/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 757 by woo409, Mon Jun 26 13:12:56 2006 UTC revision 2151 by caltinay, Wed Dec 10 06:34:25 2008 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #include "MeshAdapter.h"  /*******************************************************
3    *
4    * Copyright (c) 2003-2008 by University of Queensland
5    * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * Licensed under the Open Software License version 3.0
10    * http://www.opensource.org/licenses/osl-3.0.php
11    *
12    *******************************************************/
13    
14    
15    #include "MeshAdapter.h"
16  #include "escript/Data.h"  #include "escript/Data.h"
17  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
18    #ifdef USE_NETCDF
19    #include <netcdfcpp.h>
20    #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25    extern "C" {
26    #include "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();
# Line 70  Finley_Mesh* MeshAdapter::getFinley_Mesh Line 102  Finley_Mesh* MeshAdapter::getFinley_Mesh
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>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;     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);     TMPMEMFREE(fName);
110    }
111    
112    void MeshAdapter::Print_Mesh_Info(const bool full=false) const
113    {
114       Finley_PrintMesh_Info(m_finleyMesh.get(), full);
115    }
116    
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  //  //
# Line 165  int MeshAdapter::getDiracDeltaFunctionCo Line 643  int MeshAdapter::getDiracDeltaFunctionCo
643  //  //
644  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
645  {  {
646    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     Finley_Mesh* mesh=m_finleyMesh.get();
647    checkFinleyError();     int numDim=Finley_Mesh_getDim(mesh);
648    return numDim;     checkFinleyError();
649       return numDim;
650    }
651    
652    //
653    // Return the number of data points summed across all MPI processes
654    //
655    int MeshAdapter::getNumDataPointsGlobal() const
656    {
657       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
658  }  }
659    
660  //  //
# Line 180  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  #ifndef PASO_MPI     break;
708               numSamples=mesh->Nodes->numDegreesOfFreedom;     case(ContactElementsZero):
709  #else     if (mesh->ContactElements!=NULL) {
710               numSamples=mesh->Nodes->degreeOfFreedomDistribution->numLocal;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
711  #endif        numSamples=mesh->ContactElements->numElements;
712             }     }
713             break;     break;
714        case(ReducedDegreesOfFreedom):     case(ReducedContactElementsZero):
715             if (mesh->Nodes!=NULL) {     if (mesh->ContactElements!=NULL) {
716               numDataPointsPerSample=1;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
717  #ifndef PASO_MPI        numSamples=mesh->ContactElements->numElements;
718               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     }
719  #else     break;
720               numSamples=mesh->Nodes->reducedDegreeOfFreedomDistribution->numLocal;     case(ContactElementsOne):
721  #endif     if (mesh->ContactElements!=NULL) {
722             }        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
723             break;        numSamples=mesh->ContactElements->numElements;
724        default:     }
725          stringstream temp;     break;
726          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     case(ReducedContactElementsOne):
727          throw FinleyAdapterException(temp.str());     if (mesh->ContactElements!=NULL) {
728          break;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
729        }        numSamples=mesh->ContactElements->numElements;
730        return pair<int,int>(numDataPointsPerSample,numSamples);     }
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    escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
763    escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
764    escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
765    escriptDataC _C=C.getDataC();     escriptDataC _C=C.getDataC();
766    escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
767    escriptDataC _X=X.getDataC();     escriptDataC _X=X.getDataC();
768    escriptDataC _Y=Y.getDataC();     escriptDataC _Y=Y.getDataC();
769    escriptDataC _d=d.getDataC();     escriptDataC _d=d.getDataC();
770    escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
771    escriptDataC _d_contact=d_contact.getDataC();     escriptDataC _d_contact=d_contact.getDataC();
772    escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
773    
774     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
775    
776     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
777       checkFinleyError();
778    
779       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
780     checkFinleyError();     checkFinleyError();
781    
782     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, &_d, &_y, Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
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    
    Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , &_d_contact, &_y_contact ,             Finley_Assemble_handelShapeMissMatch_Step_out);  
800     checkFinleyError();     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  //  //
# Line 283  void MeshAdapter::addPDEToRHS( escript:: Line 808  void MeshAdapter::addPDEToRHS( escript::
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();
822    
823       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
824       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();     checkFinleyError();
856    
857     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->FaceElements,&(rhs.getDataC()),&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
858     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
859    
860       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
861     checkFinleyError();     checkFinleyError();
862     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  
863     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->ContactElements,&(rhs.getDataC()),&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
864     checkFinleyError();     checkFinleyError();
865  }  }
866    
# Line 301  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  #ifndef PASO_MPI        break;
949             case(Elements):     }
950                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     break;
951                break;     case(Elements):
952             case(FaceElements):     if (target.getFunctionSpace().getTypeCode()==Elements) {
953                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
954                break;     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
955             case(Points):        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
956                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     } else {
957                break;        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
958             case(ContactElementsZero):     }
