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

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trunk/finley/src/CPPAdapter/MeshAdapter.cpp revision 547 by gross, Tue Feb 21 06:10:54 2006 UTC temp/finley/src/CPPAdapter/MeshAdapter.cpp revision 1387 by trankine, Fri Jan 11 07:45:26 2008 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #include "MeshAdapter.h"  /* $Id$ */
3    
4    /*******************************************************
5     *
6     *           Copyright 2003-2007 by ACceSS MNRF
7     *       Copyright 2007 by University of Queensland
8     *
9     *                http://esscc.uq.edu.au
10     *        Primary Business: Queensland, Australia
11     *  Licensed under the Open Software License version 3.0
12     *     http://www.opensource.org/licenses/osl-3.0.php
13     *
14     *******************************************************/
15    
16  #include "Data.h"  #include "MeshAdapter.h"
17  #include "DataFactory.h"  #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  using namespace std;  using namespace std;
28  using namespace escript;  using namespace escript;
# Line 29  MeshAdapter::FunctionSpaceNamesMapType M Line 35  MeshAdapter::FunctionSpaceNamesMapType M
35  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
36  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
37  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
38    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
39  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
40    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
41  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
42    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
43  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
44  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
45    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
46  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
47    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
48    
49  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
50  {  {
51    setFunctionSpaceTypeNames();    setFunctionSpaceTypeNames();
52    //    //
53    // 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
54    // for us.    // for us.
55    m_finleyMesh.reset(finleyMesh,null_deleter());    m_finleyMesh.reset(finleyMesh,null_deleter());
56  }  }
# Line 58  MeshAdapter::~MeshAdapter() Line 69  MeshAdapter::~MeshAdapter()
69    // 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.
70    //  cout << "In MeshAdapter destructor." << endl;    //  cout << "In MeshAdapter destructor." << endl;
71    if (m_finleyMesh.unique()) {    if (m_finleyMesh.unique()) {
72      //   cout << "Calling dealloc." << endl;      Finley_Mesh_free(m_finleyMesh.get());
     Finley_Mesh_dealloc(m_finleyMesh.get());  
     //   cout << "Finished dealloc." << endl;  
73    }    }
74  }  }
75    
76    int MeshAdapter::getMPISize() const
77    {
78       return m_finleyMesh.get()->MPIInfo->size;
79    }
80    int MeshAdapter::getMPIRank() const
81    {
82       return m_finleyMesh.get()->MPIInfo->rank;
83    }
84    
85    
86  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
87     return m_finleyMesh.get();     return m_finleyMesh.get();
88  }  }
89    
90  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
91  {  {
92    char fName[fileName.size()+1];    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
93    strcpy(fName,fileName.c_str());    strcpy(fName,fileName.c_str());
94    Finley_Mesh_write(m_finleyMesh.get(),fName);    Finley_Mesh_write(m_finleyMesh.get(),fName);
95    checkFinleyError();    checkFinleyError();
96      TMPMEMFREE(fName);
97    }
98    
99    void MeshAdapter::Print_Mesh_Info(const bool full=false) const
100    {
101      Finley_PrintMesh_Info(m_finleyMesh.get(), full);
102    }
103    
104    void MeshAdapter::dump(const std::string& fileName) const
105    {
106    #ifdef USE_NETCDF
107       const NcDim* ncdims[12];
108       NcVar *ids, *data;
109       int *int_ptr;
110       Finley_Mesh *mesh = m_finleyMesh.get();
111       Finley_TagMap* tag_map;
112       int num_Tags = 0;
113       int mpi_size             = mesh->MPIInfo->size;
114       int mpi_rank             = mesh->MPIInfo->rank;
115       int numDim               = mesh->Nodes->numDim;
116       int numNodes             = mesh->Nodes->numNodes;
117       int num_Elements         = mesh->Elements->numElements;
118       int num_FaceElements         = mesh->FaceElements->numElements;
119       int num_ContactElements      = mesh->ContactElements->numElements;
120       int num_Points           = mesh->Points->numElements;
121       int num_Elements_numNodes        = mesh->Elements->numNodes;
122       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
123       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
124       char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);
125    
126       /* Figure out how much storage is required for tags */
127       tag_map = mesh->TagMap;
128       if (tag_map) {
129         while (tag_map) {
130        num_Tags++;
131            tag_map=tag_map->next;
132         }
133       }
134    
135       // NetCDF error handler
136       NcError err(NcError::verbose_nonfatal);
137       // Create the file.
