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

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revision 547 by gross, Tue Feb 21 06:10:54 2006 UTC revision 1796 by jfenwick, Wed Sep 17 01:45:46 2008 UTC
# Line 1  Line 1 
1  // $Id$  
2  /*  /* $Id$ */
3   ******************************************************************************  
4   *                                                                            *  /*******************************************************
5   *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *   *
6   *                                                                            *   *           Copyright 2003-2007 by ACceSS MNRF
7   * This software is the property of ACcESS. No part of this code              *   *       Copyright 2007 by University of Queensland
8   * may be copied in any form or by any means without the expressed written    *   *
9   * consent of ACcESS.  Copying, use or modification of this software          *   *                http://esscc.uq.edu.au
10   * by any unauthorised person is illegal unless that person has a software    *   *        Primary Business: Queensland, Australia
11   * license agreement with ACcESS.                                             *   *  Licensed under the Open Software License version 3.0
12   *                                                                            *   *     http://www.opensource.org/licenses/osl-3.0.php
13   ******************************************************************************   *
14  */   *******************************************************/
15    
16  #include "MeshAdapter.h"  #include "MeshAdapter.h"
17    #include "escript/Data.h"
18    #include "escript/DataFactory.h"
19    #ifdef USE_NETCDF
20    #include <netcdfcpp.h>
21    #endif
22    extern "C" {
23    #include "escript/blocktimer.h"
24    }
25    #include <vector>
26    
27  #include "Data.h"  #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256
 #include "DataFactory.h"  
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
# Line 29  MeshAdapter::FunctionSpaceNamesMapType M Line 37  MeshAdapter::FunctionSpaceNamesMapType M
37  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
38  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
39  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
40    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
41  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
42    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
43  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
44    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
45  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
46  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
47    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
48  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52  {  {
53    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
54    //     //
55    // need to use a null_deleter as Finley_Mesh_dealloc deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
56    // for us.     // for us.
57    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
58  }  }
59    
60  //  //
# Line 49  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 62  MeshAdapter::MeshAdapter(Finley_Mesh* fi
62  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
63  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
64  {  {
65    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
66  }  }
67    
68  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
69  {  {
70    //     //
71    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
72    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
73    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
74      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
75      Finley_Mesh_dealloc(m_finleyMesh.get());     }
76      //   cout << "Finished dealloc." << endl;  }
77    }  
78    int MeshAdapter::getMPISize() const
79    {
80       return m_finleyMesh.get()->MPIInfo->size;
81    }
82    int MeshAdapter::getMPIRank() const
83    {
84       return m_finleyMesh.get()->MPIInfo->rank;
85  }  }
86    
87    
88  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
89     return m_finleyMesh.get();     return m_finleyMesh.get();
90  }  }
91    
92  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
93  {  {
94    char fName[fileName.size()+1];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
95    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
96    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
97    checkFinleyError();     checkFinleyError();
98       TMPMEMFREE(fName);
99    }
100    
101    void MeshAdapter::Print_Mesh_Info(const bool full=false) const
102    {
103       Finley_PrintMesh_Info(m_finleyMesh.get(), full);
104    }
105    
106    void MeshAdapter::dump(const std::string& fileName) const
107    {
108    #ifdef USE_NETCDF
109       const NcDim* ncdims[12];
110       NcVar *ids;
111       int *int_ptr;
112       Finley_Mesh *mesh = m_finleyMesh.get();
113       Finley_TagMap* tag_map;
114       int num_Tags = 0;
115       int mpi_size             = mesh->MPIInfo->size;
116       int mpi_rank             = mesh->MPIInfo->rank;
117       int numDim               = mesh->Nodes->numDim;
118       int numNodes             = mesh->Nodes->numNodes;
119       int num_Elements         = mesh->Elements->numElements;
120       int num_FaceElements         = mesh->FaceElements->numElements;
121       int num_ContactElements      = mesh->ContactElements->numElements;
122       int num_Points           = mesh->Points->numElements;
123       int num_Elements_numNodes        = mesh->Elements->numNodes;
124       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
125       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
126    
127       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
128                                                         mpi_size, mpi_rank);
129    
130       /* Figure out how much storage is required for tags */
131       tag_map = mesh->TagMap;
132       if (tag_map) {
133          while (tag_map) {
134             num_Tags++;
135             tag_map=tag_map->next;
136          }
137       }
138    
139       // NetCDF error handler
140       NcError err(NcError::verbose_nonfatal);
141       // Create the file.
142       NcFile dataFile(newFileName, NcFile::Replace);
143       // check if writing was successful
144       if (!dataFile.is_valid())
145          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
146    
147       // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
148       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
149          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
150       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
151          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
152       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
153          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
154       if (num_Elements>0)
155          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
156             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
157       if (num_FaceElements>0)
158          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
159             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
160       if (num_ContactElements>0)
161          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
162             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
163       if (num_Points>0)
164          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
165             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
166       if (num_Elements>0)
167          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
168             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
169       if (num_FaceElements>0)
170          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
171             throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
172       if (num_ContactElements>0)
173          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
174             throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
175       if (num_Tags>0)
176          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
177             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
178    
179       // Attributes: MPI size, MPI rank, Name, order, reduced_order
180       if (!dataFile.add_att("mpi_size", mpi_size) )
181          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
182       if (!dataFile.add_att("mpi_rank", mpi_rank) )
183          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
184       if (!dataFile.add_att("Name",mesh->Name) )
185          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
186       if (!dataFile.add_att("numDim",numDim) )
187          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
188       if (!dataFile.add_att("order",mesh->order) )
189          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
190       if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
191          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
192       if (!dataFile.add_att("numNodes",numNodes) )
193          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
194       if (!dataFile.add_att("num_Elements",num_Elements) )
195          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
196       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
197          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
198       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
199          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
200       if (!dataFile.add_att("num_Points",num_Points) )
201          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
202       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
203          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
204       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
205          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
206       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
207          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
208       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
209          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
210       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
211          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
212       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
213          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
214       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
215          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
216       if (!dataFile.add_att("num_Tags", num_Tags) )
217          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
218    
219       // // // // // Nodes // // // // //
220    
221       // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
222       if (numNodes>0) {
223    
224          // Nodes Id
225          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
226             throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
227          int_ptr = &mesh->Nodes->Id[0];
228          if (! (ids->put(int_ptr, numNodes)) )
229             throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
230    
231          // Nodes Tag
232          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
233             throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
234          int_ptr = &mesh->Nodes->Tag[0];
235          if (! (ids->put(int_ptr, numNodes)) )
236             throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
237    
238          // Nodes gDOF
239          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
240             throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
241          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
242          if (! (ids->put(int_ptr, numNodes)) )
243             throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
244    
245          // Nodes global node index
246          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
247             throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
248          int_ptr = &mesh->Nodes->globalNodesIndex[0];
249          if (! (ids->put(int_ptr, numNodes)) )
250             throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
251    
252          // Nodes grDof
253          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