959             case(ContactElementsOne):     break;
960                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     case(ReducedElements):
961               break;     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
962  #else        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
963             /* need to copy Degrees of freedom data to nodal data so that the external values are available */     } else {
964             case(Elements):        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
965             {     }
966                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );     break;
967                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(nodeTemp.getDataC()),&(target.getDataC()));     case(FaceElements):
968                break;     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
969             }        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
970             case(FaceElements):     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
971             {        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
972                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );     } else {
973                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(nodeTemp.getDataC()),&(target.getDataC()));        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
974                break;     }
975             }     break;
976             case(Points):     case(ReducedFaceElements):
977             {     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
978                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
979                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(nodeTemp.getDataC()),&(target.getDataC()));     } else {
980                break;        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
981             }     }
982             case(ContactElementsZero):     break;
983             case(ContactElementsOne):     case(Points):
984             {     if (target.getFunctionSpace().getTypeCode()==Points) {
985                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
986                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(nodeTemp.getDataC()),&(target.getDataC()));     } else {
987               break;        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
988             }     }
989  #endif     break;
990             default:     case(ContactElementsZero):
991               stringstream temp;     case(ContactElementsOne):
992               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
993               throw FinleyAdapterException(temp.str());        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
994               break;     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
995          }        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
996          break;     } else {
997       case(ReducedDegreesOfFreedom):        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
998         switch(target.getFunctionSpace().getTypeCode()) {     }
999            case(ReducedDegreesOfFreedom):     break;
1000               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));     case(ReducedContactElementsZero):
1001               break;     case(ReducedContactElementsOne):
1002            case(Elements):     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1003               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1004               break;     } else {
1005            case(FaceElements):        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1006               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     }
1007               break;     break;
1008            case(Points):     case(DegreesOfFreedom):      
1009               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     switch(target.getFunctionSpace().getTypeCode()) {
1010               break;     case(ReducedDegreesOfFreedom):
1011            case(ContactElementsZero):     case(DegreesOfFreedom):
1012            case(ContactElementsOne):     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1013               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
1014               break;  
1015            case(Nodes):     case(Nodes):
1016               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");     case(ReducedNodes):
1017               break;     if (getMPISize()>1) {
1018            case(DegreesOfFreedom):        escript::Data temp=escript::Data(in);
1019               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        temp.expand();
1020               break;        escriptDataC _in2 = temp.getDataC();
1021            default:        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1022               stringstream temp;     } else {
1023               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1024               throw FinleyAdapterException(temp.str());     }
1025               break;     break;
1026         }     case(Elements):
1027         break;     case(ReducedElements):
1028       default:     if (getMPISize()>1) {
1029          stringstream temp;        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1030          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        escriptDataC _in2 = temp.getDataC();
1031          throw FinleyAdapterException(temp.str());        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1032          break;     } else {
1033    }        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1034    checkFinleyError();     }
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 471  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 492  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 533  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 545  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 589  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    escriptDataC nodeDataC;     escriptDataC _grad=grad.getDataC();
1330  #ifdef PASO_MPI     escriptDataC nodeDataC;
1331    escript::Data nodeTemp( arg, continuousFunction(asAbstractContinuousDomain()) );     escript::Data temp;
1332    if( arg.getFunctionSpace().getTypeCode() != Nodes )     if (getMPISize()>1) {
1333    {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1334      Finley_Assemble_CopyNodalData(mesh->Nodes,&(nodeTemp.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1335      nodeDataC = nodeTemp.getDataC();           nodeDataC = temp.getDataC();
1336    }        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1337    else           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1338      nodeDataC = arg.getDataC();           nodeDataC = temp.getDataC();
1339  #else        } else {
1340    nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1341  #endif        }
1342    switch(grad.getFunctionSpace().getTypeCode()) {     } else {
1343         case(Nodes):        nodeDataC = arg.getDataC();
1344            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     }
1345            break;     switch(grad.getFunctionSpace().getTypeCode()) {
1346         case(Elements):     case(Nodes):