138       NcFile dataFile(newFileName, NcFile::Replace);
139       // check if writing was successful
140       if (!dataFile.is_valid())
141            throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
142    
143       // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
144       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
145            throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
146       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
147            throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
148       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
149            throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
150       if (num_Elements>0)
151          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
152            throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
153       if (num_FaceElements>0)
154          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
155            throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
156       if (num_ContactElements>0)
157          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
158            throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
159       if (num_Points>0)
160          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
161            throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
162       if (num_Elements>0)
163          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
164            throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
165       if (num_FaceElements>0)
166          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
167            throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
168       if (num_ContactElements>0)
169          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
170            throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
171       if (num_Tags>0)
172          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
173            throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
174    
175       // Attributes: MPI size, MPI rank, Name, order, reduced_order
176       if (!dataFile.add_att("mpi_size", mpi_size) )
177            throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
178       if (!dataFile.add_att("mpi_rank", mpi_rank) )
179            throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
180       if (!dataFile.add_att("Name",mesh->Name) )
181            throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
182       if (!dataFile.add_att("numDim",numDim) )
183            throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
184       if (!dataFile.add_att("order",mesh->order) )
185            throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
186       if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
187            throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
188       if (!dataFile.add_att("numNodes",numNodes) )
189            throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
190       if (!dataFile.add_att("num_Elements",num_Elements) )
191            throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
192       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
193            throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
194       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
195            throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
196       if (!dataFile.add_att("num_Points",num_Points) )
197            throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
198       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
199            throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
200       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
201            throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
202       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
203            throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
204       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
205          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
206       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
207          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
208       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
209          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
210       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
211          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
212       if (!dataFile.add_att("num_Tags", num_Tags) )
213          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
214    
215       // // // // // Nodes // // // // //
216    
217       // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
218       if (numNodes>0) {
219    
220       // Nodes Id
221       if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
222            throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
223       int_ptr = &mesh->Nodes->Id[0];
224       if (! (ids->put(int_ptr, numNodes)) )
225            throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
226    
227       // Nodes Tag
228       if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
229            throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
230       int_ptr = &mesh->Nodes->Tag[0];
231       if (! (ids->put(int_ptr, numNodes)) )
232            throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
233    
234       // Nodes gDOF
235       if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
236            throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
237       int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
238       if (! (ids->put(int_ptr, numNodes)) )
239            throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
240    
241       // Nodes global node index
242       if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
243            throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
244       int_ptr = &mesh->Nodes->globalNodesIndex[0];
245       if (! (ids->put(int_ptr, numNodes)) )
246            throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
247    
248       // Nodes grDof
249       if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
250            throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
251       int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
252       if (! (ids->put(int_ptr, numNodes)) )
253            throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
254    
255       // Nodes grNI
256       if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
257            throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
258       int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
259       if (! (ids->put(int_ptr, numNodes)) )
260            throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
261    
262       // Nodes Coordinates
263       if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
264            throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
265       if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
266            throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
267    
268       // Nodes degreesOfFreedomDistribution
269       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
270            throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
271       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
272       if (! (ids->put(int_ptr, mpi_size+1)) )
273            throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
274    
275       }
276    
277       // // // // // Elements // // // // //
278    
279       if (num_Elements>0) {
280    
281         // Temp storage to gather node IDs
282         int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);
283    
284         // Elements_Id
285         if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
286            throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
