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

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revision 471 by jgs, Fri Jan 27 01:33:02 2006 UTC revision 2150 by caltinay, Wed Dec 10 05:57:12 2008 UTC
# Line 1  Line 1 
1  // $Id$  
2  /*  /*******************************************************
3   ******************************************************************************  *
4   *                                                                            *  * Copyright (c) 2003-2008 by University of Queensland
5   *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  * Earth Systems Science Computational Center (ESSCC)
6   *                                                                            *  * http://www.uq.edu.au/esscc
7   * This software is the property of ACcESS. No part of this code              *  *
8   * may be copied in any form or by any means without the expressed written    *  * Primary Business: Queensland, Australia
9   * consent of ACcESS.  Copying, use or modification of this software          *  * Licensed under the Open Software License version 3.0
10   * by any unauthorised person is illegal unless that person has a software    *  * http://www.opensource.org/licenses/osl-3.0.php
11   * license agreement with ACcESS.                                             *  *
12   *                                                                            *  *******************************************************/
13   ******************************************************************************  
14  */  
15    #include "MeshAdapter.h"
16    #include "escript/Data.h"
17    #include "escript/DataFactory.h"
18    #ifdef USE_NETCDF
19    #include <netcdfcpp.h>
20    #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25  extern "C" {  extern "C" {
26  #include "Finley.h"  #include "esysUtils/blocktimer.h"
 #include "Assemble.h"  
 #include "Mesh.h"  
 #include "Finley.h"  
 #include "SystemMatrix.h"  
27  }  }
28  #include "SystemMatrixAdapter.h"  #include <vector>
 #include "MeshAdapter.h"  
 #include "FinleyError.h"  
 #include "FinleyAdapterException.h"  
 #include "escript/Data/FunctionSpaceFactory.h"  
 #include "escript/Data/Data.h"  
 #include "escript/Data/DataArrayView.h"  
 #include "escript/Data/FunctionSpace.h"  
 #include "escript/Data/DataFactory.h"  
 #include <boost/python/extract.hpp>  
   
 #include <iostream>  
 #include <sstream>  
29    
30  using namespace std;  using namespace std;
31  using namespace escript;  using namespace escript;
# Line 44  MeshAdapter::FunctionSpaceNamesMapType M Line 38  MeshAdapter::FunctionSpaceNamesMapType M
38  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
39  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
40  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
41    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
42  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
43    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
44  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
45    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
46  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
47  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
48    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
49  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
50    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
51    
52  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
53  {  {
54    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
55    //     //
56    // 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
57    // for us.     // for us.
58    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
59  }  }
60    
61  //  //
# Line 64  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 63  MeshAdapter::MeshAdapter(Finley_Mesh* fi
63  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
64  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
65  {  {
66    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
67  }  }
68    
69  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
70  {  {
71    //     //
72    // 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.
73    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
74    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
75      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
76      Finley_Mesh_dealloc(m_finleyMesh.get());     }
77      //   cout << "Finished dealloc." << endl;  }
78    }  
79    int MeshAdapter::getMPISize() const
80    {
81       return m_finleyMesh.get()->MPIInfo->size;
82    }
83    int MeshAdapter::getMPIRank() const
84    {
85       return m_finleyMesh.get()->MPIInfo->rank;
86    }
87    void MeshAdapter::MPIBarrier() const
88    {
89    #ifdef PASO_MPI
90       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
91    #endif
92       return;
93    }
94    bool MeshAdapter::onMasterProcessor() const
95    {
96       return m_finleyMesh.get()->MPIInfo->rank == 0;
97  }  }
98    
99    
100  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
101     return m_finleyMesh.get();     return m_finleyMesh.get();
102  }  }
103    
104  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
105  {  {
106    char fName[fileName.size()+1];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
107    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
108    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
109    checkFinleyError();     checkFinleyError();
110       TMPMEMFREE(fName);
111    }
112    
113    void MeshAdapter::Print_Mesh_Info(const bool full=false) const
114    {
115       Finley_PrintMesh_Info(m_finleyMesh.get(), full);
116  }  }
117    
118  // void MeshAdapter::getTagList(int functionSpaceType,  void MeshAdapter::dump(const std::string& fileName) const
119  //                  int* numTags) const  {
120  // {  #ifdef USE_NETCDF
121  //   Finley_Mesh_tagList(m_finleyMesh.get(),functionSpaceType,tagList,numTags);     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
122  //   return;     NcVar *ids;
123  // }     int *int_ptr;
124       Finley_Mesh *mesh = m_finleyMesh.get();
125       Finley_TagMap* tag_map;
126       int num_Tags = 0;
127       int mpi_size             = mesh->MPIInfo->size;
128       int mpi_rank             = mesh->MPIInfo->rank;
129       int numDim               = mesh->Nodes->numDim;
130       int numNodes             = mesh->Nodes->numNodes;
131       int num_Elements         = mesh->Elements->numElements;
132       int num_FaceElements         = mesh->FaceElements->numElements;
133       int num_ContactElements      = mesh->ContactElements->numElements;
134       int num_Points           = mesh->Points->numElements;
135       int num_Elements_numNodes        = mesh->Elements->numNodes;
136       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
137       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
138    #ifdef PASO_MPI
139       MPI_Status status;
140    #endif
141    
142    /* Incoming token indicates it's my turn to write */
143    #ifdef PASO_MPI
144       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
145    #endif
146    
147       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
148                                                         mpi_size, mpi_rank);
149    
150       /* Figure out how much storage is required for tags */
151       tag_map = mesh->TagMap;
152       num_Tags = 0;
153       if (tag_map) {
154          while (tag_map) {
155             num_Tags++;
156             tag_map=tag_map->next;
157          }
158       }
159    
160       // NetCDF error handler
161       NcError err(NcError::verbose_nonfatal);
162       // Create the file.