1347            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&nodeDataC);     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1348            break;     break;
1349         case(FaceElements):     case(ReducedNodes):
1350            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&nodeDataC);     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1351            break;     break;
1352         case(Points):     case(Elements):
1353            throw FinleyAdapterException("Error - Gradient at points is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1354            break;     break;
1355         case(ContactElementsZero):     case(ReducedElements):
1356            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1357            break;     break;
1358         case(ContactElementsOne):     case(FaceElements):
1359            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1360            break;     break;
1361         case(DegreesOfFreedom):     case(ReducedFaceElements):
1362            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1363            break;     break;
1364         case(ReducedDegreesOfFreedom):     case(Points):
1365            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1366            break;     break;
1367         default:     case(ContactElementsZero):
1368            stringstream temp;     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1369            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     break;
1370            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1371            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1372    }     break;
1373    checkFinleyError();     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 649  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    escriptDataC tmp;     escriptDataC tmp;
1453    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1454    if (newDomain!=*this)     if (newDomain!=*this)
1455       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1456    tmp = new_x.getDataC();     tmp = new_x.getDataC();
1457    Finley_Mesh_setCoordinates(mesh,&tmp);     Finley_Mesh_setCoordinates(mesh,&tmp);
1458    checkFinleyError();     checkFinleyError();
1459  }  }
1460    
1461  // saves a data array in openDX format:  //
1462    // Helper for the save* methods. Extracts optional data variable names and the
1463    // corresponding pointers from python dictionary. Caller must free arrays.
1464    //
1465    void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1466    {
1467       numData = boost::python::extract<int>(arg.attr("__len__")());
1468       /* win32 refactor */
1469       names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1470       data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1471       dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1472    
1473       boost::python::list keys=arg.keys();
1474       for (int i=0; i<numData; ++i) {
1475          std::string n=boost::python::extract<std::string>(keys[i]);
1476          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1477          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1478             throw FinleyAdapterException("Error: Data must be defined on same Domain");
1479          data[i] = d.getDataC();
1480          dataPtr[i] = &(data[i]);
1481          names[i] = TMPMEMALLOC(n.length()+1, char);
1482          strcpy(names[i], n.c_str());
1483       }
1484    }
1485    
1486    //
1487    // saves mesh and optionally data arrays in openDX format
1488    //
1489  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
1490  {  {
1491      int MAX_namelength=256;     int num_data;
1492      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1493    /* win32 refactor */     escriptDataC *data;
1494    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC **ptr_data;
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1495    
1496    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1497    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1498    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;     checkFinleyError();
1499    
1500      boost::python::list keys=arg.keys();     /* win32 refactor */
1501      for (int i=0;i<num_data;++i) {     TMPMEMFREE(data);
1502           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     TMPMEMFREE(ptr_data);
1503           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     for(int i=0; i<num_data; i++)
1504               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     {
1505           data[i]=d.getDataC();        TMPMEMFREE(names[i]);
1506           ptr_data[i]=&(data[i]);     }
1507           std::string n=boost::python::extract<std::string>(keys[i]);     TMPMEMFREE(names);
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
       
       /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1508    
1509      return;     return;
1510  }  }
1511    
1512  // saves a data array in openVTK format:  //
1513    // saves mesh and optionally data arrays in VTK format
1514    //
1515  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1516  {  {
1517      int MAX_namelength=256;     int num_data;
1518      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1519    /* win32 refactor */     escriptDataC *data;
1520    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC **ptr_data;
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1521    
1522    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1523    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1524    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;     checkFinleyError();
   
     boost::python::list keys=arg.keys();  
     for (int i=0;i<num_data;++i) {  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
   /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1525    
1526      return;     /* win32 refactor */
1527       TMPMEMFREE(data);
1528       TMPMEMFREE(ptr_data);
1529       for(int i=0; i<num_data; i++)
1530       {
1531          TMPMEMFREE(names[i]);
1532       }
1533       TMPMEMFREE(names);
1534  }  }
1535                                                                                                                                                                            
1536                                                                                                                                                                            //
1537  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1538    //
1539  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1540                        const int row_blocksize,                                                   const int row_blocksize,
1541                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1542                        const int column_blocksize,                                                   const int column_blocksize,
1543                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1544                        const int type) const                                                   const int type) const
1545  {  {
1546      int reduceRowOrder=0;     int reduceRowOrder=0;
1547      int reduceColOrder=0;     int reduceColOrder=0;
1548      // is the domain right?     // is the domain right?
