187        break;     case(Nodes):
1188      case(Elements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1189        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     break;
1190        break;     case(ReducedNodes):
1191      case (FaceElements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1192        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     break;
1193        break;     case(Elements):
1194      case(Points):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1195        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     break;
1196        break;     case(ReducedElements):
1197      case (ContactElementsOne):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1198      case (ContactElementsZero):     break;
1199        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (FaceElements):
1200        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1201      case(DegreesOfFreedom):     break;
1202        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case (ReducedFaceElements):
1203        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1204      case(ReducedDegreesOfFreedom):     break;
1205        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(Points):
1206        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1207      default:     break;
1208       case (ContactElementsOne):
1209       case (ContactElementsZero):
1210       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1211       break;
1212       case (ReducedContactElementsOne):
1213       case (ReducedContactElementsZero):
1214       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1215       break;
1216       case(DegreesOfFreedom):
1217       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1218       break;
1219       case(ReducedDegreesOfFreedom):
1220       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1221       break;
1222       default:
1223        stringstream temp;        stringstream temp;
1224        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();
1225        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1226        break;        break;
1227    }     }
1228    checkFinleyError();     checkFinleyError();
1229  }  }
1230    
1231  //  //
# Line 642  void MeshAdapter::setToNormal(escript::D Line 1233  void MeshAdapter::setToNormal(escript::D
1233  //  //
1234  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1235  {  {
1236    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1237    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1238       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1239          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1240    
1241    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1242  }  }
1243    
1244  //  //
# Line 654  void MeshAdapter::interpolateACross(escr Line 1246  void MeshAdapter::interpolateACross(escr
1246  //  //
1247  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1248  {  {
1249    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1250    if (argDomain!=*this)     if (argDomain!=*this)
1251       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1252    
1253    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1254    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1255       case(Nodes):     escriptDataC _temp;
1256          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1257          break;     escriptDataC _arg=arg.getDataC();
1258       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1259          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1260          break;     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1261       case(FaceElements):     _temp=temp.getDataC();
1262          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1263          break;     break;
1264       case(Points):     case(ReducedNodes):
1265          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1266          break;     _temp=temp.getDataC();
1267       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1268          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1269          break;     case(Elements):
1270       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1271          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1272          break;     case(ReducedElements):
1273       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1274          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1275          break;     case(FaceElements):
1276       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1277          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1278          break;     case(ReducedFaceElements):
1279       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1280          stringstream temp;     break;
1281          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1282          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1283          break;     break;
1284    }     case(ContactElementsZero):
1285    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1286       break;
1287       case(ReducedContactElementsZero):
1288       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1289       break;
1290       case(ContactElementsOne):
1291       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1292       break;
1293       case(ReducedContactElementsOne):
1294       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1295       break;
1296       case(DegreesOfFreedom):
1297       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1298       _temp=temp.getDataC();
1299       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1300       break;
1301       case(ReducedDegreesOfFreedom):
1302       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1303       _temp=temp.getDataC();
1304       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1305       break;
1306       default:
1307          stringstream temp;
1308          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1309          throw FinleyAdapterException(temp.str());
1310          break;
1311       }
1312       checkFinleyError();
1313       blocktimer_increment("integrate()", blocktimer_start);
1314  }  }
1315    
1316  //  //
# Line 698  void MeshAdapter::setToIntegrals(std::ve Line 1318  void MeshAdapter::setToIntegrals(std::ve
1318  //  //
1319  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1320  {  {
1321    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1322    if (argDomain!=*this)     if (argDomain!=*this)
1323      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1324    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1325    if (gradDomain!=*this)     if (gradDomain!=*this)
1326       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1327    
1328    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1329    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1330         case(Nodes):     escriptDataC nodeDataC;