163       NcFile dataFile(newFileName, NcFile::Replace);
164       // check if writing was successful
165       if (!dataFile.is_valid())
166          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
167    
168       // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
169       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
170          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
171       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
172          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
173       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
174          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
175       if (num_Elements>0)
176          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
177             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
178       if (num_FaceElements>0)
179          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
180             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
181       if (num_ContactElements>0)
182          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
183             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
184       if (num_Points>0)
185          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
186             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
187       if (num_Elements>0)
188          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
189             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
190       if (num_FaceElements>0)
191          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
192             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
193       if (num_ContactElements>0)
194          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
195             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
196       if (num_Tags>0)
197          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
198             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
199    
200       // Attributes: MPI size, MPI rank, Name, order, reduced_order
201       if (!dataFile.add_att("mpi_size", mpi_size) )
202          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
203       if (!dataFile.add_att("mpi_rank", mpi_rank) )
204          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
205       if (!dataFile.add_att("Name",mesh->Name) )
206          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
207       if (!dataFile.add_att("numDim",numDim) )
208          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
209       if (!dataFile.add_att("order",mesh->order) )
210          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
211       if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
212          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
213       if (!dataFile.add_att("numNodes",numNodes) )
214          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
215       if (!dataFile.add_att("num_Elements",num_Elements) )
216          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
217       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
218          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
219       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
220          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
221       if (!dataFile.add_att("num_Points",num_Points) )
222          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
223       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
224          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
225       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
226          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
227       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
228          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
229       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
230          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
231       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
232          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
233       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
234          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
235       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
236          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
237       if (!dataFile.add_att("num_Tags", num_Tags) )
238          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
239    
240       // // // // // Nodes // // // // //
241    
242       // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
243       if (numNodes>0) {
244    
245          // Nodes Id
246          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
247             throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
248          int_ptr = &mesh->Nodes->Id[0];
249          if (! (ids->put(int_ptr, numNodes)) )
250             throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
251    
252          // Nodes Tag
253          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
254             throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
255          int_ptr = &mesh->Nodes->Tag[0];
256          if (! (ids->put(int_ptr, numNodes)) )
257             throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
258    
259          // Nodes gDOF
260          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
261             throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
262          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
263          if (! (ids->put(int_ptr, numNodes)) )
264             throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
265    
266          // Nodes global node index
267          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
268             throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
269          int_ptr = &mesh->Nodes->globalNodesIndex[0];
270          if (! (ids->put(int_ptr, numNodes)) )
271             throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
272    
273          // Nodes grDof
274          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
275             throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
276          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
277          if (! (ids->put(int_ptr, numNodes)) )
278             throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
279    
280          // Nodes grNI
281          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
282             throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
283          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
284          if (! (ids->put(int_ptr, numNodes)) )
285             throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
286    
287          // Nodes Coordinates
288          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
289             throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
290          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
291             throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
292    
293          // Nodes degreesOfFreedomDistribution
294          if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
295             throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
296          int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
297          if (! (ids->put(int_ptr, mpi_size+1)) )
298             throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
299    
300          // Nodes nodeDistribution
301          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
302             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
303          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
304          if (! (ids->put(int_ptr, mpi_size+1)) )
305             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
306    
307       }
308    
309       // // // // // Elements // // // // //
310    
311       if (num_Elements>0) {
312    
313          // Elements_Id
314          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
315             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
316          int_ptr = &mesh->Elements->Id[0];
317          if (! (ids->put(int_ptr, num_Elements)) )
318             throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
319    
320          // Elements_Tag
321          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
322             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
323          int_ptr = &mesh->Elements->Tag[0];
324          if (! (ids->put(int_ptr, num_Elements)) )
325             throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
326    
327          // Elements_Owner
328          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
329             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
330          int_ptr = &mesh->Elements->Owner[0];
331          if (! (ids->put(int_ptr, num_Elements)) )
332             throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
333    
334          // Elements_Color
335          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
336             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
337          int_ptr = &mesh->Elements->Color[0];
338          if (! (ids->put(int_ptr, num_Elements)) )
339             throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
340    
341          // Elements_Nodes
342          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
343             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
344          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
345             throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
346    
347       }
348    
349       // // // // // Face_Elements // // // // //
350    
351       if (num_FaceElements>0) {
352    
353          // FaceElements_Id
354          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
355             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
356          int_ptr = &mesh->FaceElements->Id[0];
357          if (! (ids->put(int_ptr, num_FaceElements)) )
358             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
359    
360          // FaceElements_Tag
361          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
362             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
363          int_ptr = &mesh->FaceElements->Tag[0];
364          if (! (ids->put(int_ptr, num_FaceElements)) )
365             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
366    
367          // FaceElements_Owner
368          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
369             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
370          int_ptr = &mesh->FaceElements->Owner[0];
371          if (! (ids->put(int_ptr, num_FaceElements)) )
372             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
373    
374          // FaceElements_Color
375          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
376             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
377          int_ptr = &mesh->FaceElements->Color[0];
378          if (! (ids->put(int_ptr, num_FaceElements)) )
379             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
380    
381          // FaceElements_Nodes
382          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
383             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
384          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
385             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
386    
387       }
388    
389       // // // // // Contact_Elements // // // // //
390    
391       if (num_ContactElements>0) {
392    
393          // ContactElements_Id
394          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
395             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
396          int_ptr = &mesh->ContactElements->Id[0];
397          if (! (ids->put(int_ptr, num_ContactElements)) )
398             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
399    
400          // ContactElements_Tag
401          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
402             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
403          int_ptr = &mesh->ContactElements->Tag[0];
404          if (! (ids->put(int_ptr, num_ContactElements)) )
405             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
406    
407          // ContactElements_Owner
408          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
409             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
410          int_ptr = &mesh->ContactElements->Owner[0];
411          if (! (ids->put(int_ptr, num_ContactElements)) )
412             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
413    
414          // ContactElements_Color
415          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
416             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
417          int_ptr = &mesh->ContactElements->Color[0];
418          if (! (ids->put(int_ptr, num_ContactElements)) )
419             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
420    
421          // ContactElements_Nodes
422          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
423             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
424          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
425             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
426    
427       }
428    
429       // // // // // Points // // // // //
430    
431       if (num_Points>0) {
432    
433          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
434    
435          // Points_Id
436          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
437             throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
438          int_ptr = &mesh->Points->Id[0];
439          if (! (ids->put(int_ptr, num_Points)) )
440             throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
441    
442          // Points_Tag
443          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
444             throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
445          int_ptr = &mesh->Points->Tag[0];
446          if (! (ids->put(int_ptr, num_Points)) )
447             throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
448    
449          // Points_Owner
450          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
451             throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
452          int_ptr = &mesh->Points->Owner[0];
453          if (! (ids->put(int_ptr, num_Points)) )
454             throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
455    