287         int_ptr = &mesh->Elements->Id[0];
288         if (! (ids->put(int_ptr, num_Elements)) )
289            throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
290    
291         // Elements_Tag
292         if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
293            throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
294         int_ptr = &mesh->Elements->Tag[0];
295         if (! (ids->put(int_ptr, num_Elements)) )
296            throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
297    
298         // Elements_Owner
299         if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
300            throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
301         int_ptr = &mesh->Elements->Owner[0];
302         if (! (ids->put(int_ptr, num_Elements)) )
303            throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
304    
305         // Elements_Color
306         if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
307            throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
308         int_ptr = &mesh->Elements->Color[0];
309         if (! (ids->put(int_ptr, num_Elements)) )
310            throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
311    
312         // Elements_Nodes
313         for (int i=0; i<num_Elements; i++)
314           for (int j=0; j<num_Elements_numNodes; j++)
315             Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];
316         if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
317            throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
318         if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )
319            throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
320    
321         TMPMEMFREE(Elements_Nodes);
322    
323       }
324    
325       // // // // // Face_Elements // // // // //
326    
327       if (num_FaceElements>0) {
328    
329         // Temp storage to gather node IDs
330         int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);
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         for (int i=0; i<num_FaceElements; i++)
362           for (int j=0; j<num_FaceElements_numNodes; j++)
363             FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];
364         if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
365            throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
366         if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
367            throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
368    
369         TMPMEMFREE(FaceElements_Nodes);
370    
371       }
372    
373       // // // // // Contact_Elements // // // // //
374    
375       if (num_ContactElements>0) {
376    
377         // Temp storage to gather node IDs
378         int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);
379    
380         // ContactElements_Id
381         if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
382            throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
383         int_ptr = &mesh->ContactElements->Id[0];
384         if (! (ids->put(int_ptr, num_ContactElements)) )
385            throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
386    
387         // ContactElements_Tag
388         if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
389            throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
390         int_ptr = &mesh->ContactElements->Tag[0];
391         if (! (ids->put(int_ptr, num_ContactElements)) )
392            throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
393    
394         // ContactElements_Owner
395         if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
396            throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
397         int_ptr = &mesh->ContactElements->Owner[0];
398         if (! (ids->put(int_ptr, num_ContactElements)) )
399            throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
400    
401         // ContactElements_Color
402         if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
403            throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
404         int_ptr = &mesh->ContactElements->Color[0];
405         if (! (ids->put(int_ptr, num_ContactElements)) )
406            throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
407    
408         // ContactElements_Nodes
409         for (int i=0; i<num_ContactElements; i++)
410           for (int j=0; j<num_ContactElements_numNodes; j++)
411             ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];
412         if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
413            throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
414         if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
415            throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
416    
417         TMPMEMFREE(ContactElements_Nodes);
418    
419       }
420    
421       // // // // // Points // // // // //
422    
423       if (num_Points>0) {
424    
425         fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
426    
427         // Temp storage to gather node IDs
428         int *Points_Nodes = TMPMEMALLOC(num_Points,int);
429    
430         // Points_Id
431         if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
432            throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
433         int_ptr = &mesh->Points->Id[0];
434         if (! (ids->put(int_ptr, num_Points)) )
435            throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
436    
437         // Points_Tag
438         if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
439            throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
440         int_ptr = &mesh->Points->Tag[0];
441         if (! (ids->put(int_ptr, num_Points)) )
442            throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
443    
444         // Points_Owner
445         if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
446            throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
447         int_ptr = &mesh->Points->Owner[0];
448         if (! (ids->put(int_ptr, num_Points)) )
449            throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
450    
451         // Points_Color
452         if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
453            throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
454         int_ptr = &mesh->Points->Color[0];
455         if (! (ids->put(int_ptr, num_Points)) )
456            throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
457    
458         // Points_Nodes
459         // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
460         for (int i=0; i<num_Points; i++)
461           Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];
462         if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
463            throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
464         if (! (ids->put(&(Points_Nodes[0]), num_Points)) )
465            throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
466    
467         TMPMEMFREE(Points_Nodes);
468    
469       }
470    
471       // // // // // TagMap // // // // //
472    
473       if (num_Tags>0) {
474    
475         // Temp storage to gather node IDs
476         int *Tags_keys = TMPMEMALLOC(num_Tags, int);
477         char name_temp[4096];
478    
479         /* Copy tag data into temp arrays */
480         tag_map = mesh->TagMap;
481         if (tag_map) {
482           int i = 0;
483           while (tag_map) {
484        Tags_keys[i++] = tag_map->tag_key;
485            tag_map=tag_map->next;
486           }
487         }
488    
489         // Tags_keys
490         if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
491            throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
492         int_ptr = &Tags_keys[0];
493         if (! (ids->put(int_ptr, num_Tags)) )