1331            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     escript::Data temp;
1332            break;     if (getMPISize()>1) {
1333         case(Elements):        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1334            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1335            break;           nodeDataC = temp.getDataC();
1336         case(FaceElements):        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1337            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1338            break;           nodeDataC = temp.getDataC();
1339         case(Points):        } else {
1340            throw FinleyAdapterException("Error - Gradient at points is not supported.");           nodeDataC = arg.getDataC();
1341            break;        }
1342         case(ContactElementsZero):     } else {
1343            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));        nodeDataC = arg.getDataC();
1344            break;     }
1345         case(ContactElementsOne):     switch(grad.getFunctionSpace().getTypeCode()) {
1346            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     case(Nodes):
1347            break;     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1348         case(DegreesOfFreedom):     break;
1349            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     case(ReducedNodes):
1350            break;     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1351         case(ReducedDegreesOfFreedom):     break;
1352            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     case(Elements):
1353            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1354         default:     break;
1355            stringstream temp;     case(ReducedElements):
1356            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1357            throw FinleyAdapterException(temp.str());     break;
1358            break;     case(FaceElements):
1359    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1360    checkFinleyError();     break;
1361       case(ReducedFaceElements):
1362       Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1363       break;
1364       case(Points):
1365       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1366       break;
1367       case(ContactElementsZero):
1368       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1369       break;
1370       case(ReducedContactElementsZero):
1371       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1372       break;
1373       case(ContactElementsOne):
1374       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1375       break;
1376       case(ReducedContactElementsOne):
1377       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1378       break;
1379       case(DegreesOfFreedom):
1380       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1381       break;
1382       case(ReducedDegreesOfFreedom):
1383       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1384       break;
1385       default:
1386          stringstream temp;
1387          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1388          throw FinleyAdapterException(temp.str());
1389          break;
1390       }
1391       checkFinleyError();
1392  }  }
1393    
1394  //  //
# Line 745  void MeshAdapter::setToGradient(escript: Line 1396  void MeshAdapter::setToGradient(escript:
1396  //  //
1397  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1398  {  {
1399    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1400    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1401    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1402         case(Nodes):     case(Nodes):
1403            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1404            break;     break;
1405         case(Elements):     case(ReducedNodes):
1406            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1407            break;     break;
1408         case(FaceElements):     case(Elements):
1409            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1410            break;     break;
1411         case(Points):     case(ReducedElements):
1412            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1413            break;     break;
1414         case(ContactElementsZero):     case(FaceElements):
1415         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1416            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1417            break;     case(ReducedFaceElements):
1418         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1419            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1420            break;     case(Points):
1421         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1422            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1423            break;     case(ContactElementsZero):
1424         default:     case(ContactElementsOne):
1425            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1426            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1427            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1428            break;     case(ReducedContactElementsOne):
1429    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1430    checkFinleyError();     break;
1431       case(DegreesOfFreedom):
1432       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1433       break;
1434       case(ReducedDegreesOfFreedom):
1435       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1436       break;
1437       default:
1438          stringstream temp;
1439          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1440          throw FinleyAdapterException(temp.str());
1441          break;
1442       }
1443       checkFinleyError();
1444  }  }
1445    
1446  // sets the location of nodes:  //
1447    // sets the location of nodes
1448    //
1449  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1450  {  {
1451    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1452    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1453    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1454       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1455    Finley_Mesh_setCoordinates(mesh,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1456    checkFinleyError();     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {
1457           tmp = new_x.getDataC();
1458           Finley_Mesh_setCoordinates(mesh,&tmp);
1459       } else {
1460           escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );
1461           tmp = new_x_inter.getDataC();
1462           Finley_Mesh_setCoordinates(mesh,&tmp);
1463       }
1464       checkFinleyError();
1465  }  }
1466    
1467  // saves a data array in openDX format:  //
1468    // Helper for the save* methods. Extracts optional data variable names and the
1469    // corresponding pointers from python dictionary. Caller must free arrays.