254             throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
255          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
256          if (! (ids->put(int_ptr, numNodes)) )
257             throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
258    
259          // Nodes grNI
260          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
261             throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
262          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
263          if (! (ids->put(int_ptr, numNodes)) )
264             throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
265    
266          // Nodes Coordinates
267          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
268             throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
269          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
270             throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
271    
272          // Nodes degreesOfFreedomDistribution
273          if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
274             throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
275          int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
276          if (! (ids->put(int_ptr, mpi_size+1)) )
277             throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
278    
279          // Nodes nodeDistribution
280          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
281             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
282          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
283          if (! (ids->put(int_ptr, mpi_size+1)) )
284             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
285    
286       }
287    
288       // // // // // Elements // // // // //
289    
290       if (num_Elements>0) {
291    
292          // Elements_Id
293          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
294             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
295          int_ptr = &mesh->Elements->Id[0];
296          if (! (ids->put(int_ptr, num_Elements)) )
297             throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
298    
299          // Elements_Tag
300          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
301             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
302          int_ptr = &mesh->Elements->Tag[0];
303          if (! (ids->put(int_ptr, num_Elements)) )
304             throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
305    
306          // Elements_Owner
307          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
308             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
309          int_ptr = &mesh->Elements->Owner[0];
310          if (! (ids->put(int_ptr, num_Elements)) )
311             throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
312    
313          // Elements_Color
314          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
315             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
316          int_ptr = &mesh->Elements->Color[0];
317          if (! (ids->put(int_ptr, num_Elements)) )
318             throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
319    
320          // Elements_Nodes
321          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
322             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
323          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
324             throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
325    
326       }
327    
328       // // // // // Face_Elements // // // // //
329    
330       if (num_FaceElements>0) {
331    
332          // FaceElements_Id
333          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
334             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
335          int_ptr = &mesh->FaceElements->Id[0];
336          if (! (ids->put(int_ptr, num_FaceElements)) )
337             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
338    
339          // FaceElements_Tag
340          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
341             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
342          int_ptr = &mesh->FaceElements->Tag[0];
343          if (! (ids->put(int_ptr, num_FaceElements)) )
344             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
345    
346          // FaceElements_Owner
347          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
348             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
349          int_ptr = &mesh->FaceElements->Owner[0];
350          if (! (ids->put(int_ptr, num_FaceElements)) )
351             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
352    
353          // FaceElements_Color
354          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
355             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
356          int_ptr = &mesh->FaceElements->Color[0];
357          if (! (ids->put(int_ptr, num_FaceElements)) )
358             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
359    
360          // FaceElements_Nodes
361          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
362             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
363          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
364             throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
365    
366       }
367    
368       // // // // // Contact_Elements // // // // //
369    
370       if (num_ContactElements>0) {
371    
372          // ContactElements_Id
373          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
374             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
375          int_ptr = &mesh->ContactElements->Id[0];
376          if (! (ids->put(int_ptr, num_ContactElements)) )
377             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
378    
379          // ContactElements_Tag
380          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
381             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
382          int_ptr = &mesh->ContactElements->Tag[0];
383          if (! (ids->put(int_ptr, num_ContactElements)) )
384             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
385    
386          // ContactElements_Owner
387          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
388             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
389          int_ptr = &mesh->ContactElements->Owner[0];
390          if (! (ids->put(int_ptr, num_ContactElements)) )
391             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
392    
393          // ContactElements_Color
394          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
395             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
396          int_ptr = &mesh->ContactElements->Color[0];
397          if (! (ids->put(int_ptr, num_ContactElements)) )
398             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
399    
400          // ContactElements_Nodes
401          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
402             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
403          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
404             throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
405    
406       }
407    
408       // // // // // Points // // // // //
409    
410       if (num_Points>0) {
411    
412          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
413    
414          // Points_Id
415          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
416             throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
417          int_ptr = &mesh->Points->Id[0];
418          if (! (ids->put(int_ptr, num_Points)) )
419             throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
420    
421          // Points_Tag
422          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
423             throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
424          int_ptr = &mesh->Points->Tag[0];
425          if (! (ids->put(int_ptr, num_Points)) )
426             throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
427    
428          // Points_Owner
429          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
430             throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
431          int_ptr = &mesh->Points->Owner[0];
432          if (! (ids->put(int_ptr, num_Points)) )
433             throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
434    
435          // Points_Color
436          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
437             throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
438          int_ptr = &mesh->Points->Color[0];
439          if (! (ids->put(int_ptr, num_Points)) )
440             throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
441    
442          // Points_Nodes
443          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
444          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
445             throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
446          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
447             throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
448    
449       }
450    
451       // // // // // TagMap // // // // //
452    
453       if (num_Tags>0) {
454    
455          // Temp storage to gather node IDs
456          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
457          char name_temp[4096];
458    
459          /* Copy tag data into temp arrays */
460          tag_map = mesh->TagMap;
461          if (tag_map) {
462             int i = 0;
463             while (tag_map) {
464                Tags_keys[i++] = tag_map->tag_key;
465                tag_map=tag_map->next;
466             }
467          }
468    
469          // Tags_keys
470          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
471             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
472          int_ptr = &Tags_keys[0];
473          if (! (ids->put(int_ptr, num_Tags)) )
474             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
475    
476          // Tags_names_*
477          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
478          // because the NetCDF manual doesn't tell how to do an array of strings
479          tag_map = mesh->TagMap;
480          if (tag_map) {
481             int i = 0;
482             while (tag_map) {
483                sprintf(name_temp, "Tags_name_%d", i);
484                if (!dataFile.add_att(name_temp, tag_map->name) )
485                   throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
486                tag_map=tag_map->next;
487                i++;
488             }
489          }
490    
491          TMPMEMFREE(Tags_keys);
492    
493       }
494    
495    
496       // NetCDF file is closed by destructor of NcFile object
497    #else
498       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
499    #endif  /* USE_NETCDF */
500       checkFinleyError();
501  }  }
502    
503  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
504  {  {
505    return "FinleyMesh";     return "FinleyMesh";
506  }  }
507    
508  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
509  {  {
510    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
511    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
512    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
513      return "Invalid function space type code.";        return "Invalid function space type code.";
514    } else {     } else {
515      return loc->second;        return loc->second;
516    }     }
517  }  }
518    
519  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
520  {  {
521    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
522    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
523    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
524  }  }
525    
526  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
527  {  {
528    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
529      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
530    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
531      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
532    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
533      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
534    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
535      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