494            throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
495    
496         // Tags_names_*
497         // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
498         // because the NetCDF manual doesn't tell how to do an array of strings
499         tag_map = mesh->TagMap;
500         if (tag_map) {
501           int i = 0;
502           while (tag_map) {
503             sprintf(name_temp, "Tags_name_%d", i);
504             if (!dataFile.add_att(name_temp, tag_map->name) )
505               throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
506             tag_map=tag_map->next;
507         i++;
508           }
509         }
510    
511         TMPMEMFREE(Tags_keys);
512    
513       }
514    
515    
516       // NetCDF file is closed by destructor of NcFile object
517    #else
518       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
519    #endif  /* USE_NETCDF */
520       checkFinleyError();
521  }  }
522    
523  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
# Line 108  void MeshAdapter::setFunctionSpaceTypeNa Line 552  void MeshAdapter::setFunctionSpaceTypeNa
552    m_functionSpaceTypeNames.insert    m_functionSpaceTypeNames.insert
553      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
554    m_functionSpaceTypeNames.insert    m_functionSpaceTypeNames.insert
555        (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
556      m_functionSpaceTypeNames.insert
557      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
558    m_functionSpaceTypeNames.insert    m_functionSpaceTypeNames.insert
559        (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
560      m_functionSpaceTypeNames.insert
561      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
562    m_functionSpaceTypeNames.insert    m_functionSpaceTypeNames.insert
563        (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
564      m_functionSpaceTypeNames.insert
565      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
566    m_functionSpaceTypeNames.insert    m_functionSpaceTypeNames.insert
567      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
568    m_functionSpaceTypeNames.insert    m_functionSpaceTypeNames.insert
569        (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
570      m_functionSpaceTypeNames.insert
571      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
572      m_functionSpaceTypeNames.insert
573        (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
574  }  }
575    
576  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
577  {  {
578    return Nodes;    return Nodes;
579  }  }
580    int MeshAdapter::getReducedContinuousFunctionCode() const
581    {
582      return ReducedNodes;
583    }
584    
585  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
586  {  {
587    return Elements;    return Elements;
588  }  }
589    int MeshAdapter::getReducedFunctionCode() const
590    {
591      return ReducedElements;
592    }
593    
594  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
595  {  {
596    return FaceElements;    return FaceElements;
597  }  }
598    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
599    {
600      return ReducedFaceElements;
601    }
602    
603  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
604  {  {
605    return ContactElementsZero;    return ContactElementsZero;
606  }  }
607    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
608    {
609      return ReducedContactElementsZero;
610    }
611    
612  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
613  {  {
614    return ContactElementsOne;    return ContactElementsOne;
615  }  }
616    int MeshAdapter::getReducedFunctionOnContactOneCode() const
617    {
618      return ReducedContactElementsOne;
619    }
620    
621  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
622  {  {
# Line 181  pair<int,int> MeshAdapter::getDataShape( Line 655  pair<int,int> MeshAdapter::getDataShape(
655     switch (functionSpaceCode) {     switch (functionSpaceCode) {
656        case(Nodes):        case(Nodes):
657             numDataPointsPerSample=1;             numDataPointsPerSample=1;
658             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
659               break;
660          case(ReducedNodes):
661               numDataPointsPerSample=1;
662               numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
663             break;             break;
664        case(Elements):        case(Elements):
665             if (mesh->Elements!=NULL) {             if (mesh->Elements!=NULL) {
# Line 189  pair<int,int> MeshAdapter::getDataShape( Line 667  pair<int,int> MeshAdapter::getDataShape(
667               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
668             }             }
669             break;             break;
670          case(ReducedElements):
671               if (mesh->Elements!=NULL) {
672                 numSamples=mesh->Elements->numElements;
673                 numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
674               }
675               break;
676        case(FaceElements):        case(FaceElements):
677             if (mesh->FaceElements!=NULL) {             if (mesh->FaceElements!=NULL) {
678                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
679                  numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
680             }             }
681             break;             break;
682          case(ReducedFaceElements):
683               if (mesh->FaceElements!=NULL) {
684                    numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
685                    numSamples=mesh->FaceElements->numElements;
686               }
687               break;
688        case(Points):        case(Points):
689             if (mesh->Points!=NULL) {             if (mesh->Points!=NULL) {
690               numDataPointsPerSample=1;               numDataPointsPerSample=1;
# Line 207  pair<int,int> MeshAdapter::getDataShape( Line 697  pair<int,int> MeshAdapter::getDataShape(
697               numSamples=mesh->ContactElements->numElements;               numSamples=mesh->ContactElements->numElements;
698             }             }
699             break;             break;
700          case(ReducedContactElementsZero):
701               if (mesh->ContactElements!=NULL) {
702                 numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
703                 numSamples=mesh->ContactElements->numElements;
704               }
705               break;
706        case(ContactElementsOne):        case(ContactElementsOne):
707             if (mesh->ContactElements!=NULL) {             if (mesh->ContactElements!=NULL) {
708               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
709               numSamples=mesh->ContactElements->numElements;               numSamples=mesh->ContactElements->numElements;
710             }             }
711             break;             break;
712          case(ReducedContactElementsOne):
713               if (mesh->ContactElements!=NULL) {
714                 numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
715                 numSamples=mesh->ContactElements->numElements;
716               }
717               break;
718        case(DegreesOfFreedom):        case(DegreesOfFreedom):
719             if (mesh->Nodes!=NULL) {             if (mesh->Nodes!=NULL) {
720               numDataPointsPerSample=1;               numDataPointsPerSample=1;
721               numSamples=mesh->Nodes->numDegreesOfFreedom;               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
722             }             }
723             break;             break;
724        case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
725             if (mesh->Nodes!=NULL) {             if (mesh->Nodes!=NULL) {
726               numDataPointsPerSample=1;               numDataPointsPerSample=1;
727               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