1470    //
1471    void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1472    {
1473       numData = boost::python::extract<int>(arg.attr("__len__")());
1474       /* win32 refactor */
1475       names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1476       data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1477       dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1478    
1479       boost::python::list keys=arg.keys();
1480       for (int i=0; i<numData; ++i) {
1481          std::string n=boost::python::extract<std::string>(keys[i]);
1482          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1483          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1484             throw FinleyAdapterException("Error: Data must be defined on same Domain");
1485          data[i] = d.getDataC();
1486          dataPtr[i] = &(data[i]);
1487          names[i] = TMPMEMALLOC(n.length()+1, char);
1488          strcpy(names[i], n.c_str());
1489       }
1490    }
1491    
1492    //
1493    // saves mesh and optionally data arrays in openDX format
1494    //
1495  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
1496  {  {
1497      int MAX_namelength=256;     int num_data;
1498      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1499      char names[num_data][MAX_namelength];     escriptDataC *data;
1500      char* c_names[num_data];     escriptDataC **ptr_data;
1501      escriptDataC data[num_data];  
1502      escriptDataC* ptr_data[num_data];     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1503       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1504      boost::python::list keys=arg.keys();     checkFinleyError();
1505      for (int i=0;i<num_data;++i) {  
1506           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     /* win32 refactor */
1507           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     TMPMEMFREE(data);
1508               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     TMPMEMFREE(ptr_data);
1509           data[i]=d.getDataC();     for(int i=0; i<num_data; i++)
1510           ptr_data[i]=&(data[i]);     {
1511           std::string n=boost::python::extract<std::string>(keys[i]);        TMPMEMFREE(names[i]);
1512           c_names[i]=&(names[i][0]);     }
1513           if (n.length()>MAX_namelength-1) {     TMPMEMFREE(names);
1514              strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
1515              c_names[i][MAX_namelength-1]='\0';     return;
1516           } else {  }
1517              strcpy(c_names[i],n.c_str());  
1518           }  //
1519      }  // saves mesh and optionally data arrays in VTK format
1520      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  //
1521      checkFinleyError();  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg,  const std::string& metadata, const std::string& metadata_schema) const
1522      return;  {
1523  }     int num_data;
1524       char **names;
1525  // saves a data array in openVTK format:     escriptDataC *data;
1526  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const     escriptDataC **ptr_data;
1527  {  
1528      int MAX_namelength=256;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1529      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());
1530      char names[num_data][MAX_namelength];     checkFinleyError();
1531      char* c_names[num_data];  
1532      escriptDataC data[num_data];     /* win32 refactor */
1533      escriptDataC* ptr_data[num_data];     TMPMEMFREE(data);
1534       TMPMEMFREE(ptr_data);
1535      boost::python::list keys=arg.keys();     for(int i=0; i<num_data; i++)
1536      for (int i=0;i<num_data;++i) {     {
1537           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);        TMPMEMFREE(names[i]);
1538           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     }
1539               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     TMPMEMFREE(names);
1540           data[i]=d.getDataC();  }
1541           ptr_data[i]=&(data[i]);  
1542           std::string n=boost::python::extract<std::string>(keys[i]);  //
1543           c_names[i]=&(names[i][0]);  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1544           if (n.length()>MAX_namelength-1) {  //
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
     return;  
 }  
                                                                                                                                                                           
                                                                                                                                                                           
 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  
1545  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1546                        const int row_blocksize,                                                   const int row_blocksize,
1547                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1548                        const int column_blocksize,                                                   const int column_blocksize,
1549                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1550                        const int type) const                                                   const int type) const
1551  {  {
1552      int reduceRowOrder=0;     int reduceRowOrder=0;
1553      int reduceColOrder=0;     int reduceColOrder=0;
1554      // is the domain right?     // is the domain right?
1555      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1556      if (row_domain!=*this)     if (row_domain!=*this)
1557            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.");
1558      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1559      if (col_domain!=*this)     if (col_domain!=*this)
1560            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.");
1561      // is the function space type right     // is the function space type right
1562      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1563          reduceRowOrder=0;        reduceRowOrder=0;
1564      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1565          reduceRowOrder=1;        reduceRowOrder=1;
1566      } else {     } else {
1567          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1568      }     }
1569      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1570          reduceColOrder=0;        reduceColOrder=0;
1571      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1572          reduceColOrder=1;        reduceColOrder=1;
1573      } else {     } else {
1574          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1575      }     }
1576      // generate matrix:     // generate matrix:
1577        
1578      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1579      checkFinleyError();     checkFinleyError();
1580      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1581      checkPasoError();     int trilinos = 0;
1582      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1583      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1584          /* Allocation Epetra_VrbMatrix here */
1585    #endif
1586       }
1587       else {
1588          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1589       }
1590       checkPasoError();
1591       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1592       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1593    }
1594    
1595    //
1596    // creates a TransportProblemAdapter
1597    //
1598    TransportProblemAdapter MeshAdapter::newTransportProblem(
1599                                                             const double theta,
1600                                                             const int blocksize,
1601                                                             const escript::FunctionSpace& functionspace,
1602                                                             const int type) const
1603    {
1604       int reduceOrder=0;
1605       // is the domain right?