536    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
537      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
538    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
539      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
540    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
541      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
542    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
543      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
544       m_functionSpaceTypeNames.insert
545       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
546       m_functionSpaceTypeNames.insert
547       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
548       m_functionSpaceTypeNames.insert
549       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
550       m_functionSpaceTypeNames.insert
551       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
552       m_functionSpaceTypeNames.insert
553       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
554  }  }
555    
556  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
557  {  {
558    return Nodes;     return Nodes;
559    }
560    int MeshAdapter::getReducedContinuousFunctionCode() const
561    {
562       return ReducedNodes;
563  }  }
564    
565  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
566  {  {
567    return Elements;     return Elements;
568    }
569    int MeshAdapter::getReducedFunctionCode() const
570    {
571       return ReducedElements;
572  }  }
573    
574  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
575  {  {
576    return FaceElements;     return FaceElements;
577    }
578    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
579    {
580       return ReducedFaceElements;
581  }  }
582    
583  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
584  {  {
585    return ContactElementsZero;     return ContactElementsZero;
586    }
587    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
588    {
589       return ReducedContactElementsZero;
590  }  }
591    
592  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
593  {  {
594    return ContactElementsOne;     return ContactElementsOne;
595    }
596    int MeshAdapter::getReducedFunctionOnContactOneCode() const
597    {
598       return ReducedContactElementsOne;
599  }  }
600    
601  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
602  {  {
603    return DegreesOfFreedom;     return DegreesOfFreedom;
604  }  }
605    
606  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
607  {  {
608    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
609  }  }
610    
611  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
612  {  {
613    return Points;     return Points;
614  }  }
615    
616  //  //
# Line 164  int MeshAdapter::getDiracDeltaFunctionCo Line 618  int MeshAdapter::getDiracDeltaFunctionCo
618  //  //
619  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
620  {  {
621    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
622    checkFinleyError();     checkFinleyError();
623    return numDim;     return numDim;
624    }
625    
626    //
627    // Return the number of data points summed across all MPI processes
628    //
629    int MeshAdapter::getNumDataPointsGlobal() const
630    {
631       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
632  }  }
633    
634  //  //
# Line 179  pair<int,int> MeshAdapter::getDataShape( Line 641  pair<int,int> MeshAdapter::getDataShape(
641     int numSamples=0;     int numSamples=0;
642     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
643     switch (functionSpaceCode) {     switch (functionSpaceCode) {
644        case(Nodes):     case(Nodes):
645             numDataPointsPerSample=1;     numDataPointsPerSample=1;
646             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
647             break;     break;
648        case(Elements):     case(ReducedNodes):
649             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
650               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
651               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
652             }     case(Elements):
653             break;     if (mesh->Elements!=NULL) {
654        case(FaceElements):        numSamples=mesh->Elements->numElements;
655             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
656                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
657                  numSamples=mesh->FaceElements->numElements;     break;
658             }     case(ReducedElements):
659             break;     if (mesh->Elements!=NULL) {
660        case(Points):        numSamples=mesh->Elements->numElements;
661             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
662               numDataPointsPerSample=1;     }
663               numSamples=mesh->Points->numElements;     break;
664             }     case(FaceElements):
665             break;     if (mesh->FaceElements!=NULL) {
666        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
667             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
668               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
669               numSamples=mesh->ContactElements->numElements;     break;
670             }     case(ReducedFaceElements):
671             break;     if (mesh->FaceElements!=NULL) {
672        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
673             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
674               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
675               numSamples=mesh->ContactElements->numElements;     break;
676             }     case(Points):
677             break;     if (mesh->Points!=NULL) {
678        case(DegreesOfFreedom):        numDataPointsPerSample=1;
679             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
680               numDataPointsPerSample=1;     }
681               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
682             }     case(ContactElementsZero):
683             break;     if (mesh->ContactElements!=NULL) {
684        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
685             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
686               numDataPointsPerSample=1;     }
687               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
688             }     case(ReducedContactElementsZero):
689             break;     if (mesh->ContactElements!=NULL) {
690        default:        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
691          stringstream temp;        numSamples=mesh->ContactElements->numElements;
692          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     }
693          throw FinleyAdapterException(temp.str());     break;
694          break;     case(ContactElementsOne):
695        }     if (mesh->ContactElements!=NULL) {
696        return pair<int,int>(numDataPointsPerSample,numSamples);        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
697          numSamples=mesh->ContactElements->numElements;
698       }
699       break;
700       case(ReducedContactElementsOne):
701       if (mesh->ContactElements!=NULL) {
702          numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
703          numSamples=mesh->ContactElements->numElements;
704       }
705       break;
706       case(DegreesOfFreedom):
707       if (mesh->Nodes!=NULL) {
708          numDataPointsPerSample=1;
709          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
710       }
711       break;
712       case(ReducedDegreesOfFreedom):
713       if (mesh->Nodes!=NULL) {
714          numDataPointsPerSample=1;
715          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
716       }
717       break;
718       default:
719          stringstream temp;
720          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
721          throw FinleyAdapterException(temp.str());
722          break;
723       }
724       return pair<int,int>(numDataPointsPerSample,numSamples);
725  }  }
726    
727  //  //
728  // 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:
729  //  //
730  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
731                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
732                       const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
733                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
734                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
735  {  {
736     Finley_Mesh* mesh=m_finleyMesh.get();     escriptDataC _rhs=rhs.getDataC();
737     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(),&(rhs.getDataC()),     escriptDataC _A  =A.getDataC();
738                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _B=B.getDataC();
739     checkFinleyError();     escriptDataC _C=C.getDataC();
740     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     escriptDataC _D=D.getDataC();
741                    mat.getPaso_SystemMatrix(),     escriptDataC _X=X.getDataC();
742                    &(rhs.getDataC()),     escriptDataC _Y=Y.getDataC();
743                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _d=d.getDataC();
744                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _y=y.getDataC();
745     checkFinleyError();     escriptDataC _d_contact=d_contact.getDataC();
746     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,     escriptDataC _y_contact=y_contact.getDataC();
747                    mat.getPaso_SystemMatrix(),  
748                    &(rhs.getDataC()),     Finley_Mesh* mesh=m_finleyMesh.get();
749                                    &(d_contact.getDataC()),  
750                    &(y_contact.getDataC()),     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
751                                    Finley_Assemble_handelShapeMissMatch_Step_out);     checkFinleyError();
752    
753       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
754       checkFinleyError();
755    
756       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
757     checkFinleyError();     checkFinleyError();
758  }  }
759    
760    void  MeshAdapter::addPDEToLumpedSystem(
761                                            escript::Data& mat,
762                                            const escript::Data& D,
763                                            const escript::Data& d) const
764    {
765       escriptDataC _mat=mat.getDataC();
766       escriptDataC _D=D.getDataC();
767       escriptDataC _d=d.getDataC();
768    
769       Finley_Mesh* mesh=m_finleyMesh.get();
770    
771       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
772       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
773    
774       checkFinleyError();
775    }
776    
777    
778  //  //
779  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
780  //  //
781  void MeshAdapter::addPDEToRHS( escript::Data& rhs,  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const
                      const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  
782  {  {
783     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
784    
785     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
786     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
787       escriptDataC _Y=Y.getDataC();
788       escriptDataC _y=y.getDataC();
789       escriptDataC _y_contact=y_contact.getDataC();
790    
791       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
792       checkFinleyError();
793    
794       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
795       checkFinleyError();
796    
797       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
798       checkFinleyError();
799    }
800    //
801    // adds PDE of second order into a transport problem
802    //
803    void MeshAdapter::addPDEToTransportProblem(
804                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
805                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
806                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
807                                               const escript::Data& d, const escript::Data& y,
808                                               const escript::Data& d_contact,const escript::Data& y_contact) const
809    {
810       DataTypes::ShapeType shape;
811       source.expand();
812       escriptDataC _source=source.getDataC();
813       escriptDataC _M=M.getDataC();
814       escriptDataC _A=A.getDataC();
815       escriptDataC _B=B.getDataC();
816       escriptDataC _C=C.getDataC();