456          // Points_Color
457          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
458             throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
459          int_ptr = &mesh->Points->Color[0];
460          if (! (ids->put(int_ptr, num_Points)) )
461             throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
462    
463          // Points_Nodes
464          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
465          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
466             throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
467          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
468             throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
469    
470       }
471    
472       // // // // // TagMap // // // // //
473    
474       if (num_Tags>0) {
475    
476          // Temp storage to gather node IDs
477          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
478          char name_temp[4096];
479    
480          /* Copy tag data into temp arrays */
481          tag_map = mesh->TagMap;
482          if (tag_map) {
483             int i = 0;
484             while (tag_map) {
485                Tags_keys[i++] = tag_map->tag_key;
486                tag_map=tag_map->next;
487             }
488          }
489    
490          // Tags_keys
491          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
492             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
493          int_ptr = &Tags_keys[0];
494          if (! (ids->put(int_ptr, num_Tags)) )
495             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
496    
497          // Tags_names_*
498          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
499          // because the NetCDF manual doesn't tell how to do an array of strings
500          tag_map = mesh->TagMap;
501          if (tag_map) {
502             int i = 0;
503             while (tag_map) {
504                sprintf(name_temp, "Tags_name_%d", i);
505                if (!dataFile.add_att(name_temp, tag_map->name) )
506                   throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
507                tag_map=tag_map->next;
508                i++;
509             }
510          }
511    
512          TMPMEMFREE(Tags_keys);
513    
514       }
515    
516    /* Send token to next MPI process so he can take his turn */
517    #ifdef PASO_MPI
518       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
519    #endif
520    
521       // NetCDF file is closed by destructor of NcFile object
522    
523    #else
524       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
525    #endif  /* USE_NETCDF */
526       checkFinleyError();
527    }
528    
529  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
530  {  {
531    return "FinleyMesh";     return "FinleyMesh";
532  }  }
533    
534  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
535  {  {
536    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
537    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
538    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
539      return "Invalid function space type code.";        return "Invalid function space type code.";
540    } else {     } else {
541      return loc->second;        return loc->second;
542    }     }
543  }  }
544    
545  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
546  {  {
547    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
548    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
549    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
550  }  }
551    
552  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
553  {  {
554    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
555      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
556    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
557      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
558    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
559      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
560    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
561      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
562    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
563      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
564    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
565      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
566    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
567      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
568    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
569      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
570       m_functionSpaceTypeNames.insert
571       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
572       m_functionSpaceTypeNames.insert
573       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
574       m_functionSpaceTypeNames.insert
575       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
576       m_functionSpaceTypeNames.insert
577       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
578       m_functionSpaceTypeNames.insert
579       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
580  }  }
581    
582  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
583  {  {
584    return Nodes;     return Nodes;
585    }
586    int MeshAdapter::getReducedContinuousFunctionCode() const
587    {
588       return ReducedNodes;
589  }  }
590    
591  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
592  {  {
593    return Elements;     return Elements;
594    }
595    int MeshAdapter::getReducedFunctionCode() const
596    {
597       return ReducedElements;
598  }  }
599    
600  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
601  {  {
602    return FaceElements;     return FaceElements;
603    }
604    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
605    {
606       return ReducedFaceElements;
607  }  }
608    
609  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
610  {  {
611    return ContactElementsZero;     return ContactElementsZero;
612    }
613    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
614    {
615       return ReducedContactElementsZero;
616  }  }
617    
618  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
619  {  {
620    return ContactElementsOne;     return ContactElementsOne;
621    }
622    int MeshAdapter::getReducedFunctionOnContactOneCode() const
623    {
624       return ReducedContactElementsOne;
625  }  }
626    
627  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
628  {  {
629    return DegreesOfFreedom;     return DegreesOfFreedom;
630  }  }
631    
632  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
633  {  {
634    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
635  }  }
636    
637  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
638  {  {
639    return Points;     return Points;
 }  
   
 //  
 // returns a pointer to the tag list of samples of functionSpaceType  
 //  
 void MeshAdapter::getTagList(int functionSpaceType, int** tagList,  
                  int* numTags) const  
 {  
   *tagList=NULL;  
   *numTags=0;  
   Finley_Mesh* mesh=m_finleyMesh.get();  
   switch (functionSpaceType) {  
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *tagList=mesh->Nodes->Tag;  
       *numTags=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *tagList=mesh->Elements->Tag;  
       *numTags=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *tagList=mesh->FaceElements->Tag;  
       *numTags=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *tagList=mesh->Points->Tag;  
       *numTags=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   if (*tagList==NULL) {  
     stringstream temp;  
     temp << "Error - no tags available for " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
   }  
   return;  
640  }  }
641    
642  //  //
643  // returns a pointer to the reference no list of samples of functionSpaceType  // return the spatial dimension of the Mesh:
644  //  //
645  void MeshAdapter::getReferenceNoList(int functionSpaceType, int** referenceNoList,  int MeshAdapter::getDim() const
                  int* numReferenceNo) const  
646  {  {
647    *referenceNoList=NULL;     Finley_Mesh* mesh=m_finleyMesh.get();
648    *numReferenceNo=0;     int numDim=Finley_Mesh_getDim(mesh);
649    Finley_Mesh* mesh=m_finleyMesh.get();     checkFinleyError();
650    switch (functionSpaceType) {     return numDim;
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=mesh->Nodes->Id;  
       *numReferenceNo=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *referenceNoList=mesh->Elements->Id;  
       *numReferenceNo=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *referenceNoList=mesh->FaceElements->Id;  
       *numReferenceNo=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *referenceNoList=mesh->Points->Id;  
       *numReferenceNo=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *referenceNoList=mesh->ContactElements->Id;  
       *numReferenceNo=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *referenceNoList=mesh->ContactElements->Id;  
       *numReferenceNo=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=NULL;  
       *numReferenceNo=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=NULL;  
       *numReferenceNo=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   if (*referenceNoList==NULL) {  
     stringstream temp;  
     temp << "Error - reference number list available for " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
   }  
   return;  
651  }  }
652    
653  //  //
654  // return the spatial dimension of the Mesh:  // Return the number of data points summed across all MPI processes
655  //  //
656  int MeshAdapter::getDim() const  int MeshAdapter::getNumDataPointsGlobal() const
657  {  {
658    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
   checkFinleyError();  
   return numDim;  
659  }  }
660    
661  //  //
# Line 345  pair<int,int> MeshAdapter::getDataShape( Line 668  pair<int,int> MeshAdapter::getDataShape(
668     int numSamples=0;     int numSamples=0;
669     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
670     switch (functionSpaceCode) {     switch (functionSpaceCode) {
671        case(Nodes):     case(Nodes):
672             numDataPointsPerSample=1;     numDataPointsPerSample=1;
673             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
674             break;     break;
675        case(Elements):     case(ReducedNodes):
676             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
677               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
678               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
679             }     case(Elements):
680             break;     if (mesh->Elements!=NULL) {
681        case(FaceElements):        numSamples=mesh->Elements->numElements;
682             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
683                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
684                  numSamples=mesh->FaceElements->numElements;     break;
685             }     case(ReducedElements):
686             break;     if (mesh->Elements!=NULL) {
687        case(Points):        numSamples=mesh->Elements->numElements;
688             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
689               numDataPointsPerSample=1;     }
690               numSamples=mesh->Points->numElements;     break;
691             }     case(FaceElements):
692             break;     if (mesh->FaceElements!=NULL) {
693        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
694             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
695               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
696               numSamples=mesh->ContactElements->numElements;     break;
697             }     case(ReducedFaceElements):
698             break;     if (mesh->FaceElements!=NULL) {
699        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
700             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
701               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
702               numSamples=mesh->ContactElements->numElements;     break;
703             }     case(Points):
704             break;     if (mesh->Points!=NULL) {
705        case(DegreesOfFreedom):        numDataPointsPerSample=1;
706             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
707               numDataPointsPerSample=1;     }
708               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
709             }     case(ContactElementsZero):
710             break;     if (mesh->ContactElements!=NULL) {
711        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
712             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
713               numDataPointsPerSample=1;     }
714               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
715             }     case(ReducedContactElementsZero):
716             break;     if (mesh->ContactElements!=NULL) {
717        default:        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
718          stringstream temp;        numSamples=mesh->ContactElements->numElements;
719          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     }
720          throw FinleyAdapterException(temp.str());     break;
721          break;     case(ContactElementsOne):
722        }     if (mesh->ContactElements!=NULL) {
723        return pair<int,int>(numDataPointsPerSample,numSamples);        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
724          numSamples=mesh->ContactElements->numElements;
725       }
726       break;
727       case(ReducedContactElementsOne):
728       if (mesh->ContactElements!=NULL) {
729          numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
730          numSamples=mesh->ContactElements->numElements;
731       }
732       break;
733       case(DegreesOfFreedom):
734       if (mesh->Nodes!=NULL) {
735          numDataPointsPerSample=1;
736          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
737       }
738       break;
739       case(ReducedDegreesOfFreedom):
740       if (mesh->Nodes!=NULL) {
741          numDataPointsPerSample=1;
742          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
743       }
744       break;
745       default:
746          stringstream temp;
747          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
748          throw FinleyAdapterException(temp.str());
749          break;
750       }
751       return pair<int,int>(numDataPointsPerSample,numSamples);
752  }  }
753    
754  //  //
755  // 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:
756  //  //
757  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