1606       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1607       if (domain!=*this)
1608          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1609       // is the function space type right
1610       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1611          reduceOrder=0;
1612       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1613          reduceOrder=1;
1614       } else {
1615          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1616       }
1617       // generate matrix:
1618    
1619       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1620       checkFinleyError();
1621       Paso_FCTransportProblem* transportProblem;
1622       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1623       checkPasoError();
1624       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1625       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1626  }  }
1627    
1628  //  //
# Line 904  SystemMatrixAdapter MeshAdapter::newSyst Line 1634  SystemMatrixAdapter MeshAdapter::newSyst
1634  // 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:
1635  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1636  {  {
1637    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1638         case(Nodes):     case(Nodes):
1639         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1640         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1641            return false;     return false;
1642            break;     break;
1643         case(Elements):     case(Elements):
1644         case(FaceElements):     case(FaceElements):
1645         case(Points):     case(Points):
1646         case(ContactElementsZero):     case(ContactElementsZero):
1647         case(ContactElementsOne):     case(ContactElementsOne):
1648            return true;     case(ReducedElements):
1649            break;     case(ReducedFaceElements):
1650         default:     case(ReducedContactElementsZero):
1651            stringstream temp;     case(ReducedContactElementsOne):
1652            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1653            throw FinleyAdapterException(temp.str());     break;
1654            break;     default:
1655    }        stringstream temp;
1656    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1657    return false;        throw FinleyAdapterException(temp.str());
1658          break;
1659       }
1660       checkFinleyError();
1661       return false;
1662  }  }
1663    
1664  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1665  {  {
1666    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1667       case(Nodes):     case(Nodes):
1668          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1669             case(Nodes):     case(Nodes):
1670             case(ReducedDegreesOfFreedom):     case(ReducedNodes):
1671             case(DegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1672             case(Elements):     case(DegreesOfFreedom):
1673             case(FaceElements):     case(Elements):
1674             case(Points):     case(ReducedElements):
1675             case(ContactElementsZero):     case(FaceElements):
1676             case(ContactElementsOne):     case(ReducedFaceElements):
1677                 return true;     case(Points):
1678             default:     case(ContactElementsZero):
1679                 stringstream temp;     case(ReducedContactElementsZero):
1680                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(ContactElementsOne):
1681                 throw FinleyAdapterException(temp.str());     case(ReducedContactElementsOne):
1682          }     return true;
1683          break;     default:
1684       case(Elements):        stringstream temp;
1685          if (functionSpaceType_target==Elements) {        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1686             return true;        throw FinleyAdapterException(temp.str());
1687          } else {     }
1688             return false;     break;
1689          }     case(ReducedNodes):
1690       case(FaceElements):     switch(functionSpaceType_target) {
1691          if (functionSpaceType_target==FaceElements) {     case(ReducedNodes):
1692             return true;     case(ReducedDegreesOfFreedom):
1693          } else {     case(Elements):
1694             return false;     case(ReducedElements):
1695          }     case(FaceElements):
1696       case(Points):     case(ReducedFaceElements):
1697          if (functionSpaceType_target==Points) {     case(Points):
1698             return true;     case(ContactElementsZero):
1699          } else {     case(ReducedContactElementsZero):
1700             return false;     case(ContactElementsOne):
1701          }     case(ReducedContactElementsOne):
1702       case(ContactElementsZero):     return true;
1703       case(ContactElementsOne):     case(Nodes):
1704          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     case(DegreesOfFreedom):
1705             return true;     return false;
1706          } else {     default:
1707             return false;        stringstream temp;
1708          }        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1709       case(DegreesOfFreedom):        throw FinleyAdapterException(temp.str());
1710          switch(functionSpaceType_target) {     }
1711             case(ReducedDegreesOfFreedom):     break;
1712             case(DegreesOfFreedom):     case(Elements):
1713             case(Nodes):     if (functionSpaceType_target==Elements) {
1714             case(Elements):        return true;
1715             case(FaceElements):     } else if (functionSpaceType_target==ReducedElements) {