817       escriptDataC _D=D.getDataC();
818       escriptDataC _X=X.getDataC();
819       escriptDataC _Y=Y.getDataC();
820       escriptDataC _d=d.getDataC();
821       escriptDataC _y=y.getDataC();
822       escriptDataC _d_contact=d_contact.getDataC();
823       escriptDataC _y_contact=y_contact.getDataC();
824    
825       Finley_Mesh* mesh=m_finleyMesh.get();
826       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
827    
828       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
829     checkFinleyError();     checkFinleyError();
830    
831     // 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 );
832     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
833    
834       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
835     checkFinleyError();     checkFinleyError();
836     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  
837     // 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 );
838     checkFinleyError();     checkFinleyError();
839  }  }
840    
# Line 288  void MeshAdapter::addPDEToRHS( escript:: Line 843  void MeshAdapter::addPDEToRHS( escript::
843  //  //
844  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
845  {  {
846    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
847    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
848    if (inDomain!=*this)     if (inDomain!=*this)  
849       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
850    if (targetDomain!=*this)     if (targetDomain!=*this)
851       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
852    
853    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
854    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
855       case(Nodes):     escriptDataC _in=in.getDataC();
856          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
857             case(Nodes):     case(Nodes):
858             case(ReducedDegreesOfFreedom):     switch(target.getFunctionSpace().getTypeCode()) {
859             case(DegreesOfFreedom):     case(Nodes):
860                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));     case(ReducedNodes):
861                 break;     case(DegreesOfFreedom):
862             case(Elements):     case(ReducedDegreesOfFreedom):
863                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
864                 break;     break;
865             case(FaceElements):     case(Elements):
866                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     case(ReducedElements):
867                 break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
868             case(Points):     break;
869                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     case(FaceElements):
870                 break;     case(ReducedFaceElements):
871             case(ContactElementsZero):     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
872                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
873                 break;     case(Points):
874             case(ContactElementsOne):     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
875                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
876                 break;     case(ContactElementsZero):
877             default:     case(ReducedContactElementsZero):
878                 stringstream temp;     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
879                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     break;
880                 throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
881                 break;     case(ReducedContactElementsOne):
882          }     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
883          break;     break;
884       case(Elements):     default:
885          if (target.getFunctionSpace().getTypeCode()==Elements) {        stringstream temp;
886             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();
887          } else {        throw FinleyAdapterException(temp.str());
888             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        break;
889          }     }
890          break;     break;
891       case(FaceElements):     case(ReducedNodes):
892          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     switch(target.getFunctionSpace().getTypeCode()) {
893             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));     case(Nodes):
894          } else {     case(ReducedNodes):
895             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");     case(DegreesOfFreedom):
896             break;     case(ReducedDegreesOfFreedom):
897         }     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
898       case(Points):     break;
899          if (target.getFunctionSpace().getTypeCode()==Points) {     case(Elements):
900             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));     case(ReducedElements):
901          } else {     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
902             throw FinleyAdapterException("Error - No interpolation with data on points possible.");     break;
903             break;     case(FaceElements):
904          }     case(ReducedFaceElements):
905          break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
906       case(ContactElementsZero):     break;
907       case(ContactElementsOne):     case(Points):
908          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
909             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));     break;
910          } else {     case(ContactElementsZero):
911             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");     case(ReducedContactElementsZero):
912             break;     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
913          }     break;
914          break;     case(ContactElementsOne):
915       case(DegreesOfFreedom):     case(ReducedContactElementsOne):
916          switch(target.getFunctionSpace().getTypeCode()) {     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
917             case(ReducedDegreesOfFreedom):     break;
918             case(DegreesOfFreedom):     default:
919             case(Nodes):        stringstream temp;
920                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();
921                break;        throw FinleyAdapterException(temp.str());
922             case(Elements):        break;
923                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     }
924                break;     break;
925             case(FaceElements):     case(Elements):
926                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     if (target.getFunctionSpace().getTypeCode()==Elements) {
927                break;        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
928             case(Points):     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
929                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
930                break;     } else {
931             case(ContactElementsZero):        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
932             case(ContactElementsOne):     }
933                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     break;
934               break;     case(ReducedElements):
935             default:     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
936               stringstream temp;        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
937               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();     } else {
938               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
939               break;     }
940          }     break;
941          break;     case(FaceElements):
942       case(ReducedDegreesOfFreedom):     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
943         switch(target.getFunctionSpace().getTypeCode()) {        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
944            case(ReducedDegreesOfFreedom):     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
945               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
946               break;     } else {
947            case(Elements):        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
948               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));     }
949               break;     break;
950            case(FaceElements):     case(ReducedFaceElements):
951               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
952               break;        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
953            case(Points):     } else {
954               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.");
955               break;     }
956            case(ContactElementsZero):     break;
957            case(ContactElementsOne):     case(Points):
958               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     if (target.getFunctionSpace().getTypeCode()==Points) {
959               break;        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
960            case(Nodes):     } else {
961               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.");
962               break;     }
963            case(DegreesOfFreedom):     break;
964               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsZero):
965               break;     case(ContactElementsOne):
966            default:     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
967               stringstream temp;        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
968               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) {
969               throw FinleyAdapterException(temp.str());        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
970               break;     } else {
971         }        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
972         break;     }
973       default:     break;
974          stringstream temp;     case(ReducedContactElementsZero):
975          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();     case(ReducedContactElementsOne):
976          throw FinleyAdapterException(temp.str());     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
977          break;        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
978    }     } else {
979    checkFinleyError();        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
980       }
981       break;
982       case(DegreesOfFreedom):      
983       switch(target.getFunctionSpace().getTypeCode()) {
984       case(ReducedDegreesOfFreedom):
985       case(DegreesOfFreedom):
986       Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
987       break;
988    
989       case(Nodes):
990       case(ReducedNodes):
991       if (getMPISize()>1) {
992          escript::Data temp=escript::Data(in);
993          temp.expand();
994          escriptDataC _in2 = temp.getDataC();
995          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
996       } else {
997          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
998       }
999       break;
1000       case(Elements):
1001       case(ReducedElements):
1002       if (getMPISize()>1) {
1003          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1004          escriptDataC _in2 = temp.getDataC();
1005          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1006       } else {
1007          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1008       }
1009       break;
1010       case(FaceElements):
1011       case(ReducedFaceElements):
1012       if (getMPISize()>1) {
1013          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1014          escriptDataC _in2 = temp.getDataC();
1015          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1016    
1017       } else {
1018          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1019       }
1020       break;
1021       case(Points):
1022       if (getMPISize()>1) {
1023          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1024          escriptDataC _in2 = temp.getDataC();
1025       } else {
1026          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1027       }
1028       break;
1029       case(ContactElementsZero):
1030       case(ContactElementsOne):
1031       case(ReducedContactElementsZero):
1032       case(ReducedContactElementsOne):
1033       if (getMPISize()>1) {
1034          escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1035          escriptDataC _in2 = temp.getDataC();
1036          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1037       } else {