758                       SystemMatrixAdapter& mat, Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
759                       const Data& A, const Data& B, const Data& C,const  Data& D,const  Data& X,const  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,
760                       const Data& d, const Data& y,                                   const escript::Data& d, const escript::Data& y,
761                       const Data& d_contact,const Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
762  {  {
763       escriptDataC _rhs=rhs.getDataC();
764       escriptDataC _A  =A.getDataC();
765       escriptDataC _B=B.getDataC();
766       escriptDataC _C=C.getDataC();
767       escriptDataC _D=D.getDataC();
768       escriptDataC _X=X.getDataC();
769       escriptDataC _Y=Y.getDataC();
770       escriptDataC _d=d.getDataC();
771       escriptDataC _y=y.getDataC();
772       escriptDataC _d_contact=d_contact.getDataC();
773       escriptDataC _y_contact=y_contact.getDataC();
774    
775     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
776     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(),&(rhs.getDataC()),  
777                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
778     checkFinleyError();     checkFinleyError();
779     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,  
780                    mat.getPaso_SystemMatrix(),     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
781                    &(rhs.getDataC()),     checkFinleyError();
782                                    &(d.getDataC()),&(y.getDataC()),  
783                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
    checkFinleyError();  
    Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,  
                   mat.getPaso_SystemMatrix(),  
                   &(rhs.getDataC()),  
                                   &(d_contact.getDataC()),  
                   &(y_contact.getDataC()),  
                                   Finley_Assemble_handelShapeMissMatch_Step_out);  
784     checkFinleyError();     checkFinleyError();
785  }  }
786    
787    void  MeshAdapter::addPDEToLumpedSystem(
788                                            escript::Data& mat,
789                                            const escript::Data& D,
790                                            const escript::Data& d) const
791    {
792       escriptDataC _mat=mat.getDataC();
793       escriptDataC _D=D.getDataC();
794       escriptDataC _d=d.getDataC();
795    
796       Finley_Mesh* mesh=m_finleyMesh.get();
797    
798       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
799       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
800    
801       checkFinleyError();
802    }
803    
804    
805  //  //
806  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
807  //  //
808  void MeshAdapter::addPDEToRHS( Data& rhs,  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const
                      const  Data& X,const  Data& Y, const Data& y, const Data& y_contact) const  
809  {  {
810     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
811    
812     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
813     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
814       escriptDataC _Y=Y.getDataC();
815       escriptDataC _y=y.getDataC();
816       escriptDataC _y_contact=y_contact.getDataC();
817    
818       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
819       checkFinleyError();
820    
821       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
822       checkFinleyError();
823    
824       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
825       checkFinleyError();
826    }
827    //
828    // adds PDE of second order into a transport problem
829    //
830    void MeshAdapter::addPDEToTransportProblem(
831                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
832                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
833                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
834                                               const escript::Data& d, const escript::Data& y,
835                                               const escript::Data& d_contact,const escript::Data& y_contact) const
836    {
837       DataTypes::ShapeType shape;
838       source.expand();
839       escriptDataC _source=source.getDataC();
840       escriptDataC _M=M.getDataC();
841       escriptDataC _A=A.getDataC();
842       escriptDataC _B=B.getDataC();
843       escriptDataC _C=C.getDataC();
844       escriptDataC _D=D.getDataC();
845       escriptDataC _X=X.getDataC();
846       escriptDataC _Y=Y.getDataC();
847       escriptDataC _d=d.getDataC();
848       escriptDataC _y=y.getDataC();
849       escriptDataC _d_contact=d_contact.getDataC();
850       escriptDataC _y_contact=y_contact.getDataC();
851    
852       Finley_Mesh* mesh=m_finleyMesh.get();
853       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
854    
855       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
856     checkFinleyError();     checkFinleyError();
857    
858     // 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 );
859     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
860    
861       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
862     checkFinleyError();     checkFinleyError();
863     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  
864     // 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 );
865     checkFinleyError();     checkFinleyError();
866  }  }
867    
868  //  //
869  // interpolates data between different function spaces:  // interpolates data between different function spaces:
870  //  //
871  void MeshAdapter::interpolateOnDomain(Data& target,const Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
872  {  {
873    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
874    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
875    if (inDomain!=*this)     if (inDomain!=*this)  
876       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
877    if (targetDomain!=*this)     if (targetDomain!=*this)
878       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
879    
880    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
881    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
882       case(Nodes):     escriptDataC _in=in.getDataC();
883          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
884             case(Nodes):     case(Nodes):
885             case(ReducedDegreesOfFreedom):     switch(target.getFunctionSpace().getTypeCode()) {
886             case(DegreesOfFreedom):     case(Nodes):
887                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));     case(ReducedNodes):
888                 break;     case(DegreesOfFreedom):
889             case(Elements):     case(ReducedDegreesOfFreedom):
890                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
891                 break;     break;
892             case(FaceElements):     case(Elements):
893                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     case(ReducedElements):
894                 break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
895             case(Points):     break;
896                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     case(FaceElements):
897                 break;     case(ReducedFaceElements):
898             case(ContactElementsZero):     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
899                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
900                 break;     case(Points):
901             case(ContactElementsOne):     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
902                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
903                 break;     case(ContactElementsZero):
904             default:     case(ReducedContactElementsZero):
905                 stringstream temp;     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
906                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     break;
907                 throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
908                 break;     case(ReducedContactElementsOne):
909          }     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
910          break;     break;
911       case(Elements):     default:
912          if (target.getFunctionSpace().getTypeCode()==Elements) {        stringstream temp;
913             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();
914          } else {        throw FinleyAdapterException(temp.str());
915             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        break;
916          }     }
917          break;     break;
918       case(FaceElements):     case(ReducedNodes):
919          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     switch(target.getFunctionSpace().getTypeCode()) {
920             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));     case(Nodes):
921          } else {     case(ReducedNodes):
922             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");     case(DegreesOfFreedom):
923             break;     case(ReducedDegreesOfFreedom):
924         }     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
925       case(Points):     break;
926          if (target.getFunctionSpace().getTypeCode()==Points) {     case(Elements):
927             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));     case(ReducedElements):
928          } else {     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
929             throw FinleyAdapterException("Error - No interpolation with data on points possible.");     break;
930             break;     case(FaceElements):
931          }     case(ReducedFaceElements):
932          break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
933       case(ContactElementsZero):     break;
934       case(ContactElementsOne):     case(Points):
935          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
936             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));     break;
937          } else {     case(ContactElementsZero):
938             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");     case(ReducedContactElementsZero):
939             break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
940          }     break;
941          break;     case(ContactElementsOne):
942       case(DegreesOfFreedom):     case(ReducedContactElementsOne):
943          switch(target.getFunctionSpace().getTypeCode()) {     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
944             case(ReducedDegreesOfFreedom):     break;
945             case(DegreesOfFreedom):     default:
946             case(Nodes):        stringstream temp;
947                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();
948                break;        throw FinleyAdapterException(temp.str());
949             case(Elements):        break;
950                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     }
951                break;     break;
952             case(FaceElements):     case(Elements):
953                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     if (target.getFunctionSpace().getTypeCode()==Elements) {
954                break;        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
955             case(Points):     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
956                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
957                break;     } else {
958             case(ContactElementsZero):        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
959             case(ContactElementsOne):     }
960                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
961               break;     case(ReducedElements):
962             default:     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
963               stringstream temp;        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
964               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     } else {
965               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
966               break;     }
967          }     break;
968          break;     case(FaceElements):
969       case(ReducedDegreesOfFreedom):     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
970         switch(target.getFunctionSpace().getTypeCode()) {        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
971            case(ReducedDegreesOfFreedom):     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
972               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
973               break;     } else {
974            case(Elements):        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
975               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     }
976               break;     break;
977            case(FaceElements):     case(ReducedFaceElements):
978               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
979               break;        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
980            case(Points):     } else {
981               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
982               break;     }
983            case(ContactElementsZero):     break;
984            case(ContactElementsOne):     case(Points):
985               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     if (target.getFunctionSpace().getTypeCode()==Points) {
986               break;        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
987            case(Nodes):     } else {
988               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
989               break;     }
990            case(DegreesOfFreedom):     break;
991               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsZero):
992               break;     case(ContactElementsOne):
993            default:     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
994               stringstream temp;        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
995               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
996               throw FinleyAdapterException(temp.str());        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
997               break;     } else {
998         }        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
999         break;     }
1000       default:     break;
1001          stringstream temp;     case(ReducedContactElementsZero):
1002          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();     case(ReducedContactElementsOne):
1003          throw FinleyAdapterException(temp.str());     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1004          break;        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1005    }     } else {