1549      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1550      if (row_domain!=*this)     if (row_domain!=*this)
1551            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.");
1552      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1553      if (col_domain!=*this)     if (col_domain!=*this)
1554            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.");
1555      // is the function space type right     // is the function space type right
1556      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1557          reduceRowOrder=0;        reduceRowOrder=0;
1558      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1559          reduceRowOrder=1;        reduceRowOrder=1;
1560      } else {     } else {
1561          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1562      }     }
1563      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1564          reduceColOrder=0;        reduceColOrder=0;
1565      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1566          reduceColOrder=1;        reduceColOrder=1;
1567      } else {     } else {
1568          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1569      }     }
1570      // generate matrix:     // generate matrix:
1571        
1572      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1573      checkFinleyError();     checkFinleyError();
1574      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1575      checkPasoError();     int trilinos = 0;
1576      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1577      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1578          /* Allocation Epetra_VrbMatrix here */
1579    #endif
1580       }
1581       else {
1582          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1583       }
1584       checkPasoError();
1585       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1586       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1587    }
1588    
1589    //
1590    // creates a TransportProblemAdapter
1591    //
1592    TransportProblemAdapter MeshAdapter::newTransportProblem(
1593                                                             const double theta,
1594                                                             const int blocksize,
1595                                                             const escript::FunctionSpace& functionspace,
1596                                                             const int type) const
1597    {
1598       int reduceOrder=0;
1599       // is the domain right?
1600       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1601       if (domain!=*this)
1602          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1603       // is the function space type right
1604       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1605          reduceOrder=0;
1606       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1607          reduceOrder=1;
1608       } else {
1609          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1610       }
1611       // generate matrix:
1612    
1613       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1614       checkFinleyError();
1615       Paso_FCTransportProblem* transportProblem;
1616       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1617       checkPasoError();
1618       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1619       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1620  }  }
1621    
1622  //  //
# Line 843  SystemMatrixAdapter MeshAdapter::newSyst Line 1628  SystemMatrixAdapter MeshAdapter::newSyst
1628  // 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:
1629  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1630  {  {
1631    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1632         case(Nodes):     case(Nodes):
1633         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1634         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1635            return false;     return false;
1636            break;     break;
1637         case(Elements):     case(Elements):
1638         case(FaceElements):     case(FaceElements):
1639         case(Points):     case(Points):
1640         case(ContactElementsZero):     case(ContactElementsZero):
1641         case(ContactElementsOne):     case(ContactElementsOne):
1642            return true;     case(ReducedElements):
1643            break;     case(ReducedFaceElements):
1644         default:     case(ReducedContactElementsZero):
1645            stringstream temp;     case(ReducedContactElementsOne):
1646            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1647            throw FinleyAdapterException(temp.str());     break;
1648            break;     default:
1649    }        stringstream temp;
1650    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1651    return false;        throw FinleyAdapterException(temp.str());
1652          break;
1653       }
1654       checkFinleyError();
1655       return false;
1656  }  }
1657    
1658  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1659  {  {
1660    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1661       case(Nodes):     case(Nodes):
1662          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1663             case(Nodes):     case(Nodes):