1716             case(Points):        return true;
1717             case(ContactElementsZero):     } else {
1718             case(ContactElementsOne):        return false;
1719                return true;     }
1720             default:     case(ReducedElements):
1721               stringstream temp;     if (functionSpaceType_target==ReducedElements) {
1722               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;        return true;
1723               throw FinleyAdapterException(temp.str());     } else {
1724          }        return false;
1725          break;     }
1726       case(ReducedDegreesOfFreedom):     case(FaceElements):
1727         switch(functionSpaceType_target) {     if (functionSpaceType_target==FaceElements) {
1728            case(ReducedDegreesOfFreedom):        return true;
1729            case(Elements):     } else if (functionSpaceType_target==ReducedFaceElements) {
1730            case(FaceElements):        return true;
1731            case(Points):     } else {
1732            case(ContactElementsZero):        return false;
1733            case(ContactElementsOne):     }
1734                return true;     case(ReducedFaceElements):
1735            case(Nodes):     if (functionSpaceType_target==ReducedFaceElements) {
1736            case(DegreesOfFreedom):        return true;
1737               return false;     } else {
1738            default:        return false;
1739               stringstream temp;     }
1740               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1741               throw FinleyAdapterException(temp.str());     if (functionSpaceType_target==Points) {
1742         }        return true;
1743         break;     } else {
1744       default:        return false;
1745          stringstream temp;     }
1746          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1747          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1748          break;     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1749    }        return true;
1750    checkFinleyError();     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1751    return false;        return true;
1752       } else {
1753          return false;
1754       }
1755       case(ReducedContactElementsZero):
1756       case(ReducedContactElementsOne):
1757       if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1758          return true;
1759       } else {
1760          return false;
1761       }
1762       case(DegreesOfFreedom):
1763       switch(functionSpaceType_target) {
1764       case(ReducedDegreesOfFreedom):
1765       case(DegreesOfFreedom):
1766       case(Nodes):
1767       case(ReducedNodes):
1768       case(Elements):
1769       case(ReducedElements):
1770       case(Points):
1771       case(FaceElements):
1772       case(ReducedFaceElements):
1773       case(ContactElementsZero):
1774       case(ReducedContactElementsZero):
1775       case(ContactElementsOne):
1776       case(ReducedContactElementsOne):
1777       return true;
1778       default:
1779          stringstream temp;
1780          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1781          throw FinleyAdapterException(temp.str());
1782       }
1783       break;
1784       case(ReducedDegreesOfFreedom):
1785       switch(functionSpaceType_target) {
1786       case(ReducedDegreesOfFreedom):
1787       case(ReducedNodes):
1788       case(Elements):
1789       case(ReducedElements):
1790       case(FaceElements):
1791       case(ReducedFaceElements):
1792       case(Points):
1793       case(ContactElementsZero):
1794       case(ReducedContactElementsZero):
1795       case(ContactElementsOne):
1796       case(ReducedContactElementsOne):
1797       return true;
1798       case(Nodes):
1799       case(DegreesOfFreedom):
1800       return false;
1801       default:
1802          stringstream temp;
1803          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1804          throw FinleyAdapterException(temp.str());
1805       }
1806       break;
1807       default:
1808          stringstream temp;
1809          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1810          throw FinleyAdapterException(temp.str());
1811          break;
1812       }
1813       checkFinleyError();
1814       return false;
1815  }  }
1816    
1817  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
1818  {  {
1819      return false;     return false;
1820  }  }
1821    
1822  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1823  {  {
1824    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1825    if (temp!=0) {     if (temp!=0) {
1826      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1827    } else {     } else {
1828      return false;        return false;
1829    }     }
1830  }  }
1831    
1832  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1833  {  {
1834    return !(operator==(other));     return !(operator==(other));
1835  }  }
1836    
1837  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
1838    {
1839       Finley_Mesh* mesh=m_finleyMesh.get();
1840       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
1841       checkPasoError();
1842       return out;
1843    }
1844    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1845  {  {
1846     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
1847       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
1848     checkPasoError();     checkPasoError();
1849     return out;     return out;
1850  }  }
1851    
1852  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1853  {  {
1854    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1855  }  }