1006    checkFinleyError();        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1007       }
1008       break;
1009       case(DegreesOfFreedom):      
1010       switch(target.getFunctionSpace().getTypeCode()) {
1011       case(ReducedDegreesOfFreedom):
1012       case(DegreesOfFreedom):
1013       Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1014       break;
1015    
1016       case(Nodes):
1017       case(ReducedNodes):
1018       if (getMPISize()>1) {
1019          escript::Data temp=escript::Data(in);
1020          temp.expand();
1021          escriptDataC _in2 = temp.getDataC();
1022          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1023       } else {
1024          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1025       }
1026       break;
1027       case(Elements):
1028       case(ReducedElements):
1029       if (getMPISize()>1) {
1030          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1031          escriptDataC _in2 = temp.getDataC();
1032          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1033       } else {
1034          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1035       }
1036       break;
1037       case(FaceElements):
1038       case(ReducedFaceElements):
1039       if (getMPISize()>1) {
1040          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1041          escriptDataC _in2 = temp.getDataC();
1042          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1043    
1044       } else {
1045          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1046       }
1047       break;
1048       case(Points):
1049       if (getMPISize()>1) {
1050          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1051          escriptDataC _in2 = temp.getDataC();
1052       } else {
1053          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1054       }
1055       break;
1056       case(ContactElementsZero):
1057       case(ContactElementsOne):
1058       case(ReducedContactElementsZero):
1059       case(ReducedContactElementsOne):
1060       if (getMPISize()>1) {
1061          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1062          escriptDataC _in2 = temp.getDataC();
1063          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1064       } else {
1065          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1066       }
1067       break;
1068       default:
1069          stringstream temp;
1070          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1071          throw FinleyAdapterException(temp.str());
1072          break;
1073       }
1074       break;
1075       case(ReducedDegreesOfFreedom):
1076       switch(target.getFunctionSpace().getTypeCode()) {
1077       case(Nodes):
1078       throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1079       break;
1080       case(ReducedNodes):
1081       if (getMPISize()>1) {
1082          escript::Data temp=escript::Data(in);
1083          temp.expand();
1084          escriptDataC _in2 = temp.getDataC();
1085          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1086       } else {
1087          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1088       }
1089       break;
1090       case(DegreesOfFreedom):
1091       throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1092       break;
1093       case(ReducedDegreesOfFreedom):
1094       Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1095       break;
1096       case(Elements):
1097       case(ReducedElements):
1098       if (getMPISize()>1) {
1099          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1100          escriptDataC _in2 = temp.getDataC();
1101          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1102       } else {
1103          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1104       }
1105       break;
1106       case(FaceElements):
1107       case(ReducedFaceElements):
1108       if (getMPISize()>1) {
1109          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1110          escriptDataC _in2 = temp.getDataC();
1111          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1112       } else {
1113          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1114       }
1115       break;
1116       case(Points):
1117       if (getMPISize()>1) {
1118          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1119          escriptDataC _in2 = temp.getDataC();
1120          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1121       } else {
1122          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1123       }
1124       break;
1125       case(ContactElementsZero):
1126       case(ContactElementsOne):
1127       case(ReducedContactElementsZero):
1128       case(ReducedContactElementsOne):
1129       if (getMPISize()>1) {
1130          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1131          escriptDataC _in2 = temp.getDataC();
1132          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1133       } else {
1134          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1135       }
1136       break;
1137       default:
1138          stringstream temp;
1139          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1140          throw FinleyAdapterException(temp.str());
1141          break;
1142       }
1143       break;
1144       default:
1145          stringstream temp;
1146          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1147          throw FinleyAdapterException(temp.str());
1148          break;
1149       }
1150       checkFinleyError();
1151  }  }
1152    
1153  //  //
1154  // copies the locations of sample points into x:  // copies the locations of sample points into x:
1155  //  //
1156  void MeshAdapter::setToX(Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1157  {  {
1158    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1159    if (argDomain!=*this)     if (argDomain!=*this)
1160       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1161    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1162    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1163    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1164       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1165    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1166       Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1167       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1168       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1169       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1170    }        // this is then interpolated onto arg:
1171    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1172       }
1173       checkFinleyError();
1174  }  }
1175    
1176  //  //
1177  // return the normal vectors at the location of data points as a Data object:  // return the normal vectors at the location of data points as a Data object:
1178  //  //
1179  void MeshAdapter::setToNormal(Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1180  {  {
1181    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1182    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1183       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1184    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1185    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1186      case(Nodes):     escriptDataC _normal=normal.getDataC();
1187        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     switch(normal.getFunctionSpace().getTypeCode()) {
1188        break;     case(Nodes):
1189      case(Elements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1190        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     break;
1191        break;     case(ReducedNodes):
1192      case (FaceElements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1193        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     break;
1194        break;     case(Elements):
1195      case(Points):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1196        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     break;
1197        break;     case(ReducedElements):
1198      case (ContactElementsOne):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1199      case (ContactElementsZero):     break;
1200        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (FaceElements):
1201        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1202      case(DegreesOfFreedom):     break;
1203        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case (ReducedFaceElements):
1204        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1205      case(ReducedDegreesOfFreedom):     break;
1206        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(Points):
1207        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1208      default:     break;
1209       case (ContactElementsOne):
1210       case (ContactElementsZero):
1211       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1212       break;
1213       case (ReducedContactElementsOne):
1214       case (ReducedContactElementsZero):
1215       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1216       break;
1217       case(DegreesOfFreedom):
1218       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1219       break;
1220       case(ReducedDegreesOfFreedom):
1221       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1222       break;
1223       default:
1224        stringstream temp;        stringstream temp;
1225        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();
1226        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1227        break;        break;
1228    }     }
1229    checkFinleyError();     checkFinleyError();
1230  }  }
1231    
1232  //  //
1233  // interpolates data to other domain:  // interpolates data to other domain:
1234  //  //
1235  void MeshAdapter::interpolateACross(Data& target,const Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1236  {  {
1237    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1238    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1239       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1240          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1241    
1242    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1243  }  }
1244    
1245  //  //
1246  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1247  //  //
1248  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1249  {  {
1250    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1251    if (argDomain!=*this)     if (argDomain!=*this)
1252       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1253    
1254    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1255    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1256       case(Nodes):     escriptDataC _temp;
1257          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1258          break;     escriptDataC _arg=arg.getDataC();
1259       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1260          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1261          break;     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1262       case(FaceElements):     _temp=temp.getDataC();
1263          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1264          break;     break;
1265       case(Points):     case(ReducedNodes):
1266          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1267          break;     _temp=temp.getDataC();
1268       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1269          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1270          break;     case(Elements):
1271       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1272          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1273          break;     case(ReducedElements):
1274       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1275          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1276          break;     case(FaceElements):
1277       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1278          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1279          break;     case(ReducedFaceElements):
1280       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1281          stringstream temp;     break;
1282          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1283          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1284          break;     break;
1285    }     case(ContactElementsZero):
1286    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287       break;
1288       case(ReducedContactElementsZero):
1289       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1290       break;
1291       case(ContactElementsOne):
1292       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1293       break;
1294       case(ReducedContactElementsOne):
1295       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1296       break;
1297       case(DegreesOfFreedom):
1298       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1299       _temp=temp.getDataC();
1300       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1301       break;
1302       case(ReducedDegreesOfFreedom):
1303       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1304       _temp=temp.getDataC();
1305       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1306       break;
1307       default:
1308          stringstream temp;
1309          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1310          throw FinleyAdapterException(temp.str());
1311          break;
1312       }
1313       checkFinleyError();
1314       blocktimer_increment("integrate()", blocktimer_start);
1315  }  }
1316    
1317  //  //
1318  // calculates the gradient of arg:  // calculates the gradient of arg:
1319  //  //
1320  void MeshAdapter::setToGradient(Data& grad,const Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1321  {  {
1322    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1323    if (argDomain!=*this)     if (argDomain!=*this)
1324      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1325    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1326    if (gradDomain!=*this)     if (gradDomain!=*this)
1327       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1328    
1329    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1330    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1331         case(Nodes):     escriptDataC nodeDataC;
1332            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     escript::Data temp;
1333            break;     if (getMPISize()>1) {