1664             case(ReducedDegreesOfFreedom):     case(ReducedNodes):
1665             case(DegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1666             case(Elements):     case(DegreesOfFreedom):
1667             case(FaceElements):     case(Elements):
1668             case(Points):     case(ReducedElements):
1669             case(ContactElementsZero):     case(FaceElements):
1670             case(ContactElementsOne):     case(ReducedFaceElements):
1671                 return true;     case(Points):
1672             default:     case(ContactElementsZero):
1673                 stringstream temp;     case(ReducedContactElementsZero):
1674                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(ContactElementsOne):
1675                 throw FinleyAdapterException(temp.str());     case(ReducedContactElementsOne):
1676          }     return true;
1677          break;     default:
1678       case(Elements):        stringstream temp;
1679          if (functionSpaceType_target==Elements) {        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1680             return true;        throw FinleyAdapterException(temp.str());
1681          } else {     }
1682             return false;     break;
1683          }     case(ReducedNodes):
1684       case(FaceElements):     switch(functionSpaceType_target) {
1685          if (functionSpaceType_target==FaceElements) {     case(ReducedNodes):
1686             return true;     case(ReducedDegreesOfFreedom):
1687          } else {     case(Elements):
1688             return false;     case(ReducedElements):
1689          }     case(FaceElements):
1690       case(Points):     case(ReducedFaceElements):
1691          if (functionSpaceType_target==Points) {     case(Points):
1692             return true;     case(ContactElementsZero):
1693          } else {     case(ReducedContactElementsZero):
1694             return false;     case(ContactElementsOne):
1695          }     case(ReducedContactElementsOne):
1696       case(ContactElementsZero):     return true;
1697       case(ContactElementsOne):     case(Nodes):
1698          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     case(DegreesOfFreedom):
1699             return true;     return false;
1700          } else {     default:
1701             return false;        stringstream temp;
1702          }        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1703       case(DegreesOfFreedom):        throw FinleyAdapterException(temp.str());
1704          switch(functionSpaceType_target) {     }
1705             case(ReducedDegreesOfFreedom):     break;
1706             case(DegreesOfFreedom):     case(Elements):
1707             case(Nodes):     if (functionSpaceType_target==Elements) {
1708             case(Elements):        return true;
1709             case(FaceElements):     } else if (functionSpaceType_target==ReducedElements) {
1710             case(Points):        return true;
1711             case(ContactElementsZero):     } else {
1712             case(ContactElementsOne):        return false;
1713                return true;     }
1714             default:     case(ReducedElements):
1715               stringstream temp;     if (functionSpaceType_target==ReducedElements) {
1716               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;        return true;
1717               throw FinleyAdapterException(temp.str());     } else {
1718          }        return false;
1719          break;     }
1720       case(ReducedDegreesOfFreedom):     case(FaceElements):
1721         switch(functionSpaceType_target) {     if (functionSpaceType_target==FaceElements) {
1722            case(ReducedDegreesOfFreedom):        return true;
1723            case(Elements):     } else if (functionSpaceType_target==ReducedFaceElements) {
1724            case(FaceElements):        return true;
1725            case(Points):     } else {
1726            case(ContactElementsZero):        return false;
1727            case(ContactElementsOne):     }
1728                return true;     case(ReducedFaceElements):
1729            case(Nodes):     if (functionSpaceType_target==ReducedFaceElements) {
1730            case(DegreesOfFreedom):        return true;
1731               return false;     } else {
1732            default:        return false;
1733               stringstream temp;     }
1734               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1735               throw FinleyAdapterException(temp.str());     if (functionSpaceType_target==Points) {
1736         }        return true;
1737         break;     } else {
1738       default:        return false;
1739          stringstream temp;     }
1740          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1741          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1742          break;     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1743    }        return true;
1744    checkFinleyError();     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1745    return false;        return true;
1746       } else {
1747          return false;
1748       }
1749       case(ReducedContactElementsZero):
1750       case(ReducedContactElementsOne):