1038          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1039       }
1040       break;
1041       default:
1042          stringstream temp;
1043          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1044          throw FinleyAdapterException(temp.str());
1045          break;
1046       }
1047       break;
1048       case(ReducedDegreesOfFreedom):
1049       switch(target.getFunctionSpace().getTypeCode()) {
1050       case(Nodes):
1051       throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1052       break;
1053       case(ReducedNodes):
1054       if (getMPISize()>1) {
1055          escript::Data temp=escript::Data(in);
1056          temp.expand();
1057          escriptDataC _in2 = temp.getDataC();
1058          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1059       } else {
1060          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1061       }
1062       break;
1063       case(DegreesOfFreedom):
1064       throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1065       break;
1066       case(ReducedDegreesOfFreedom):
1067       Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1068       break;
1069       case(Elements):
1070       case(ReducedElements):
1071       if (getMPISize()>1) {
1072          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1073          escriptDataC _in2 = temp.getDataC();
1074          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1075       } else {
1076          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1077       }
1078       break;
1079       case(FaceElements):
1080       case(ReducedFaceElements):
1081       if (getMPISize()>1) {
1082          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1083          escriptDataC _in2 = temp.getDataC();
1084          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1085       } else {
1086          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1087       }
1088       break;
1089       case(Points):
1090       if (getMPISize()>1) {
1091          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1092          escriptDataC _in2 = temp.getDataC();
1093          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1094       } else {
1095          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1096       }
1097       break;
1098       case(ContactElementsZero):
1099       case(ContactElementsOne):
1100       case(ReducedContactElementsZero):
1101       case(ReducedContactElementsOne):
1102       if (getMPISize()>1) {
1103          escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1104          escriptDataC _in2 = temp.getDataC();
1105          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1106       } else {
1107          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1108       }
1109       break;
1110       default:
1111          stringstream temp;
1112          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1113          throw FinleyAdapterException(temp.str());
1114          break;
1115       }
1116       break;
1117       default:
1118          stringstream temp;
1119          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1120          throw FinleyAdapterException(temp.str());
1121          break;
1122       }
1123       checkFinleyError();
1124  }  }
1125    
1126  //  //
# Line 429  void MeshAdapter::interpolateOnDomain(es Line 1128  void MeshAdapter::interpolateOnDomain(es
1128  //  //
1129  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1130  {  {
1131    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1132    if (argDomain!=*this)     if (argDomain!=*this)
1133       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1134    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1135    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1136    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1137       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1138    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1139       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1140       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1141       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1142       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1143    }        // this is then interpolated onto arg:
1144    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1145       }
1146       checkFinleyError();
1147  }  }
1148    
1149  //  //
# Line 450  void MeshAdapter::setToX(escript::Data& Line 1151  void MeshAdapter::setToX(escript::Data&
1151  //  //
1152  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1153  {  {
1154    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());
1155    if (normalDomain!=*this)     if (normalDomain!=*this)
1156       throw FinleyAdapterException("Error - Illegal domain of normal locations");        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1157    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1158    switch(normal.getFunctionSpace().getTypeCode()) {     escriptDataC _normal=normal.getDataC();
1159      case(Nodes):     switch(normal.getFunctionSpace().getTypeCode()) {
1160        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     case(Nodes):
1161        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1162      case(Elements):     break;
1163        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     case(ReducedNodes):
1164        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1165      case (FaceElements):     break;
1166        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     case(Elements):
1167        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1168      case(Points):     break;
1169        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     case(ReducedElements):
1170        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1171      case (ContactElementsOne):     break;
1172      case (ContactElementsZero):     case (FaceElements):
1173        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1174        break;     break;
1175      case(DegreesOfFreedom):     case (ReducedFaceElements):
1176        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1177        break;     break;
1178      case(ReducedDegreesOfFreedom):     case(Points):
1179        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1180        break;     break;
1181      default:     case (ContactElementsOne):
1182       case (ContactElementsZero):
1183       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1184       break;
1185       case (ReducedContactElementsOne):
1186       case (ReducedContactElementsZero):
1187       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1188       break;
1189       case(DegreesOfFreedom):
1190       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1191       break;
1192       case(ReducedDegreesOfFreedom):
1193       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1194       break;
1195       default:
1196        stringstream temp;        stringstream temp;
1197        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();
1198        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1199        break;        break;
1200    }     }
1201    checkFinleyError();     checkFinleyError();
1202  }  }
1203    
1204  //  //
# Line 491  void MeshAdapter::setToNormal(escript::D Line 1206  void MeshAdapter::setToNormal(escript::D
1206  //  //
1207  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1208  {  {
1209    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
1210    if (targetDomain!=*this)     if (targetDomain!=*this)
1211       throw FinleyAdapterException("Error - Illegal domain of interpolation target");        throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1212    
1213    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1214  }  }
1215    
1216  //  //
# Line 503  void MeshAdapter::interpolateACross(escr Line 1218  void MeshAdapter::interpolateACross(escr
1218  //  //
1219  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1220  {  {
1221    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1222    if (argDomain!=*this)     if (argDomain!=*this)
1223       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1224    
1225    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1226    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1227       case(Nodes):     escriptDataC _temp;
1228          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1229          break;     escriptDataC _arg=arg.getDataC();
1230       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1231          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1232          break;     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1233       case(FaceElements):     _temp=temp.getDataC();
1234          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1235          break;     break;
1236       case(Points):     case(ReducedNodes):
1237          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1238          break;     _temp=temp.getDataC();
1239       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1240          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1241          break;     case(Elements):
1242       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1243          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1244          break;     case(ReducedElements):
1245       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1246          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1247          break;     case(FaceElements):
1248       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1249          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1250          break;     case(ReducedFaceElements):
1251       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1252          stringstream temp;     break;
1253          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1254          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1255          break;     break;
1256    }     case(ContactElementsZero):
1257    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1258       break;
1259       case(ReducedContactElementsZero):
1260       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1261       break;
1262       case(ContactElementsOne):
1263       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1264       break;
1265       case(ReducedContactElementsOne):
1266       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1267       break;
1268       case(DegreesOfFreedom):
1269       temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1270       _temp=temp.getDataC();
1271       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1272       break;
1273       case(ReducedDegreesOfFreedom):
1274       temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1275       _temp=temp.getDataC();
1276       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1277       break;
1278       default:
1279          stringstream temp;
1280          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1281          throw FinleyAdapterException(temp.str());
1282          break;
1283       }
1284       checkFinleyError();
1285       blocktimer_increment("integrate()", blocktimer_start);
1286  }  }
1287    
1288  //  //
# Line 547  void MeshAdapter::setToIntegrals(std::ve Line 1290  void MeshAdapter::setToIntegrals(std::ve
1290  //  //
1291  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1292  {  {
1293    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1294    if (argDomain!=*this)     if (argDomain!=*this)
1295      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1296    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());
1297    if (gradDomain!=*this)     if (gradDomain!=*this)
1298       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1299    
1300    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1301    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1302         case(Nodes):     escriptDataC nodeDataC;
1303            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     escript::Data temp;
1304            break;     if (getMPISize()>1) {
1305         case(Elements):        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1306            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1307            break;           nodeDataC = temp.getDataC();
1308         case(FaceElements):        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1309            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1310            break;           nodeDataC = temp.getDataC();