728             }             }
729             break;             break;
730        default:        default:
# Line 243  void MeshAdapter::addPDEToSystem( Line 745  void MeshAdapter::addPDEToSystem(
745                       const escript::Data& d, const escript::Data& y,                       const escript::Data& d, const escript::Data& y,
746                       const escript::Data& d_contact,const escript::Data& y_contact) const                       const escript::Data& d_contact,const escript::Data& y_contact) const
747  {  {
748       escriptDataC _rhs=rhs.getDataC();
749       escriptDataC _A  =A.getDataC();
750       escriptDataC _B=B.getDataC();
751       escriptDataC _C=C.getDataC();
752       escriptDataC _D=D.getDataC();
753       escriptDataC _X=X.getDataC();
754       escriptDataC _Y=Y.getDataC();
755       escriptDataC _d=d.getDataC();
756       escriptDataC _y=y.getDataC();
757       escriptDataC _d_contact=d_contact.getDataC();
758       escriptDataC _y_contact=y_contact.getDataC();
759    
760     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
761     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(),&(rhs.getDataC()),  
762                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
763       checkFinleyError();
764    
765       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
766       checkFinleyError();
767    
768       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
769     checkFinleyError();     checkFinleyError();
770     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,  }
771                    mat.getPaso_SystemMatrix(),  
772                    &(rhs.getDataC()),  void  MeshAdapter::addPDEToLumpedSystem(
773                                    &(d.getDataC()),&(y.getDataC()),                       escript::Data& mat,
774                                    Finley_Assemble_handelShapeMissMatch_Mean_out);                       const escript::Data& D,
775     checkFinleyError();                       const escript::Data& d) const
776     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,  {
777                    mat.getPaso_SystemMatrix(),     escriptDataC _mat=mat.getDataC();
778                    &(rhs.getDataC()),     escriptDataC _D=D.getDataC();
779                                    &(d_contact.getDataC()),     escriptDataC _d=d.getDataC();
780                    &(y_contact.getDataC()),  
781                                    Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Mesh* mesh=m_finleyMesh.get();
782    
783       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
784       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
785    
786     checkFinleyError();     checkFinleyError();
787  }  }
788    
789    
790  //  //
791  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
792  //  //
793  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  
794  {  {
795     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
796    
797     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
798     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
799       escriptDataC _Y=Y.getDataC();
800       escriptDataC _y=y.getDataC();
801       escriptDataC _y_contact=y_contact.getDataC();
802    
803       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
804     checkFinleyError();     checkFinleyError();
805    
806     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->FaceElements,&(rhs.getDataC()),&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
807     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
808    
809       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
810     checkFinleyError();     checkFinleyError();
811     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  }
812     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->ContactElements,&(rhs.getDataC()),&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  //
813    // adds PDE of second order into a transport problem
814    //
815    void MeshAdapter::addPDEToTransportProblem(
816                         TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
817                         const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
818                         const escript::Data& d, const escript::Data& y,
819                         const escript::Data& d_contact,const escript::Data& y_contact) const
820    {
821       DataArrayView::ShapeType shape;
822       source.expand();
823       escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true);
824       escriptDataC _source=source.getDataC();
825       escriptDataC _tmp=tmp.getDataC();
826       escriptDataC _M=M.getDataC();
827       escriptDataC _A=A.getDataC();
828       escriptDataC _B=B.getDataC();
829       escriptDataC _C=C.getDataC();
830       escriptDataC _D=D.getDataC();
831       escriptDataC _X=X.getDataC();
832       escriptDataC _Y=Y.getDataC();
833       escriptDataC _d=d.getDataC();
834       escriptDataC _y=y.getDataC();
835       escriptDataC _d_contact=d_contact.getDataC();
836       escriptDataC _y_contact=y_contact.getDataC();
837    
838       Finley_Mesh* mesh=m_finleyMesh.get();
839       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
840      
841    
842       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_tmp, &_M);
843       checkFinleyError();
844       /* add mass matix to lumped mass matrix of transport problem */
845       double* tmp_prt=getSampleData(&_tmp,0);
846       int i;
847       int n=Paso_FCTransportProblem_getTotalNumRows(_tp);
848       #pragma omp parallel for private(i) schedule(static)
849       for (i=0;i<n ;++i) _tp->lumped_mass_matrix[i]+=tmp_prt[i];
850    
851       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, 0, 0, &_D, &_X, &_Y );
852       checkFinleyError();
853    
854       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->flux_matrix, &_source, 0, &_B, &_C, 0, 0, 0 );
855       checkFinleyError();
856    
857       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
858       checkFinleyError();
859    
860       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
861     checkFinleyError();     checkFinleyError();
862  }  }
863    
# Line 290  void MeshAdapter::interpolateOnDomain(es Line 868  void MeshAdapter::interpolateOnDomain(es
868  {  {
869    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
870    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
871    if (inDomain!=*this)    if (inDomain!=*this)  
872       throw FinleyAdapterException("Error - Illegal domain of interpolant.");      throw FinleyAdapterException("Error - Illegal domain of interpolant.");
873    if (targetDomain!=*this)    if (targetDomain!=*this)
874       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
875    
876    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
877      escriptDataC _target=target.getDataC();
878      escriptDataC _in=in.getDataC();
879    switch(in.getFunctionSpace().getTypeCode()) {    switch(in.getFunctionSpace().getTypeCode()) {
880       case(Nodes):       case(Nodes):
881          switch(target.getFunctionSpace().getTypeCode()) {          switch(target.getFunctionSpace().getTypeCode()) {
882             case(Nodes):             case(Nodes):
883               case(ReducedNodes):
884               case(DegreesOfFreedom):
885             case(ReducedDegreesOfFreedom):             case(ReducedDegreesOfFreedom):
886                   Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
887                   break;
888               case(Elements):
889               case(ReducedElements):
890                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
891                   break;
892               case(FaceElements):
893               case(ReducedFaceElements):
894                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
895                   break;
896               case(Points):
897                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