1856    
1857  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1858  {  {
1859    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1860  }  }
1861    
1862  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1863  {  {
1864    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1865  }  }
1866    
1867    const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1868    {
1869       int *out = NULL;
1870       Finley_Mesh* mesh=m_finleyMesh.get();
1871       switch (functionSpaceType) {
1872       case(Nodes):
1873       out=mesh->Nodes->Id;
1874       break;
1875       case(ReducedNodes):
1876       out=mesh->Nodes->reducedNodesId;
1877       break;
1878       case(Elements):
1879       out=mesh->Elements->Id;
1880       break;
1881       case(ReducedElements):
1882       out=mesh->Elements->Id;
1883       break;
1884       case(FaceElements):
1885       out=mesh->FaceElements->Id;
1886       break;
1887       case(ReducedFaceElements):
1888       out=mesh->FaceElements->Id;
1889       break;
1890       case(Points):
1891       out=mesh->Points->Id;
1892       break;
1893       case(ContactElementsZero):
1894       out=mesh->ContactElements->Id;
1895       break;
1896       case(ReducedContactElementsZero):
1897       out=mesh->ContactElements->Id;
1898       break;
1899       case(ContactElementsOne):
1900       out=mesh->ContactElements->Id;
1901       break;
1902       case(ReducedContactElementsOne):
1903       out=mesh->ContactElements->Id;
1904       break;
1905       case(DegreesOfFreedom):
1906       out=mesh->Nodes->degreesOfFreedomId;
1907       break;
1908       case(ReducedDegreesOfFreedom):
1909       out=mesh->Nodes->reducedDegreesOfFreedomId;
1910       break;
1911       default:
1912          stringstream temp;
1913          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1914          throw FinleyAdapterException(temp.str());
1915          break;
1916       }
1917       return out;
1918    }
1919  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1920  {  {
1921    int* tagList;     int out=0;
1922    int numTags;     Finley_Mesh* mesh=m_finleyMesh.get();
1923    getTagList(functionSpaceType, &tagList, &numTags);     switch (functionSpaceType) {
1924    return tagList[sampleNo];     case(Nodes):
1925       out=mesh->Nodes->Tag[sampleNo];
1926       break;
1927       case(ReducedNodes):
1928       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1929       break;
1930       case(Elements):
1931       out=mesh->Elements->Tag[sampleNo];
1932       break;
1933       case(ReducedElements):
1934       out=mesh->Elements->Tag[sampleNo];
1935       break;
1936       case(FaceElements):
1937       out=mesh->FaceElements->Tag[sampleNo];
1938       break;
1939       case(ReducedFaceElements):
1940       out=mesh->FaceElements->Tag[sampleNo];
1941       break;
1942       case(Points):
1943       out=mesh->Points->Tag[sampleNo];
1944       break;
1945       case(ContactElementsZero):
1946       out=mesh->ContactElements->Tag[sampleNo];
1947       break;
1948       case(ReducedContactElementsZero):
1949       out=mesh->ContactElements->Tag[sampleNo];
1950       break;
1951       case(ContactElementsOne):
1952       out=mesh->ContactElements->Tag[sampleNo];
1953       break;
1954       case(ReducedContactElementsOne):
1955       out=mesh->ContactElements->Tag[sampleNo];
1956       break;
1957       case(DegreesOfFreedom):
1958       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1959       break;
1960       case(ReducedDegreesOfFreedom):
1961       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1962       break;
1963       default:
1964          stringstream temp;
1965          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1966          throw FinleyAdapterException(temp.str());
1967          break;
1968       }
1969       return out;
1970    }
1971    
1972    
1973    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1974    {
1975       Finley_Mesh* mesh=m_finleyMesh.get();
1976       escriptDataC tmp=mask.getDataC();
1977       switch(functionSpaceType) {
1978       case(Nodes):
1979       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1980       break;
1981       case(ReducedNodes):
1982       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1983       break;
1984       case(DegreesOfFreedom):
1985       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1986       break;
1987       case(ReducedDegreesOfFreedom):
1988       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1989       break;
1990       case(Elements):
1991       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1992       break;
1993       case(ReducedElements):
1994       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1995       break;
1996       case(FaceElements):
1997       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1998       break;
1999       case(ReducedFaceElements):
2000       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2001       break;
2002       case(Points):
2003       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2004       break;
2005       case(ContactElementsZero):
2006       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2007       break;
2008       case(ReducedContactElementsZero):
2009       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2010       break;
2011       case(ContactElementsOne):
2012       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2013       break;
2014       case(ReducedContactElementsOne):
2015       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2016       break;