1334         case(Elements):        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1335            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1336            break;           nodeDataC = temp.getDataC();
1337         case(FaceElements):        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1338            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1339            break;           nodeDataC = temp.getDataC();
1340         case(Points):        } else {
1341            throw FinleyAdapterException("Error - Gradient at points is not supported.");           nodeDataC = arg.getDataC();
1342            break;        }
1343         case(ContactElementsZero):     } else {
1344            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));        nodeDataC = arg.getDataC();
1345            break;     }
1346         case(ContactElementsOne):     switch(grad.getFunctionSpace().getTypeCode()) {
1347            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     case(Nodes):
1348            break;     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1349         case(DegreesOfFreedom):     break;
1350            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     case(ReducedNodes):
1351            break;     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1352         case(ReducedDegreesOfFreedom):     break;
1353            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     case(Elements):
1354            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1355         default:     break;
1356            stringstream temp;     case(ReducedElements):
1357            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1358            throw FinleyAdapterException(temp.str());     break;
1359            break;     case(FaceElements):
1360    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1361    checkFinleyError();     break;
1362       case(ReducedFaceElements):
1363       Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1364       break;
1365       case(Points):
1366       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1367       break;
1368       case(ContactElementsZero):
1369       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370       break;
1371       case(ReducedContactElementsZero):
1372       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1373       break;
1374       case(ContactElementsOne):
1375       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1376       break;
1377       case(ReducedContactElementsOne):
1378       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1379       break;
1380       case(DegreesOfFreedom):
1381       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1382       break;
1383       case(ReducedDegreesOfFreedom):
1384       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1385       break;
1386       default:
1387          stringstream temp;
1388          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1389          throw FinleyAdapterException(temp.str());
1390          break;
1391       }
1392       checkFinleyError();
1393  }  }
1394    
1395  //  //
1396  // returns the size of elements:  // returns the size of elements:
1397  //  //
1398  void MeshAdapter::setToSize(Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1399  {  {
1400    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1401    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1402    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1403         case(Nodes):     case(Nodes):
1404            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1405            break;     break;
1406         case(Elements):     case(ReducedNodes):
1407            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1408            break;     break;
1409         case(FaceElements):     case(Elements):
1410            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1411            break;     break;
1412         case(Points):     case(ReducedElements):
1413            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1414            break;     break;
1415         case(ContactElementsZero):     case(FaceElements):
1416         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1417            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1418            break;     case(ReducedFaceElements):
1419         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1420            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1421            break;     case(Points):
1422         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1423            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1424            break;     case(ContactElementsZero):
1425         default:     case(ContactElementsOne):
1426            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1427            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1428            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1429            break;     case(ReducedContactElementsOne):
1430    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1431    checkFinleyError();     break;
1432       case(DegreesOfFreedom):
1433       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1434       break;
1435       case(ReducedDegreesOfFreedom):
1436       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1437       break;
1438       default:
1439          stringstream temp;
1440          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1441          throw FinleyAdapterException(temp.str());
1442          break;
1443       }
1444       checkFinleyError();
1445  }  }
1446    
1447  // sets the location of nodes:  // sets the location of nodes:
1448  void MeshAdapter::setNewX(const Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1449  {  {
1450    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1451    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1452    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1453       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1454    Finley_NodeFile_setCoordinates(mesh->Nodes,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1455    checkFinleyError();     tmp = new_x.getDataC();
1456       Finley_Mesh_setCoordinates(mesh,&tmp);
1457       checkFinleyError();
1458  }  }
1459    
1460  // saves a data array in openDX format:  // saves a data array in openDX format:
1461  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1462  {  {
1463      int MAX_namelength=256;     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1464      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     /* win32 refactor */
1465      char names[num_data][MAX_namelength];     char **names = (num_data>0) ? TMPMEMALLOC(num_data, char*) : (char**)NULL;
1466      char* c_names[num_data];  
1467      escriptDataC data[num_data];     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1468      escriptDataC* ptr_data[num_data];     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1469    
1470      boost::python::list keys=arg.keys();     boost::python::list keys=arg.keys();
1471      for (int i=0;i<num_data;++i) {     for (int i=0; i<num_data; ++i) {
1472           Data& d=boost::python::extract<Data&>(arg[keys[i]]);        std::string n=boost::python::extract<std::string>(keys[i]);
1473           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1474               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1475           data[i]=d.getDataC();           throw FinleyAdapterException("Error in saveDX: Data must be defined on same Domain");
1476           ptr_data[i]=&(data[i]);        data[i]=d.getDataC();
1477           std::string n=boost::python::extract<std::string>(keys[i]);        ptr_data[i]= &(data[i]);
1478           c_names[i]=&(names[i][0]);        names[i] = TMPMEMALLOC(n.length()+1, char);
1479           if (n.length()>MAX_namelength-1) {        strcpy(names[i], n.c_str());
1480              strncpy(c_names[i],n.c_str(),MAX_namelength-1);     }
1481              c_names[i][MAX_namelength-1]='\0';     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1482           } else {     checkFinleyError();
1483              strcpy(c_names[i],n.c_str());  
1484           }     /* win32 refactor */
1485      }     TMPMEMFREE(data);
1486      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);     TMPMEMFREE(ptr_data);
1487      checkFinleyError();     for(int i=0; i<num_data; i++)
1488      return;     {
1489          TMPMEMFREE(names[i]);
1490       }
1491       TMPMEMFREE(names);
1492    
1493       return;
1494  }  }
1495    
1496  // saves a data array in openVTK format:  // saves a data array in openVTK format:
1497  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
1498  {  {
1499      int MAX_namelength=256;     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1500      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     /* win32 refactor */
1501      char names[num_data][MAX_namelength];     char **names = (num_data>0) ? TMPMEMALLOC(num_data, char*) : (char**)NULL;
1502      char* c_names[num_data];  
1503      escriptDataC data[num_data];     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1504      escriptDataC* ptr_data[num_data];     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1505    
1506      boost::python::list keys=arg.keys();     boost::python::list keys=arg.keys();
1507      for (int i=0;i<num_data;++i) {     for (int i=0;i<num_data;++i) {
1508           Data& d=boost::python::extract<Data&>(arg[keys[i]]);        std::string n=boost::python::extract<std::string>(keys[i]);
1509           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1510               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1511           data[i]=d.getDataC();           throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1512           ptr_data[i]=&(data[i]);        data[i]=d.getDataC();
1513           std::string n=boost::python::extract<std::string>(keys[i]);        ptr_data[i]=&(data[i]);
1514           c_names[i]=&(names[i][0]);        names[i] = TMPMEMALLOC(n.length()+1, char);
1515           if (n.length()>MAX_namelength-1) {        strcpy(names[i],n.c_str());
1516              strncpy(c_names[i],n.c_str(),MAX_namelength-1);     }
1517              c_names[i][MAX_namelength-1]='\0';     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1518           } else {  
1519              strcpy(c_names[i],n.c_str());     checkFinleyError();
1520           }     /* win32 refactor */
1521      }     TMPMEMFREE(data);
1522      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);     TMPMEMFREE(ptr_data);
1523      checkFinleyError();     for(int i=0;i<num_data;i++)
1524      return;     {
1525          TMPMEMFREE(names[i]);
1526       }
1527       TMPMEMFREE(names);
1528    
1529       return;
1530  }  }
1531                                                                                                                                                                                                                                                                                                                                                
1532                                                                                                                                                                                                                                                                                                                                                
1533  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1534  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1535                        const int row_blocksize,                                                   const int row_blocksize,
1536                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1537                        const int column_blocksize,                                                   const int column_blocksize,
1538                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1539                        const int type) const                                                   const int type) const
1540  {  {
1541      int reduceRowOrder=0;     int reduceRowOrder=0;
1542      int reduceColOrder=0;     int reduceColOrder=0;
1543      // is the domain right?     // is the domain right?
1544      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1545      if (row_domain!=*this)     if (row_domain!=*this)
1546            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.");
1547      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1548      if (col_domain!=*this)     if (col_domain!=*this)
1549            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.");
1550      // is the function space type right     // is the function space type right
1551      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1552          reduceRowOrder=0;        reduceRowOrder=0;
1553      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1554          reduceRowOrder=1;        reduceRowOrder=1;
1555      } else {     } else {
1556          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1557      }     }
1558      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1559          reduceColOrder=0;        reduceColOrder=0;
1560      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1561          reduceColOrder=1;        reduceColOrder=1;
1562      } else {     } else {
1563          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1564      }     }
1565      // generate matrix:     // generate matrix:
1566        
1567      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1568      checkFinleyError();     checkFinleyError();
1569      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1570      checkPasoError();     int trilinos = 0;
1571      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1572      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1573          /* Allocation Epetra_VrbMatrix here */
1574    #endif
1575       }
1576       else {
1577          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1578       }
1579       checkPasoError();
1580       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1581       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1582    }
1583    // creates a TransportProblemAdapter
1584    TransportProblemAdapter MeshAdapter::newTransportProblem(
1585                                                             const double theta,
1586                                                             const int blocksize,
1587                                                             const escript::FunctionSpace& functionspace,
1588                                                             const int type) const
1589    {
1590       int reduceOrder=0;
1591       // is the domain right?