1311         case(Points):        } else {
1312            throw FinleyAdapterException("Error - Gradient at points is not supported.");           nodeDataC = arg.getDataC();
1313            break;        }
1314         case(ContactElementsZero):     } else {
1315            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));        nodeDataC = arg.getDataC();
1316            break;     }
1317         case(ContactElementsOne):     switch(grad.getFunctionSpace().getTypeCode()) {
1318            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     case(Nodes):
1319            break;     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1320         case(DegreesOfFreedom):     break;
1321            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     case(ReducedNodes):
1322            break;     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1323         case(ReducedDegreesOfFreedom):     break;
1324            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     case(Elements):
1325            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1326         default:     break;
1327            stringstream temp;     case(ReducedElements):
1328            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1329            throw FinleyAdapterException(temp.str());     break;
1330            break;     case(FaceElements):
1331    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1332    checkFinleyError();     break;
1333       case(ReducedFaceElements):
1334       Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1335       break;
1336       case(Points):
1337       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1338       break;
1339       case(ContactElementsZero):
1340       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1341       break;
1342       case(ReducedContactElementsZero):
1343       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1344       break;
1345       case(ContactElementsOne):
1346       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1347       break;
1348       case(ReducedContactElementsOne):
1349       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1350       break;
1351       case(DegreesOfFreedom):
1352       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1353       break;
1354       case(ReducedDegreesOfFreedom):
1355       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1356       break;
1357       default:
1358          stringstream temp;
1359          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1360          throw FinleyAdapterException(temp.str());
1361          break;
1362       }
1363       checkFinleyError();
1364  }  }
1365    
1366  //  //
# Line 594  void MeshAdapter::setToGradient(escript: Line 1368  void MeshAdapter::setToGradient(escript:
1368  //  //
1369  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1370  {  {
1371    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1372    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1373    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1374         case(Nodes):     case(Nodes):
1375            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1376            break;     break;
1377         case(Elements):     case(ReducedNodes):
1378            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1379            break;     break;
1380         case(FaceElements):     case(Elements):
1381            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1382            break;     break;
1383         case(Points):     case(ReducedElements):
1384            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1385            break;     break;
1386         case(ContactElementsZero):     case(FaceElements):
1387         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1388            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1389            break;     case(ReducedFaceElements):
1390         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1391            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1392            break;     case(Points):
1393         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1394            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1395            break;     case(ContactElementsZero):
1396         default:     case(ContactElementsOne):
1397            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1398            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1399            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1400            break;     case(ReducedContactElementsOne):
1401    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1402    checkFinleyError();     break;
1403       case(DegreesOfFreedom):
1404       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1405       break;
1406       case(ReducedDegreesOfFreedom):
1407       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1408       break;
1409       default:
1410          stringstream temp;
1411          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1412          throw FinleyAdapterException(temp.str());
1413          break;
1414       }
1415       checkFinleyError();
1416  }  }
1417    
1418  // sets the location of nodes:  // sets the location of nodes:
1419  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1420  {  {
1421    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1422    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1423    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1424       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1425    Finley_Mesh_setCoordinates(mesh,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1426    checkFinleyError();     tmp = new_x.getDataC();
1427       Finley_Mesh_setCoordinates(mesh,&tmp);
1428       checkFinleyError();
1429  }  }
1430    
1431  // saves a data array in openDX format:  // saves a data array in openDX format:
1432  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
1433  {  {
1434      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1435      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1436      char names[num_data][MAX_namelength];     /* win32 refactor */
1437      char* c_names[num_data];     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1438      escriptDataC data[num_data];     for(int i=0;i<num_data;i++)
1439      escriptDataC* ptr_data[num_data];     {
1440          names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1441      boost::python::list keys=arg.keys();     }
1442      for (int i=0;i<num_data;++i) {  
1443           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1444           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1445               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
1446           data[i]=d.getDataC();     boost::python::list keys=arg.keys();
1447           ptr_data[i]=&(data[i]);     for (int i=0;i<num_data;++i) {
1448           std::string n=boost::python::extract<std::string>(keys[i]);        std::string n=boost::python::extract<std::string>(keys[i]);
1449           c_names[i]=&(names[i][0]);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1450           if (n.length()>MAX_namelength-1) {        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1451              strncpy(c_names[i],n.c_str(),MAX_namelength-1);           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1452              c_names[i][MAX_namelength-1]='\0';        data[i]=d.getDataC();
1453           } else {        ptr_data[i]= &(data[i]);
1454              strcpy(c_names[i],n.c_str());        if (n.length()>MAX_namelength-1) {
1455           }           strncpy(names[i],n.c_str(),MAX_namelength-1);
1456      }           names[i][MAX_namelength-1]='\0';
1457      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);        } else {
1458      checkFinleyError();           strcpy(names[i],n.c_str());
1459      return;        }
1460       }
1461       Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1462       checkFinleyError();
1463    
1464       /* win32 refactor */
1465       TMPMEMFREE(data);
1466       TMPMEMFREE(ptr_data);
1467       for(int i=0;i<num_data;i++)
1468       {
1469          TMPMEMFREE(names[i]);
1470       }
1471       TMPMEMFREE(names);
1472    
1473       return;
1474  }  }
1475    
1476  // saves a data array in openVTK format:  // saves a data array in openVTK format:
1477  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
1478  {  {
1479      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1480      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1481      char names[num_data][MAX_namelength];     /* win32 refactor */
1482      char* c_names[num_data];     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1483      escriptDataC data[num_data];     for(int i=0;i<num_data;i++)
1484      escriptDataC* ptr_data[num_data];     {
1485          names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1486      boost::python::list keys=arg.keys();     }
1487      for (int i=0;i<num_data;++i) {  
1488           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1489           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1490               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
1491           data[i]=d.getDataC();     boost::python::list keys=arg.keys();
1492           ptr_data[i]=&(data[i]);     for (int i=0;i<num_data;++i) {
1493           std::string n=boost::python::extract<std::string>(keys[i]);        std::string n=boost::python::extract<std::string>(keys[i]);
1494           c_names[i]=&(names[i][0]);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1495           if (n.length()>MAX_namelength-1) {        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1496              strncpy(c_names[i],n.c_str(),MAX_namelength-1);           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1497              c_names[i][MAX_namelength-1]='\0';        data[i]=d.getDataC();
1498           } else {        ptr_data[i]=&(data[i]);
1499              strcpy(c_names[i],n.c_str());        if (n.length()>MAX_namelength-1) {
1500           }           strncpy(names[i],n.c_str(),MAX_namelength-1);
1501      }           names[i][MAX_namelength-1]='\0';
1502      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);        } else {
1503      checkFinleyError();           strcpy(names[i],n.c_str());
1504      return;        }
1505       }
1506       Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1507    
1508       checkFinleyError();
1509       /* win32 refactor */
1510       TMPMEMFREE(data);
1511       TMPMEMFREE(ptr_data);
1512       for(int i=0;i<num_data;i++)
1513       {
1514          TMPMEMFREE(names[i]);
1515       }
1516       TMPMEMFREE(names);
1517    
1518       return;
1519  }  }
1520                                                                                                                                                                                                                                                                                                                                                
1521                                                                                                                                                                                                                                                                                                                                                
1522  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1523  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1524                        const int row_blocksize,                                                   const int row_blocksize,
1525                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1526                        const int column_blocksize,                                                   const int column_blocksize,
1527                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1528                        const int type) const                                                   const int type) const
1529  {  {
1530      int reduceRowOrder=0;     int reduceRowOrder=0;
1531      int reduceColOrder=0;     int reduceColOrder=0;
1532      // is the domain right?     // is the domain right?
1533      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());
1534      if (row_domain!=*this)     if (row_domain!=*this)
1535            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.");