1751       if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1752          return true;
1753       } else {
1754          return false;
1755       }
1756       case(DegreesOfFreedom):
1757       switch(functionSpaceType_target) {
1758       case(ReducedDegreesOfFreedom):
1759       case(DegreesOfFreedom):
1760       case(Nodes):
1761       case(ReducedNodes):
1762       case(Elements):
1763       case(ReducedElements):
1764       case(Points):
1765       case(FaceElements):
1766       case(ReducedFaceElements):
1767       case(ContactElementsZero):
1768       case(ReducedContactElementsZero):
1769       case(ContactElementsOne):
1770       case(ReducedContactElementsOne):
1771       return true;
1772       default:
1773          stringstream temp;
1774          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1775          throw FinleyAdapterException(temp.str());
1776       }
1777       break;
1778       case(ReducedDegreesOfFreedom):
1779       switch(functionSpaceType_target) {
1780       case(ReducedDegreesOfFreedom):
1781       case(ReducedNodes):
1782       case(Elements):
1783       case(ReducedElements):
1784       case(FaceElements):
1785       case(ReducedFaceElements):
1786       case(Points):
1787       case(ContactElementsZero):
1788       case(ReducedContactElementsZero):
1789       case(ContactElementsOne):
1790       case(ReducedContactElementsOne):
1791       return true;
1792       case(Nodes):
1793       case(DegreesOfFreedom):
1794       return false;
1795       default:
1796          stringstream temp;
1797          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1798          throw FinleyAdapterException(temp.str());
1799       }
1800       break;
1801       default:
1802          stringstream temp;
1803          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1804          throw FinleyAdapterException(temp.str());
1805          break;
1806       }
1807       checkFinleyError();
1808       return false;
1809  }  }
1810    
1811  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
1812  {  {
1813      return false;     return false;
1814  }  }
1815    
1816  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1817  {  {
1818    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1819    if (temp!=0) {     if (temp!=0) {
1820      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1821    } else {     } else {
1822      return false;        return false;
1823    }     }
1824  }  }
1825    
1826  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1827  {  {
1828    return !(operator==(other));     return !(operator==(other));
1829  }  }
1830    
1831  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
1832    {
1833       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1834       checkPasoError();
1835       return out;
1836    }
1837    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1838  {  {
1839     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1840     checkPasoError();     checkPasoError();
1841     return out;     return out;
1842  }  }
1843    
1844  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1845  {  {
1846    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1847  }  }
1848    
1849  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1850  {  {
1851    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1852  }  }
1853    
1854  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1855  {  {
1856    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1857  }  }
1858    
1859    int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1860    {
1861       int *out = NULL;
1862       Finley_Mesh* mesh=m_finleyMesh.get();
1863       switch (functionSpaceType) {
1864       case(Nodes):
1865       out=mesh->Nodes->Id;
1866       break;
1867       case(ReducedNodes):
1868       out=mesh->Nodes->reducedNodesId;
1869       break;
1870       case(Elements):
1871       out=mesh->Elements->Id;
1872       break;
1873       case(ReducedElements):
1874       out=mesh->Elements->Id;
1875       break;
1876       case(FaceElements):
1877       out=mesh->FaceElements->Id;
1878       break;
1879       case(ReducedFaceElements):
1880       out=mesh->FaceElements->Id;
1881       break;
1882       case(Points):
1883       out=mesh->Points->Id;
1884       break;
1885       case(ContactElementsZero):
1886       out=mesh->ContactElements->Id;
1887       break;
1888       case(ReducedContactElementsZero):
1889       out=mesh->ContactElements->Id;
1890       break;
1891       case(ContactElementsOne):
1892       out=mesh->ContactElements->Id;
1893       break;
1894       case(ReducedContactElementsOne):
1895       out=mesh->ContactElements->Id;
1896       break;
1897       case(DegreesOfFreedom):
1898       out=mesh->Nodes->degreesOfFreedomId;
1899       break;
1900       case(ReducedDegreesOfFreedom):
1901       out=mesh->Nodes->reducedDegreesOfFreedomId;
1902       break;
1903       default:
1904          stringstream temp;
1905          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1906          throw FinleyAdapterException(temp.str());
1907          break;
1908       }
1909       return out;
1910    }
1911  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1912  {  {
1913    int out=0;     int out=0;
1914       Finley_Mesh* mesh=m_finleyMesh.get();