1592       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1593       if (domain!=*this)
1594          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1595       // is the function space type right
1596       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1597          reduceOrder=0;
1598       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1599          reduceOrder=1;
1600       } else {
1601          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1602       }
1603       // generate matrix:
1604    
1605       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1606       checkFinleyError();
1607       Paso_FCTransportProblem* transportProblem;
1608       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1609       checkPasoError();
1610       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1611       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1612  }  }
1613    
1614  //  //
# Line 919  SystemMatrixAdapter MeshAdapter::newSyst Line 1620  SystemMatrixAdapter MeshAdapter::newSyst
1620  // 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:
1621  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1622  {  {
1623    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1624         case(Nodes):     case(Nodes):
1625         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1626         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1627            return false;     return false;
1628            break;     break;
1629         case(Elements):     case(Elements):
1630         case(FaceElements):     case(FaceElements):
1631         case(Points):     case(Points):
1632         case(ContactElementsZero):     case(ContactElementsZero):
1633         case(ContactElementsOne):     case(ContactElementsOne):
1634            return true;     case(ReducedElements):
1635            break;     case(ReducedFaceElements):
1636         default:     case(ReducedContactElementsZero):
1637            stringstream temp;     case(ReducedContactElementsOne):
1638            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1639            throw FinleyAdapterException(temp.str());     break;
1640            break;     default:
1641    }        stringstream temp;
1642    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1643    return false;        throw FinleyAdapterException(temp.str());
1644          break;
1645       }
1646       checkFinleyError();
1647       return false;
1648  }  }
1649    
1650  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1651  {  {
1652    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1653       case(Nodes):     case(Nodes):
1654          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1655             case(Nodes):     case(Nodes):
1656             case(ReducedDegreesOfFreedom):     case(ReducedNodes):
1657             case(DegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1658             case(Elements):     case(DegreesOfFreedom):
1659             case(FaceElements):     case(Elements):
1660             case(Points):     case(ReducedElements):
1661             case(ContactElementsZero):     case(FaceElements):
1662             case(ContactElementsOne):     case(ReducedFaceElements):
1663                 return true;     case(Points):
1664             default:     case(ContactElementsZero):
1665                 stringstream temp;     case(ReducedContactElementsZero):
1666                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(ContactElementsOne):
1667                 throw FinleyAdapterException(temp.str());     case(ReducedContactElementsOne):
1668          }     return true;
1669          break;     default:
1670       case(Elements):        stringstream temp;
1671          if (functionSpaceType_target==Elements) {        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1672             return true;        throw FinleyAdapterException(temp.str());
1673          } else {     }
1674             return false;     break;
1675          }     case(ReducedNodes):
1676       case(FaceElements):     switch(functionSpaceType_target) {
1677          if (functionSpaceType_target==FaceElements) {     case(ReducedNodes):
1678             return true;     case(ReducedDegreesOfFreedom):
1679          } else {     case(Elements):
1680             return false;     case(ReducedElements):
1681          }     case(FaceElements):
1682       case(Points):     case(ReducedFaceElements):
1683          if (functionSpaceType_target==Points) {     case(Points):
1684             return true;     case(ContactElementsZero):
1685          } else {     case(ReducedContactElementsZero):
1686             return false;     case(ContactElementsOne):
1687          }     case(ReducedContactElementsOne):
1688       case(ContactElementsZero):     return true;
1689       case(ContactElementsOne):     case(Nodes):
1690          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     case(DegreesOfFreedom):
1691             return true;     return false;
1692          } else {     default:
1693             return false;        stringstream temp;
1694          }        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1695       case(DegreesOfFreedom):        throw FinleyAdapterException(temp.str());
1696          switch(functionSpaceType_target) {     }
1697             case(ReducedDegreesOfFreedom):     break;
1698             case(DegreesOfFreedom):     case(Elements):
1699             case(Nodes):     if (functionSpaceType_target==Elements) {
1700             case(Elements):        return true;
1701             case(FaceElements):     } else if (functionSpaceType_target==ReducedElements) {
1702             case(Points):        return true;
1703             case(ContactElementsZero):     } else {
1704             case(ContactElementsOne):        return false;
1705                return true;     }
1706             default:     case(ReducedElements):
1707               stringstream temp;     if (functionSpaceType_target==ReducedElements) {
1708               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;        return true;
1709               throw FinleyAdapterException(temp.str());     } else {
1710          }        return false;
1711          break;     }
1712       case(ReducedDegreesOfFreedom):     case(FaceElements):
1713         switch(functionSpaceType_target) {     if (functionSpaceType_target==FaceElements) {
1714            case(ReducedDegreesOfFreedom):        return true;
1715            case(Elements):     } else if (functionSpaceType_target==ReducedFaceElements) {
1716            case(FaceElements):        return true;
1717            case(Points):     } else {
1718            case(ContactElementsZero):        return false;
1719            case(ContactElementsOne):     }
1720                return true;     case(ReducedFaceElements):
1721            case(Nodes):     if (functionSpaceType_target==ReducedFaceElements) {
1722            case(DegreesOfFreedom):        return true;
1723               return false;     } else {
1724            default:        return false;
1725               stringstream temp;     }
1726               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1727               throw FinleyAdapterException(temp.str());     if (functionSpaceType_target==Points) {
1728         }        return true;
1729         break;     } else {
1730       default:        return false;
1731          stringstream temp;     }
1732          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1733          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1734          break;     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1735    }        return true;
1736    checkFinleyError();     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1737    return false;        return true;
1738       } else {
1739          return false;
1740       }
1741       case(ReducedContactElementsZero):
1742       case(ReducedContactElementsOne):
1743       if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1744          return true;
1745       } else {
1746          return false;
1747       }
1748       case(DegreesOfFreedom):
1749       switch(functionSpaceType_target) {
1750       case(ReducedDegreesOfFreedom):
1751       case(DegreesOfFreedom):
1752       case(Nodes):
1753       case(ReducedNodes):
1754       case(Elements):
1755       case(ReducedElements):
1756       case(Points):
1757       case(FaceElements):
1758       case(ReducedFaceElements):
1759       case(ContactElementsZero):
1760       case(ReducedContactElementsZero):
1761       case(ContactElementsOne):
1762       case(ReducedContactElementsOne):
1763       return true;
1764       default:
1765          stringstream temp;
1766          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1767          throw FinleyAdapterException(temp.str());
1768       }
1769       break;
1770       case(ReducedDegreesOfFreedom):
1771       switch(functionSpaceType_target) {
1772       case(ReducedDegreesOfFreedom):
1773       case(ReducedNodes):
1774       case(Elements):
1775       case(ReducedElements):
1776       case(FaceElements):
1777       case(ReducedFaceElements):
1778       case(Points):
1779       case(ContactElementsZero):
1780       case(ReducedContactElementsZero):
1781       case(ContactElementsOne):
1782       case(ReducedContactElementsOne):
1783       return true;
1784       case(Nodes):
1785       case(DegreesOfFreedom):
1786       return false;
1787       default:
1788          stringstream temp;
1789          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1790          throw FinleyAdapterException(temp.str());
1791       }
1792       break;
1793       default:
1794          stringstream temp;
1795          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1796          throw FinleyAdapterException(temp.str());
1797          break;
1798       }
1799       checkFinleyError();
1800       return false;
1801  }  }
1802    
1803  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
1804  {  {
1805      return false;     return false;
1806  }  }
1807    
1808  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1809  {  {
1810    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1811    if (temp!=0) {     if (temp!=0) {
1812      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1813    } else {     } else {
1814      return false;        return false;
1815    }     }
1816  }  }
1817    
1818  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1819  {  {
1820    return !(operator==(other));     return !(operator==(other));
1821  }  }
1822    
1823  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
1824    {
1825       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1826       checkPasoError();
1827       return out;
1828    }
1829    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1830  {  {
1831     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);
1832     checkPasoError();     checkPasoError();
1833     return out;     return out;
1834  }  }
1835    
1836  Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1837  {  {
1838    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1839  }  }
1840    