1536      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());
1537      if (col_domain!=*this)     if (col_domain!=*this)
1538            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.");
1539      // is the function space type right     // is the function space type right
1540      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1541          reduceRowOrder=0;        reduceRowOrder=0;
1542      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1543          reduceRowOrder=1;        reduceRowOrder=1;
1544      } else {     } else {
1545          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1546      }     }
1547      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1548          reduceColOrder=0;        reduceColOrder=0;
1549      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1550          reduceColOrder=1;        reduceColOrder=1;
1551      } else {     } else {
1552          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1553      }     }
1554      // generate matrix:     // generate matrix:
1555        
1556      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1557      checkFinleyError();     checkFinleyError();
1558      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1559      checkPasoError();     int trilinos = 0;
1560      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1561      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1562          /* Allocation Epetra_VrbMatrix here */
1563    #endif
1564       }
1565       else {
1566          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1567       }
1568       checkPasoError();
1569       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1570       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1571    }
1572    // creates a TransportProblemAdapter
1573    TransportProblemAdapter MeshAdapter::newTransportProblem(
1574                                                             const double theta,
1575                                                             const int blocksize,
1576                                                             const escript::FunctionSpace& functionspace,
1577                                                             const int type) const
1578    {
1579       int reduceOrder=0;
1580       // is the domain right?
1581       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1582       if (domain!=*this)
1583          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1584       // is the function space type right
1585       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1586          reduceOrder=0;
1587       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1588          reduceOrder=1;
1589       } else {
1590          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1591       }
1592       // generate matrix:
1593    
1594       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1595       checkFinleyError();
1596       Paso_FCTransportProblem* transportProblem;
1597       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1598       checkPasoError();
1599       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1600       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1601  }  }
1602    
1603  //  //
# Line 753  SystemMatrixAdapter MeshAdapter::newSyst Line 1609  SystemMatrixAdapter MeshAdapter::newSyst
1609  // 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:
1610  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1611  {  {
1612    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1613         case(Nodes):     case(Nodes):
1614         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1615         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1616            return false;     return false;
1617            break;     break;
1618         case(Elements):     case(Elements):
1619         case(FaceElements):     case(FaceElements):
1620         case(Points):     case(Points):
1621         case(ContactElementsZero):     case(ContactElementsZero):
1622         case(ContactElementsOne):     case(ContactElementsOne):
1623            return true;     case(ReducedElements):
1624            break;     case(ReducedFaceElements):
1625         default:     case(ReducedContactElementsZero):
1626            stringstream temp;     case(ReducedContactElementsOne):
1627            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1628            throw FinleyAdapterException(temp.str());     break;
1629            break;     default:
1630    }        stringstream temp;
1631    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1632    return false;        throw FinleyAdapterException(temp.str());
1633          break;
1634       }
1635       checkFinleyError();
1636       return false;
1637  }  }
1638    
1639  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1640  {  {
1641    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1642       case(Nodes):     case(Nodes):
1643          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1644             case(Nodes):     case(Nodes):
1645             case(ReducedDegreesOfFreedom):     case(ReducedNodes):
1646             case(DegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1647             case(Elements):     case(DegreesOfFreedom):
1648             case(FaceElements):     case(Elements):
1649             case(Points):     case(ReducedElements):
1650             case(ContactElementsZero):     case(FaceElements):
1651             case(ContactElementsOne):     case(ReducedFaceElements):
1652                 return true;     case(Points):
1653             default:     case(ContactElementsZero):
1654                 stringstream temp;     case(ReducedContactElementsZero):
1655                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(ContactElementsOne):
1656                 throw FinleyAdapterException(temp.str());     case(ReducedContactElementsOne):
1657          }     return true;
1658          break;     default:
1659       case(Elements):        stringstream temp;
1660          if (functionSpaceType_target==Elements) {        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1661             return true;        throw FinleyAdapterException(temp.str());
1662          } else {     }
1663             return false;     break;
1664          }     case(ReducedNodes):
1665       case(FaceElements):     switch(functionSpaceType_target) {
1666          if (functionSpaceType_target==FaceElements) {     case(ReducedNodes):
1667             return true;     case(ReducedDegreesOfFreedom):
1668          } else {     case(Elements):
1669             return false;     case(ReducedElements):
1670          }     case(FaceElements):
1671       case(Points):     case(ReducedFaceElements):
1672          if (functionSpaceType_target==Points) {     case(Points):
1673             return true;     case(ContactElementsZero):
1674          } else {     case(ReducedContactElementsZero):
1675             return false;     case(ContactElementsOne):
1676          }     case(ReducedContactElementsOne):
1677       case(ContactElementsZero):     return true;
1678       case(ContactElementsOne):     case(Nodes):
1679          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     case(DegreesOfFreedom):
1680             return true;     return false;
1681          } else {     default:
1682             return false;        stringstream temp;
1683          }        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1684       case(DegreesOfFreedom):        throw FinleyAdapterException(temp.str());
1685          switch(functionSpaceType_target) {     }
1686             case(ReducedDegreesOfFreedom):     break;
1687             case(DegreesOfFreedom):     case(Elements):
1688             case(Nodes):     if (functionSpaceType_target==Elements) {
1689             case(Elements):        return true;
1690             case(FaceElements):     } else if (functionSpaceType_target==ReducedElements) {
1691             case(Points):        return true;
1692             case(ContactElementsZero):     } else {
1693             case(ContactElementsOne):        return false;
1694                return true;     }
1695             default:     case(ReducedElements):
1696               stringstream temp;     if (functionSpaceType_target==ReducedElements) {
1697               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;        return true;
1698               throw FinleyAdapterException(temp.str());     } else {
1699          }        return false;
1700          break;     }
1701       case(ReducedDegreesOfFreedom):     case(FaceElements):
1702         switch(functionSpaceType_target) {     if (functionSpaceType_target==FaceElements) {
1703            case(ReducedDegreesOfFreedom):        return true;
1704            case(Elements):     } else if (functionSpaceType_target==ReducedFaceElements) {
1705            case(FaceElements):        return true;
1706            case(Points):     } else {
1707            case(ContactElementsZero):        return false;
1708            case(ContactElementsOne):     }
1709                return true;     case(ReducedFaceElements):
1710            case(Nodes):     if (functionSpaceType_target==ReducedFaceElements) {
1711            case(DegreesOfFreedom):        return true;
1712               return false;     } else {
1713            default:        return false;
1714               stringstream temp;     }
1715               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1716               throw FinleyAdapterException(temp.str());     if (functionSpaceType_target==Points) {
1717         }        return true;
1718         break;     } else {
1719       default:        return false;
1720          stringstream temp;     }
1721          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1722          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1723          break;     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1724    }        return true;
1725    checkFinleyError();     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1726    return false;        return true;
1727       } else {
1728          return false;
1729       }
1730       case(ReducedContactElementsZero):
1731       case(ReducedContactElementsOne):
1732       if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1733          return true;
1734       } else {
1735          return false;
1736       }
1737       case(DegreesOfFreedom):
1738       switch(functionSpaceType_target) {
1739       case(ReducedDegreesOfFreedom):
1740       case(DegreesOfFreedom):
1741       case(Nodes):
1742       case(ReducedNodes):
1743       case(Elements):
1744       case(ReducedElements):
1745       case(Points):
1746       case(FaceElements):
1747       case(ReducedFaceElements):
1748       case(ContactElementsZero):
1749       case(ReducedContactElementsZero):
1750       case(ContactElementsOne):
1751       case(ReducedContactElementsOne):
1752       return true;
1753       default:
1754          stringstream temp;
1755          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1756          throw FinleyAdapterException(temp.str());
1757       }
1758       break;
1759       case(ReducedDegreesOfFreedom):
1760       switch(functionSpaceType_target) {
1761       case(ReducedDegreesOfFreedom):
1762       case(ReducedNodes):
1763       case(Elements):
1764       case(ReducedElements):
1765       case(FaceElements):
1766       case(ReducedFaceElements):
1767       case(Points):
1768       case(ContactElementsZero):
1769       case(ReducedContactElementsZero):
1770       case(ContactElementsOne):
1771       case(ReducedContactElementsOne):
1772       return true;
1773       case(Nodes):
1774       case(DegreesOfFreedom):
1775       return false;
1776       default:
1777          stringstream temp;
1778          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1779          throw FinleyAdapterException(temp.str());
1780       }
1781       break;
1782       default:
1783          stringstream temp;
1784          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1785          throw FinleyAdapterException(temp.str());
1786          break;
1787       }
1788       checkFinleyError();
1789       return false;
1790  }  }
1791    
1792  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
1793  {  {
1794      return false;     return false;
1795  }  }
1796    
1797  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1798  {  {
1799    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1800    if (temp!=0) {     if (temp!=0) {