1915       switch (functionSpaceType) {
1916       case(Nodes):
1917       out=mesh->Nodes->Tag[sampleNo];
1918       break;
1919       case(ReducedNodes):
1920       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1921       break;
1922       case(Elements):
1923       out=mesh->Elements->Tag[sampleNo];
1924       break;
1925       case(ReducedElements):
1926       out=mesh->Elements->Tag[sampleNo];
1927       break;
1928       case(FaceElements):
1929       out=mesh->FaceElements->Tag[sampleNo];
1930       break;
1931       case(ReducedFaceElements):
1932       out=mesh->FaceElements->Tag[sampleNo];
1933       break;
1934       case(Points):
1935       out=mesh->Points->Tag[sampleNo];
1936       break;
1937       case(ContactElementsZero):
1938       out=mesh->ContactElements->Tag[sampleNo];
1939       break;
1940       case(ReducedContactElementsZero):
1941       out=mesh->ContactElements->Tag[sampleNo];
1942       break;
1943       case(ContactElementsOne):
1944       out=mesh->ContactElements->Tag[sampleNo];
1945       break;
1946       case(ReducedContactElementsOne):
1947       out=mesh->ContactElements->Tag[sampleNo];
1948       break;
1949       case(DegreesOfFreedom):
1950       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1951       break;
1952       case(ReducedDegreesOfFreedom):
1953       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1954       break;
1955       default:
1956          stringstream temp;
1957          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1958          throw FinleyAdapterException(temp.str());
1959          break;
1960       }
1961       return out;
1962    }
1963    
1964    
1965    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1966    {
1967       Finley_Mesh* mesh=m_finleyMesh.get();
1968       escriptDataC tmp=mask.getDataC();
1969       switch(functionSpaceType) {
1970       case(Nodes):
1971       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1972       break;
1973       case(ReducedNodes):
1974       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1975       break;
1976       case(DegreesOfFreedom):
1977       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1978       break;
1979       case(ReducedDegreesOfFreedom):
1980       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1981       break;
1982       case(Elements):
1983       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1984       break;
1985       case(ReducedElements):
1986       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1987       break;
1988       case(FaceElements):
1989       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1990       break;
1991       case(ReducedFaceElements):
1992       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1993       break;
1994       case(Points):
1995       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1996       break;
1997       case(ContactElementsZero):
1998       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1999       break;
2000       case(ReducedContactElementsZero):
2001       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2002       break;
2003       case(ContactElementsOne):
2004       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2005       break;
2006       case(ReducedContactElementsOne):
2007       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2008       break;
2009       default:
2010          stringstream temp;
2011          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2012          throw FinleyAdapterException(temp.str());
2013       }
2014       checkFinleyError();
2015       return;
2016    }
2017    
2018    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2019    {
2020       Finley_Mesh* mesh=m_finleyMesh.get();
2021       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2022       checkPasoError();
2023       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2024    }
2025    
2026    int MeshAdapter::getTag(const std::string& name) const
2027    {
2028       Finley_Mesh* mesh=m_finleyMesh.get();
2029       int tag=0;
2030       tag=Finley_Mesh_getTag(mesh, name.c_str());
2031       checkPasoError();
2032       // throwStandardException("MeshAdapter::getTag is not implemented.");
2033       return tag;
2034    }
2035    
2036    bool MeshAdapter::isValidTagName(const std::string& name) const
2037    {
2038       Finley_Mesh* mesh=m_finleyMesh.get();
2039       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2040    }
2041    
2042    std::string MeshAdapter::showTagNames() const
2043    {
2044       stringstream temp;
2045       Finley_Mesh* mesh=m_finleyMesh.get();
2046       Finley_TagMap* tag_map=mesh->TagMap;
2047       while (tag_map) {
2048          temp << tag_map->name;
2049          tag_map=tag_map->next;
2050          if (tag_map) temp << ", ";
2051       }
2052       return temp.str();
2053    }
2054    
2055    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2056    {
2057    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2058    switch (functionSpaceType) {    dim_t numTags=0;
2059    case(Nodes):    switch(functionSpaceCode) {
2060      out=mesh->Nodes->Tag[sampleNo];     case(Nodes):
2061      break;            numTags=mesh->Nodes->numTagsInUse;