1841  Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1842  {  {
1843    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1844  }  }
1845    
1846  Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1847  {  {
1848    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1849  }  }
1850    
1851    int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1852    {
1853       int *out = NULL;
1854       Finley_Mesh* mesh=m_finleyMesh.get();
1855       switch (functionSpaceType) {
1856       case(Nodes):
1857       out=mesh->Nodes->Id;
1858       break;
1859       case(ReducedNodes):
1860       out=mesh->Nodes->reducedNodesId;
1861       break;
1862       case(Elements):
1863       out=mesh->Elements->Id;
1864       break;
1865       case(ReducedElements):
1866       out=mesh->Elements->Id;
1867       break;
1868       case(FaceElements):
1869       out=mesh->FaceElements->Id;
1870       break;
1871       case(ReducedFaceElements):
1872       out=mesh->FaceElements->Id;
1873       break;
1874       case(Points):
1875       out=mesh->Points->Id;
1876       break;
1877       case(ContactElementsZero):
1878       out=mesh->ContactElements->Id;
1879       break;
1880       case(ReducedContactElementsZero):
1881       out=mesh->ContactElements->Id;
1882       break;
1883       case(ContactElementsOne):
1884       out=mesh->ContactElements->Id;
1885       break;
1886       case(ReducedContactElementsOne):
1887       out=mesh->ContactElements->Id;
1888       break;
1889       case(DegreesOfFreedom):
1890       out=mesh->Nodes->degreesOfFreedomId;
1891       break;
1892       case(ReducedDegreesOfFreedom):
1893       out=mesh->Nodes->reducedDegreesOfFreedomId;
1894       break;
1895       default:
1896          stringstream temp;
1897          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1898          throw FinleyAdapterException(temp.str());
1899          break;
1900       }
1901       return out;
1902    }
1903  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1904  {  {
1905    int* tagList;     int out=0;
1906    int numTags;     Finley_Mesh* mesh=m_finleyMesh.get();
1907    getTagList(functionSpaceType, &tagList, &numTags);     switch (functionSpaceType) {
1908    return tagList[sampleNo];     case(Nodes):
1909       out=mesh->Nodes->Tag[sampleNo];
1910       break;
1911       case(ReducedNodes):
1912       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1913       break;
1914       case(Elements):
1915       out=mesh->Elements->Tag[sampleNo];
1916       break;
1917       case(ReducedElements):
1918       out=mesh->Elements->Tag[sampleNo];
1919       break;
1920       case(FaceElements):
1921       out=mesh->FaceElements->Tag[sampleNo];
1922       break;
1923       case(ReducedFaceElements):
1924       out=mesh->FaceElements->Tag[sampleNo];
1925       break;
1926       case(Points):
1927       out=mesh->Points->Tag[sampleNo];
1928       break;
1929       case(ContactElementsZero):
1930       out=mesh->ContactElements->Tag[sampleNo];
1931       break;
1932       case(ReducedContactElementsZero):
1933       out=mesh->ContactElements->Tag[sampleNo];
1934       break;
1935       case(ContactElementsOne):
1936       out=mesh->ContactElements->Tag[sampleNo];
1937       break;
1938       case(ReducedContactElementsOne):
1939       out=mesh->ContactElements->Tag[sampleNo];
1940       break;
1941       case(DegreesOfFreedom):
1942       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1943       break;
1944       case(ReducedDegreesOfFreedom):
1945       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1946       break;
1947       default:
1948          stringstream temp;
1949          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1950          throw FinleyAdapterException(temp.str());
1951          break;
1952       }
1953       return out;
1954    }
1955    
1956    
1957    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1958    {
1959       Finley_Mesh* mesh=m_finleyMesh.get();
1960       escriptDataC tmp=mask.getDataC();
1961       switch(functionSpaceType) {
1962       case(Nodes):
1963       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1964       break;
1965       case(ReducedNodes):
1966       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1967       break;
1968       case(DegreesOfFreedom):
1969       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1970       break;
1971       case(ReducedDegreesOfFreedom):
1972       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1973       break;
1974       case(Elements):
1975       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1976       break;
1977       case(ReducedElements):
1978       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1979       break;
1980       case(FaceElements):
1981       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1982       break;
1983       case(ReducedFaceElements):
1984       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1985       break;
1986       case(Points):
1987       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1988       break;
1989       case(ContactElementsZero):
1990       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1991       break;
1992       case(ReducedContactElementsZero):
1993       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1994       break;
1995       case(ContactElementsOne):
1996       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1997       break;
1998       case(ReducedContactElementsOne):
1999       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2000       break;
2001       default:
2002          stringstream temp;
2003          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2004          throw FinleyAdapterException(temp.str());
2005       }
2006       checkFinleyError();
2007       return;
2008    }
2009    
2010    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2011    {
2012       Finley_Mesh* mesh=m_finleyMesh.get();
2013       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2014       checkPasoError();
2015       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2016    }
2017    
2018    int MeshAdapter::getTag(const std::string& name) const
2019    {
2020       Finley_Mesh* mesh=m_finleyMesh.get();
2021       int tag=0;
2022       tag=Finley_Mesh_getTag(mesh, name.c_str());
2023       checkPasoError();
2024       // throwStandardException("MeshAdapter::getTag is not implemented.");
2025       return tag;
2026    }
2027    
2028    bool MeshAdapter::isValidTagName(const std::string& name) const
2029    {
2030       Finley_Mesh* mesh=m_finleyMesh.get();
2031       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2032  }  }
2033    
2034  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  std::string MeshAdapter::showTagNames() const
2035  {  {
2036    int* referenceNoList;     stringstream temp;
2037    int numReferenceNo;     Finley_Mesh* mesh=m_finleyMesh.get();
2038    getReferenceNoList(functionSpaceType, &referenceNoList, &numReferenceNo);     Finley_TagMap* tag_map=mesh->TagMap;
2039    return referenceNoList[sampleNo];     while (tag_map) {
2040          temp << tag_map->name;
2041          tag_map=tag_map->next;
2042          if (tag_map) temp << ", ";
2043       }
2044       return temp.str();
2045  }  }
2046    
2047    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2048    {
2049      Finley_Mesh* mesh=m_finleyMesh.get();
2050      dim_t numTags=0;
2051      switch(functionSpaceCode) {
2052       case(Nodes):
2053              numTags=mesh->Nodes->numTagsInUse;
2054              break;
2055       case(ReducedNodes):
2056              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2057              break;
2058       case(DegreesOfFreedom):
2059              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2060              break;
2061       case(ReducedDegreesOfFreedom):
2062              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2063              break;
2064       case(Elements):
2065       case(ReducedElements):
2066              numTags=mesh->Elements->numTagsInUse;
2067              break;
2068       case(FaceElements):
2069       case(ReducedFaceElements):
2070              numTags=mesh->FaceElements->numTagsInUse;
2071              break;
2072       case(Points):
2073              numTags=mesh->Points->numTagsInUse;
2074              break;
2075       case(ContactElementsZero):
2076       case(ReducedContactElementsZero):
2077       case(ContactElementsOne):
2078       case(ReducedContactElementsOne):
2079              numTags=mesh->ContactElements->numTagsInUse;
2080              break;
2081       default:
2082          stringstream temp;
2083          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2084          throw FinleyAdapterException(temp.str());
2085      }
2086      return numTags;
2087    }
2088    int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2089    {
2090      Finley_Mesh* mesh=m_finleyMesh.get();
2091      index_t* tags=NULL;
2092      switch(functionSpaceCode) {
2093       case(Nodes):
2094              tags=mesh->Nodes->tagsInUse;
2095              break;
2096       case(ReducedNodes):
2097              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2098              break;
2099       case(DegreesOfFreedom):
2100              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2101              break;
2102       case(ReducedDegreesOfFreedom):
2103              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2104              break;
2105       case(Elements):
2106       case(ReducedElements):
2107              tags=mesh->Elements->tagsInUse;
2108              break;
2109       case(FaceElements):
2110       case(ReducedFaceElements):
2111              tags=mesh->FaceElements->tagsInUse;
2112              break;
2113       case(Points):
2114              tags=mesh->Points->tagsInUse;
2115              break;
2116       case(ContactElementsZero):
2117       case(ReducedContactElementsZero):
2118       case(ContactElementsOne):
2119       case(ReducedContactElementsOne):
2120              tags=mesh->ContactElements->tagsInUse;
2121              break;
2122       default:
2123          stringstream temp;
2124          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2125          throw FinleyAdapterException(temp.str());
2126      }
2127      return tags;
2128    }
2129    
2130    
2131    bool MeshAdapter::canTag(int functionSpaceCode) const
2132    {
2133      switch(functionSpaceCode) {
2134       case(Nodes):
2135       case(Elements):
2136       case(ReducedElements):
2137       case(FaceElements):
2138       case(ReducedFaceElements):
2139       case(Points):
2140       case(ContactElementsZero):
2141       case(ReducedContactElementsZero):
2142       case(ContactElementsOne):
2143       case(ReducedContactElementsOne):
2144              return true;
2145       case(ReducedNodes):
2146       case(DegreesOfFreedom):
2147       case(ReducedDegreesOfFreedom):
2148          return false;
2149       default:
2150        return false;
2151      }
2152    }
2153    
2154    
2155  }  // end of namespace  }  // end of namespace

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