898                   break;
899               case(ContactElementsZero):
900               case(ReducedContactElementsZero):
901                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
902                   break;
903               case(ContactElementsOne):
904               case(ReducedContactElementsOne):
905                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
906                   break;
907               default:
908                   stringstream temp;
909                   temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
910                   throw FinleyAdapterException(temp.str());
911                   break;
912            }
913            break;
914         case(ReducedNodes):
915            switch(target.getFunctionSpace().getTypeCode()) {
916               case(Nodes):
917               case(ReducedNodes):
918             case(DegreesOfFreedom):             case(DegreesOfFreedom):
919                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));             case(ReducedDegreesOfFreedom):
920                   Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
921                 break;                 break;
922             case(Elements):             case(Elements):
923                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));             case(ReducedElements):
924                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
925                 break;                 break;
926             case(FaceElements):             case(FaceElements):
927                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));             case(ReducedFaceElements):
928                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
929                 break;                 break;
930             case(Points):             case(Points):
931                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
932                 break;                 break;
933             case(ContactElementsZero):             case(ContactElementsZero):
934                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));             case(ReducedContactElementsZero):
935                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
936                 break;                 break;
937             case(ContactElementsOne):             case(ContactElementsOne):
938                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));             case(ReducedContactElementsOne):
939                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
940                 break;                 break;
941             default:             default:
942                 stringstream temp;                 stringstream temp;
# Line 328  void MeshAdapter::interpolateOnDomain(es Line 947  void MeshAdapter::interpolateOnDomain(es
947          break;          break;
948       case(Elements):       case(Elements):
949          if (target.getFunctionSpace().getTypeCode()==Elements) {          if (target.getFunctionSpace().getTypeCode()==Elements) {
950             Finley_Assemble_CopyElementData(mesh->Elements,&(target.getDataC()),&(in.getDataC()));             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
951            } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
952               Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
953          } else {          } else {
954             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
955          }          }
956          break;          break;
957         case(ReducedElements):
958            if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
959               Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
960            } else {
961               throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
962            }
963            break;
964       case(FaceElements):       case(FaceElements):
965          if (target.getFunctionSpace().getTypeCode()==FaceElements) {          if (target.getFunctionSpace().getTypeCode()==FaceElements) {
966             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
967            } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
968               Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
969          } else {          } else {
970             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
971             break;          }
972            break;
973         case(ReducedFaceElements):
974            if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
975               Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
976            } else {
977               throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
978         }         }
979           break;
980       case(Points):       case(Points):
981          if (target.getFunctionSpace().getTypeCode()==Points) {          if (target.getFunctionSpace().getTypeCode()==Points) {
982             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
983          } else {          } else {
984             throw FinleyAdapterException("Error - No interpolation with data on points possible.");             throw FinleyAdapterException("Error - No interpolation with data on points possible.");
            break;  
985          }          }
986          break;          break;
987       case(ContactElementsZero):       case(ContactElementsZero):
988       case(ContactElementsOne):       case(ContactElementsOne):
989          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
990             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
991            } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
992               Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
993          } else {          } else {
994             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
            break;  
995          }          }
996          break;          break;
997       case(DegreesOfFreedom):       case(ReducedContactElementsZero):
998         case(ReducedContactElementsOne):
999            if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1000               Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1001            } else {
1002               throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1003            }
1004            break;
1005         case(DegreesOfFreedom):      
1006          switch(target.getFunctionSpace().getTypeCode()) {          switch(target.getFunctionSpace().getTypeCode()) {
1007             case(ReducedDegreesOfFreedom):             case(ReducedDegreesOfFreedom):
1008             case(DegreesOfFreedom):             case(DegreesOfFreedom):
1009                  Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1010                  break;
1011    
1012             case(Nodes):             case(Nodes):
1013                Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));             case(ReducedNodes):
1014                  if (getMPISize()>1) {
1015                      escript::Data temp=escript::Data(in);
1016                      temp.expand();
1017                      escriptDataC _in2 = temp.getDataC();
1018                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1019                  } else {
1020                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1021                  }
1022                break;                break;
1023             case(Elements):             case(Elements):
1024                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));             case(ReducedElements):
1025                  if (getMPISize()>1) {
1026                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1027                     escriptDataC _in2 = temp.getDataC();
1028                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1029                  } else {
1030                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1031                  }