2017       default:
2018          stringstream temp;
2019          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2020          throw FinleyAdapterException(temp.str());
2021       }
2022       checkFinleyError();
2023       return;
2024    }
2025    
2026    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2027    {
2028       Finley_Mesh* mesh=m_finleyMesh.get();
2029       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2030       checkPasoError();
2031       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2032    }
2033    
2034    int MeshAdapter::getTag(const std::string& name) const
2035    {
2036       Finley_Mesh* mesh=m_finleyMesh.get();
2037       int tag=0;
2038       tag=Finley_Mesh_getTag(mesh, name.c_str());
2039       checkPasoError();
2040       // throwStandardException("MeshAdapter::getTag is not implemented.");
2041       return tag;
2042    }
2043    
2044    bool MeshAdapter::isValidTagName(const std::string& name) const
2045    {
2046       Finley_Mesh* mesh=m_finleyMesh.get();
2047       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2048    }
2049    
2050    std::string MeshAdapter::showTagNames() const
2051    {
2052       stringstream temp;
2053       Finley_Mesh* mesh=m_finleyMesh.get();
2054       Finley_TagMap* tag_map=mesh->TagMap;
2055       while (tag_map) {
2056          temp << tag_map->name;
2057          tag_map=tag_map->next;
2058          if (tag_map) temp << ", ";
2059       }
2060       return temp.str();
2061    }
2062    
2063    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2064    {
2065      Finley_Mesh* mesh=m_finleyMesh.get();
2066      dim_t numTags=0;
2067      switch(functionSpaceCode) {
2068       case(Nodes):
2069              numTags=mesh->Nodes->numTagsInUse;
2070              break;
2071       case(ReducedNodes):
2072              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2073              break;
2074       case(DegreesOfFreedom):
2075              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2076              break;
2077       case(ReducedDegreesOfFreedom):
2078              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2079              break;
2080       case(Elements):
2081       case(ReducedElements):
2082              numTags=mesh->Elements->numTagsInUse;
2083              break;
2084       case(FaceElements):
2085       case(ReducedFaceElements):
2086              numTags=mesh->FaceElements->numTagsInUse;
2087              break;
2088       case(Points):
2089              numTags=mesh->Points->numTagsInUse;
2090              break;
2091       case(ContactElementsZero):
2092       case(ReducedContactElementsZero):
2093       case(ContactElementsOne):
2094       case(ReducedContactElementsOne):
2095              numTags=mesh->ContactElements->numTagsInUse;
2096              break;
2097       default:
2098          stringstream temp;
2099          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2100          throw FinleyAdapterException(temp.str());
2101      }
2102      return numTags;
2103    }
2104    
2105    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2106    {
2107      Finley_Mesh* mesh=m_finleyMesh.get();
2108      index_t* tags=NULL;
2109      switch(functionSpaceCode) {
2110       case(Nodes):
2111              tags=mesh->Nodes->tagsInUse;
2112              break;
2113       case(ReducedNodes):
2114              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2115              break;
2116       case(DegreesOfFreedom):
2117              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2118              break;
2119       case(ReducedDegreesOfFreedom):
2120              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2121              break;
2122       case(Elements):
2123       case(ReducedElements):
2124              tags=mesh->Elements->tagsInUse;
2125              break;
2126       case(FaceElements):
2127       case(ReducedFaceElements):
2128              tags=mesh->FaceElements->tagsInUse;
2129              break;
2130       case(Points):
2131              tags=mesh->Points->tagsInUse;
2132              break;
2133       case(ContactElementsZero):
2134       case(ReducedContactElementsZero):
2135       case(ContactElementsOne):
2136       case(ReducedContactElementsOne):
2137              tags=mesh->ContactElements->tagsInUse;
2138              break;
2139       default:
2140          stringstream temp;
2141          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2142          throw FinleyAdapterException(temp.str());
2143      }
2144      return tags;
2145  }  }
2146    
2147  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  
2148  {  bool MeshAdapter::canTag(int functionSpaceCode) const
2149    int* referenceNoList;  {
2150    int numReferenceNo;    switch(functionSpaceCode) {
2151    getReferenceNoList(functionSpaceType, &referenceNoList, &numReferenceNo);     case(Nodes):
2152    return referenceNoList[sampleNo];     case(Elements):
2153       case(ReducedElements):
2154       case(FaceElements):
2155       case(ReducedFaceElements):
2156       case(Points):
2157       case(ContactElementsZero):
2158       case(ReducedContactElementsZero):
2159       case(ContactElementsOne):
2160       case(ReducedContactElementsOne):
2161              return true;
2162       case(ReducedNodes):
2163       case(DegreesOfFreedom):
2164       case(ReducedDegreesOfFreedom):
2165          return false;
2166       default:
2167        return false;
2168      }
2169  }  }
2170    
2171    
2172  }  // end of namespace  }  // end of namespace

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