1801      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1802    } else {     } else {
1803      return false;        return false;
1804    }     }
1805  }  }
1806    
1807  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1808  {  {
1809    return !(operator==(other));     return !(operator==(other));
1810  }  }
1811    
1812  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const
# Line 895  int MeshAdapter::getSystemMatrixTypeId(c Line 1818  int MeshAdapter::getSystemMatrixTypeId(c
1818    
1819  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1820  {  {
1821    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1822  }  }
1823    
1824  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1825  {  {
1826    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1827  }  }
1828    
1829  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1830  {  {
1831    return function(asAbstractContinuousDomain()).getSize();     return function(asAbstractContinuousDomain()).getSize();
1832  }  }
1833    
1834    int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1835    {
1836       int *out = NULL;
1837       Finley_Mesh* mesh=m_finleyMesh.get();
1838       switch (functionSpaceType) {
1839       case(Nodes):
1840       out=mesh->Nodes->Id;
1841       break;
1842       case(ReducedNodes):
1843       out=mesh->Nodes->reducedNodesId;
1844       break;
1845       case(Elements):
1846       out=mesh->Elements->Id;
1847       break;
1848       case(ReducedElements):
1849       out=mesh->Elements->Id;
1850       break;
1851       case(FaceElements):
1852       out=mesh->FaceElements->Id;
1853       break;
1854       case(ReducedFaceElements):
1855       out=mesh->FaceElements->Id;
1856       break;
1857       case(Points):
1858       out=mesh->Points->Id;
1859       break;
1860       case(ContactElementsZero):
1861       out=mesh->ContactElements->Id;
1862       break;
1863       case(ReducedContactElementsZero):
1864       out=mesh->ContactElements->Id;
1865       break;
1866       case(ContactElementsOne):
1867       out=mesh->ContactElements->Id;
1868       break;
1869       case(ReducedContactElementsOne):
1870       out=mesh->ContactElements->Id;
1871       break;
1872       case(DegreesOfFreedom):
1873       out=mesh->Nodes->degreesOfFreedomId;
1874       break;
1875       case(ReducedDegreesOfFreedom):
1876       out=mesh->Nodes->reducedDegreesOfFreedomId;
1877       break;
1878       default:
1879          stringstream temp;
1880          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1881          throw FinleyAdapterException(temp.str());
1882          break;
1883       }
1884       return out;
1885    }
1886  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1887  {  {
1888    int out=0;     int out=0;
1889       Finley_Mesh* mesh=m_finleyMesh.get();
1890       switch (functionSpaceType) {
1891       case(Nodes):
1892       out=mesh->Nodes->Tag[sampleNo];
1893       break;
1894       case(ReducedNodes):
1895       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1896       break;
1897       case(Elements):
1898       out=mesh->Elements->Tag[sampleNo];
1899       break;
1900       case(ReducedElements):
1901       out=mesh->Elements->Tag[sampleNo];
1902       break;
1903       case(FaceElements):
1904       out=mesh->FaceElements->Tag[sampleNo];
1905       break;
1906       case(ReducedFaceElements):
1907       out=mesh->FaceElements->Tag[sampleNo];
1908       break;
1909       case(Points):
1910       out=mesh->Points->Tag[sampleNo];
1911       break;
1912       case(ContactElementsZero):
1913       out=mesh->ContactElements->Tag[sampleNo];
1914       break;
1915       case(ReducedContactElementsZero):
1916       out=mesh->ContactElements->Tag[sampleNo];
1917       break;
1918       case(ContactElementsOne):
1919       out=mesh->ContactElements->Tag[sampleNo];
1920       break;
1921       case(ReducedContactElementsOne):
1922       out=mesh->ContactElements->Tag[sampleNo];
1923       break;
1924       case(DegreesOfFreedom):
1925       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1926       break;
1927       case(ReducedDegreesOfFreedom):
1928       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1929       break;
1930       default:
1931          stringstream temp;
1932          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1933          throw FinleyAdapterException(temp.str());
1934          break;
1935       }
1936       return out;
1937    }
1938    
1939    
1940    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1941    {
1942       Finley_Mesh* mesh=m_finleyMesh.get();
1943       escriptDataC tmp=mask.getDataC();
1944       switch(functionSpaceType) {
1945       case(Nodes):
1946       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1947       break;
1948       case(ReducedNodes):
1949       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1950       break;
1951       case(DegreesOfFreedom):
1952       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1953       break;
1954       case(ReducedDegreesOfFreedom):
1955       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1956       break;
1957       case(Elements):
1958       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1959       break;
1960       case(ReducedElements):
1961       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1962       break;
1963       case(FaceElements):
1964       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1965       break;
1966       case(ReducedFaceElements):
1967       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1968       break;
1969       case(Points):
1970       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1971       break;
1972       case(ContactElementsZero):
1973       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1974       break;
1975       case(ReducedContactElementsZero):
1976       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1977       break;
1978       case(ContactElementsOne):
1979       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1980       break;
1981       case(ReducedContactElementsOne):
1982       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1983       break;
1984       default:
1985          stringstream temp;
1986          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1987          throw FinleyAdapterException(temp.str());
1988       }
1989       checkFinleyError();
1990       return;
1991    }
1992    
1993    void MeshAdapter::setTagMap(const std::string& name,  int tag)
1994    {
1995       Finley_Mesh* mesh=m_finleyMesh.get();
1996       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
1997       checkPasoError();
1998       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
1999    }
2000    
2001    int MeshAdapter::getTag(const std::string& name) const
2002    {
2003       Finley_Mesh* mesh=m_finleyMesh.get();
2004       int tag=0;
2005       tag=Finley_Mesh_getTag(mesh, name.c_str());
2006       checkPasoError();
2007       // throwStandardException("MeshAdapter::getTag is not implemented.");
2008       return tag;
2009    }
2010    
2011    bool MeshAdapter::isValidTagName(const std::string& name) const
2012    {
2013       Finley_Mesh* mesh=m_finleyMesh.get();
2014       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2015    }
2016    
2017    std::string MeshAdapter::showTagNames() const
2018    {
2019       stringstream temp;
2020       Finley_Mesh* mesh=m_finleyMesh.get();
2021       Finley_TagMap* tag_map=mesh->TagMap;
2022       while (tag_map) {
2023          temp << tag_map->name;
2024          tag_map=tag_map->next;
2025          if (tag_map) temp << ", ";
2026       }
2027       return temp.str();
2028    }
2029    
2030    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2031    {
2032    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2033    switch (functionSpaceType) {    dim_t numTags=0;
2034    case(Nodes):    switch(functionSpaceCode) {
2035      out=mesh->Nodes->Tag[sampleNo];     case(Nodes):
2036      break;            numTags=mesh->Nodes->numTagsInUse;
2037    case(Elements):            break;
2038      out=mesh->Elements->Tag[sampleNo];     case(ReducedNodes):
2039      break;            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2040    case(FaceElements):            break;
2041      out=mesh->FaceElements->Tag[sampleNo];     case(DegreesOfFreedom):
2042      break;            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2043    case(Points):            break;
2044      out=mesh->Points->Tag[sampleNo];     case(ReducedDegreesOfFreedom):
2045      break;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2046    case(ContactElementsZero):            break;
2047      out=mesh->ContactElements->Tag[sampleNo];     case(Elements):
2048      break;     case(ReducedElements):
2049    case(ContactElementsOne):            numTags=mesh->Elements->numTagsInUse;
2050      out=mesh->ContactElements->Tag[sampleNo];            break;
2051      break;     case(FaceElements):
2052    case(DegreesOfFreedom):     case(ReducedFaceElements):
2053      break;            numTags=mesh->FaceElements->numTagsInUse;
2054    case(ReducedDegreesOfFreedom):            break;
2055      break;     case(Points):
2056    default:            numTags=mesh->Points->numTagsInUse;
2057      stringstream temp;            break;
2058      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();     case(ContactElementsZero):
2059      throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
2060      break;     case(ContactElementsOne):
2061       case(ReducedContactElementsOne):
2062              numTags=mesh->ContactElements->numTagsInUse;
2063              break;
2064       default:
2065          stringstream temp;
2066          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2067          throw FinleyAdapterException(temp.str());
2068    }    }
2069    return out;    return numTags;
2070  }  }
2071  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2072  {  {
   int out=0,i;  
2073    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2074    switch (functionSpaceType) {    index_t* tags=NULL;
2075    case(Nodes):    switch(functionSpaceCode) {
2076      if (mesh->Nodes!=NULL) {     case(Nodes):
2077        out=mesh->Nodes->Id[sampleNo];            tags=mesh->Nodes->tagsInUse;
2078        break;            break;
2079      }     case(ReducedNodes):
2080    case(Elements):            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2081      out=mesh->Elements->Id[sampleNo];            break;
2082      break;     case(DegreesOfFreedom):
2083    case(FaceElements):            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2084      out=mesh->FaceElements->Id[sampleNo];            break;
2085      break;     case(ReducedDegreesOfFreedom):
2086    case(Points):            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2087      out=mesh->Points->Id[sampleNo];            break;
2088      break;     case(Elements):
2089    case(ContactElementsZero):     case(ReducedElements):
2090      out=mesh->ContactElements->Id[sampleNo];            tags=mesh->Elements->tagsInUse;
2091      break;            break;
2092    case(ContactElementsOne):     case(FaceElements):
2093      out=mesh->ContactElements->Id[sampleNo];     case(ReducedFaceElements):
2094      break;            tags=mesh->FaceElements->tagsInUse;
2095    case(DegreesOfFreedom):            break;
2096      for (i=0;i<mesh->Nodes->numNodes; ++i) {     case(Points):
2097         if (mesh->Nodes->degreeOfFreedom[i]==sampleNo) {            tags=mesh->Points->tagsInUse;
2098            out=mesh->Nodes->Id[i];            break;
2099            break;     case(ContactElementsZero):
2100         }     case(ReducedContactElementsZero):
2101      }     case(ContactElementsOne):
2102      break;     case(ReducedContactElementsOne):
2103    case(ReducedDegreesOfFreedom):            tags=mesh->ContactElements->tagsInUse;
2104      for (i=0;i<mesh->Nodes->numNodes; ++i) {            break;
2105         if (mesh->Nodes->reducedDegreeOfFreedom[i]==sampleNo) {     default:
2106            out=mesh->Nodes->Id[i];        stringstream temp;
2107            break;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2108         }        throw FinleyAdapterException(temp.str());
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
2109    }    }
2110    return out;    return tags;
2111  }  }
2112    
2113    
2114  }  // end of namespace  }  // end of namespace

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