1032                break;                break;
1033             case(FaceElements):             case(FaceElements):
1034                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));             case(ReducedFaceElements):
1035                  if (getMPISize()>1) {
1036                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1037                     escriptDataC _in2 = temp.getDataC();
1038                     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1039    
1040                  } else {
1041                     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1042                  }
1043                break;                break;
1044             case(Points):             case(Points):
1045                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));                if (getMPISize()>1) {
1046                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1047                     escriptDataC _in2 = temp.getDataC();
1048                  } else {
1049                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1050                  }
1051                break;                break;
1052             case(ContactElementsZero):             case(ContactElementsZero):
1053             case(ContactElementsOne):             case(ContactElementsOne):
1054                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));             case(ReducedContactElementsZero):
1055               case(ReducedContactElementsOne):
1056                  if (getMPISize()>1) {
1057                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1058                     escriptDataC _in2 = temp.getDataC();
1059                     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1060                  } else {
1061                     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1062                  }
1063               break;               break;
1064             default:             default:
1065               stringstream temp;               stringstream temp;
# Line 386  void MeshAdapter::interpolateOnDomain(es Line 1070  void MeshAdapter::interpolateOnDomain(es
1070          break;          break;
1071       case(ReducedDegreesOfFreedom):       case(ReducedDegreesOfFreedom):
1072         switch(target.getFunctionSpace().getTypeCode()) {         switch(target.getFunctionSpace().getTypeCode()) {
1073              case(Nodes):
1074                 throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1075                 break;
1076              case(ReducedNodes):
1077                  if (getMPISize()>1) {
1078                      escript::Data temp=escript::Data(in);
1079                      temp.expand();
1080                      escriptDataC _in2 = temp.getDataC();
1081                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1082                  } else {
1083                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1084                  }
1085                  break;
1086              case(DegreesOfFreedom):
1087                 throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1088                 break;
1089            case(ReducedDegreesOfFreedom):            case(ReducedDegreesOfFreedom):
1090               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1091               break;               break;
1092            case(Elements):            case(Elements):
1093               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));            case(ReducedElements):
1094                  if (getMPISize()>1) {
1095                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1096                     escriptDataC _in2 = temp.getDataC();
1097                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1098                  } else {
1099                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1100                 }
1101               break;               break;
1102            case(FaceElements):            case(FaceElements):
1103               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));            case(ReducedFaceElements):
1104                  if (getMPISize()>1) {
1105                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1106                     escriptDataC _in2 = temp.getDataC();
1107                     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1108                  } else {
1109                     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1110                  }
1111               break;               break;
1112            case(Points):            case(Points):
1113               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));                if (getMPISize()>1) {
1114                     escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1115                     escriptDataC _in2 = temp.getDataC();
1116                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1117                  } else {
1118                     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1119                 }
1120               break;               break;
1121            case(ContactElementsZero):            case(ContactElementsZero):
1122            case(ContactElementsOne):            case(ContactElementsOne):
1123               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));            case(ReducedContactElementsZero):
1124               break;            case(ReducedContactElementsOne):
1125            case(Nodes):                if (getMPISize()>1) {
1126               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1127               break;                   escriptDataC _in2 = temp.getDataC();
1128            case(DegreesOfFreedom):                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1129               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                } else {
1130                     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1131                 }
1132               break;               break;
1133            default:            default:
1134               stringstream temp;               stringstream temp;
# Line 435  void MeshAdapter::setToX(escript::Data& Line 1157  void MeshAdapter::setToX(escript::Data&
1157    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
1158    // in case of values node coordinates we can do the job directly:    // in case of values node coordinates we can do the job directly:
1159    if (arg.getFunctionSpace().getTypeCode()==Nodes) {    if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1160       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));       escriptDataC _arg=arg.getDataC();
1161         Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1162    } else {    } else {
1163       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1164       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));       escriptDataC _tmp_data=tmp_data.getDataC();
1165         Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1166       // this is then interpolated onto arg:       // this is then interpolated onto arg:
1167       interpolateOnDomain(arg,tmp_data);       interpolateOnDomain(arg,tmp_data);
1168    }    }
# Line 454  void MeshAdapter::setToNormal(escript::D Line 1178  void MeshAdapter::setToNormal(escript::D
1178    if (normalDomain!=*this)    if (normalDomain!=*this)
1179       throw FinleyAdapterException("Error - Illegal domain of normal locations");       throw FinleyAdapterException("Error - Illegal domain of normal locations");
1180    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
1181      escriptDataC _normal=normal.getDataC();
1182    switch(normal.getFunctionSpace().getTypeCode()) {    switch(normal.getFunctionSpace().getTypeCode()) {
1183      case(Nodes):      case(Nodes):
1184        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1185        break;        break;
1186        case(ReducedNodes):