2062    case(Elements):            break;
2063      out=mesh->Elements->Tag[sampleNo];     case(ReducedNodes):
2064      break;            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2065    case(FaceElements):            break;
2066      out=mesh->FaceElements->Tag[sampleNo];     case(DegreesOfFreedom):
2067      break;            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2068    case(Points):            break;
2069      out=mesh->Points->Tag[sampleNo];     case(ReducedDegreesOfFreedom):
2070      break;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2071    case(ContactElementsZero):            break;
2072      out=mesh->ContactElements->Tag[sampleNo];     case(Elements):
2073      break;     case(ReducedElements):
2074    case(ContactElementsOne):            numTags=mesh->Elements->numTagsInUse;
2075      out=mesh->ContactElements->Tag[sampleNo];            break;
2076      break;     case(FaceElements):
2077    case(DegreesOfFreedom):     case(ReducedFaceElements):
2078      break;            numTags=mesh->FaceElements->numTagsInUse;
2079    case(ReducedDegreesOfFreedom):            break;
2080      break;     case(Points):
2081    default:            numTags=mesh->Points->numTagsInUse;
2082      stringstream temp;            break;
2083      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();     case(ContactElementsZero):
2084      throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
2085      break;     case(ContactElementsOne):
2086       case(ReducedContactElementsOne):
2087              numTags=mesh->ContactElements->numTagsInUse;
2088              break;
2089       default:
2090          stringstream temp;
2091          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2092          throw FinleyAdapterException(temp.str());
2093    }    }
2094    return out;    return numTags;
2095  }  }
2096  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2097  {  {
   int out=0,i;  
2098    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2099    switch (functionSpaceType) {    index_t* tags=NULL;
2100    case(Nodes):    switch(functionSpaceCode) {
2101      if (mesh->Nodes!=NULL) {     case(Nodes):
2102        out=mesh->Nodes->Id[sampleNo];            tags=mesh->Nodes->tagsInUse;
2103        break;            break;
2104      }     case(ReducedNodes):
2105    case(Elements):            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2106      out=mesh->Elements->Id[sampleNo];            break;
2107      break;     case(DegreesOfFreedom):
2108    case(FaceElements):            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
     out=mesh->FaceElements->Id[sampleNo];  
     break;  
   case(Points):  
     out=mesh->Points->Id[sampleNo];  
     break;  
   case(ContactElementsZero):  
     out=mesh->ContactElements->Id[sampleNo];  
     break;  
   case(ContactElementsOne):  
     out=mesh->ContactElements->Id[sampleNo];  
     break;  
   case(DegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->degreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
2109            break;            break;
2110         }     case(ReducedDegreesOfFreedom):
2111      }            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
     break;  
   case(ReducedDegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->reducedDegreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
2112            break;            break;
2113         }     case(Elements):
2114      }     case(ReducedElements):
2115      break;            tags=mesh->Elements->tagsInUse;
2116    default:            break;
2117      stringstream temp;     case(FaceElements):
2118      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();     case(ReducedFaceElements):
2119      throw FinleyAdapterException(temp.str());            tags=mesh->FaceElements->tagsInUse;
2120      break;            break;
2121       case(Points):
2122              tags=mesh->Points->tagsInUse;
2123              break;
2124       case(ContactElementsZero):
2125       case(ReducedContactElementsZero):
2126       case(ContactElementsOne):
2127       case(ReducedContactElementsOne):
2128              tags=mesh->ContactElements->tagsInUse;
2129              break;
2130       default:
2131          stringstream temp;
2132          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2133          throw FinleyAdapterException(temp.str());
2134    }    }
2135    return out;    return tags;
2136  }  }
2137    
2138    
2139    bool MeshAdapter::canTag(int functionSpaceCode) const
2140    {
2141      switch(functionSpaceCode) {
2142       case(Nodes):
2143       case(Elements):
2144       case(ReducedElements):
2145       case(FaceElements):
2146       case(ReducedFaceElements):
2147       case(Points):
2148       case(ContactElementsZero):
2149       case(ReducedContactElementsZero):
2150       case(ContactElementsOne):
2151       case(ReducedContactElementsOne):
2152              return true;
2153       case(ReducedNodes):
2154       case(DegreesOfFreedom):
2155       case(ReducedDegreesOfFreedom):
2156          return false;
2157       default:
2158        return false;
2159      }
2160    }
2161    
2162    
2163  }  // end of namespace  }  // end of namespace

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