1187          throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1188          break;
1189      case(Elements):      case(Elements):
1190        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1191        break;        break;
1192        case(ReducedElements):
1193          throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1194          break;
1195      case (FaceElements):      case (FaceElements):
1196        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1197          break;
1198        case (ReducedFaceElements):
1199          Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1200        break;        break;
1201      case(Points):      case(Points):
1202        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1203        break;        break;
1204      case (ContactElementsOne):      case (ContactElementsOne):
1205      case (ContactElementsZero):      case (ContactElementsZero):
1206        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1207          break;
1208        case (ReducedContactElementsOne):
1209        case (ReducedContactElementsZero):
1210          Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1211        break;        break;
1212      case(DegreesOfFreedom):      case(DegreesOfFreedom):
1213        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
# Line 507  void MeshAdapter::setToIntegrals(std::ve Line 1245  void MeshAdapter::setToIntegrals(std::ve
1245    if (argDomain!=*this)    if (argDomain!=*this)
1246       throw FinleyAdapterException("Error - Illegal domain of integration kernel");       throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1247    
1248      double blocktimer_start = blocktimer_time();
1249    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
1250      escriptDataC _temp;
1251      escript::Data temp;
1252      escriptDataC _arg=arg.getDataC();
1253    switch(arg.getFunctionSpace().getTypeCode()) {    switch(arg.getFunctionSpace().getTypeCode()) {
1254       case(Nodes):       case(Nodes):
1255          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1256            _temp=temp.getDataC();
1257            Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1258            break;
1259         case(ReducedNodes):
1260            temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1261            _temp=temp.getDataC();
1262            Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1263          break;          break;
1264       case(Elements):       case(Elements):
1265          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1266            break;
1267         case(ReducedElements):
1268            Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1269          break;          break;
1270       case(FaceElements):       case(FaceElements):
1271          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1272            break;
1273         case(ReducedFaceElements):
1274            Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1275          break;          break;
1276       case(Points):       case(Points):
1277          throw FinleyAdapterException("Error - Integral of data on points is not supported.");          throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1278          break;          break;
1279       case(ContactElementsZero):       case(ContactElementsZero):
1280          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1281            break;
1282         case(ReducedContactElementsZero):
1283            Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1284          break;          break;
1285       case(ContactElementsOne):       case(ContactElementsOne):
1286          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287            break;
1288         case(ReducedContactElementsOne):
1289            Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1290          break;          break;
1291       case(DegreesOfFreedom):       case(DegreesOfFreedom):
1292          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1293            _temp=temp.getDataC();
1294            Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1295          break;          break;
1296       case(ReducedDegreesOfFreedom):       case(ReducedDegreesOfFreedom):
1297          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1298            _temp=temp.getDataC();
1299            Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1300          break;          break;
1301       default:       default:
1302          stringstream temp;          stringstream temp;
# Line 540  void MeshAdapter::setToIntegrals(std::ve Line 1305  void MeshAdapter::setToIntegrals(std::ve
1305          break;          break;
1306    }    }
1307    checkFinleyError();    checkFinleyError();
1308      blocktimer_increment("integrate()", blocktimer_start);
1309  }  }
1310    
1311  //  //
# Line 555  void MeshAdapter::setToGradient(escript: Line 1321  void MeshAdapter::setToGradient(escript:
1321       throw FinleyAdapterException("Error - Illegal domain of gradient");       throw FinleyAdapterException("Error - Illegal domain of gradient");
1322    
1323    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
1324      escriptDataC _grad=grad.getDataC();
1325      escriptDataC nodeDataC;
1326      escript::Data temp;
1327      if (getMPISize()>1) {
1328          if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1329            temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1330            nodeDataC = temp.getDataC();
1331          } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1332            temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1333            nodeDataC = temp.getDataC();
1334          } else {
1335            nodeDataC = arg.getDataC();
1336          }
1337      } else {
1338         nodeDataC = arg.getDataC();
1339      }
1340    switch(grad.getFunctionSpace().getTypeCode()) {    switch(grad.getFunctionSpace().getTypeCode()) {
1341         case(Nodes):         case(Nodes):
1342            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1343            break;            break;
1344           case(ReducedNodes):
1345              throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1346              break;
1347         case(Elements):         case(Elements):
1348            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1349              break;
1350           case(ReducedElements):
1351              Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1352            break;            break;
1353         case(FaceElements):         case(FaceElements):
1354            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1355              break;
1356           case(ReducedFaceElements):
1357              Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1358            break;            break;
1359         case(Points):         case(Points):
1360            throw FinleyAdapterException("Error - Gradient at points is not supported.");            throw FinleyAdapterException("Error - Gradient at points is not supported.");
1361            break;            break;
1362         case(ContactElementsZero):         case(ContactElementsZero):
1363            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1364              break;
1365           case(ReducedContactElementsZero):
1366              Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1367            break;            break;
1368         case(ContactElementsOne):         case(ContactElementsOne):
1369            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370              break;
1371           case(ReducedContactElementsOne):
1372              Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1373            break;            break;
1374         case(DegreesOfFreedom):         case(DegreesOfFreedom):
1375            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
# Line 600  void MeshAdapter::setToSize(escript::Dat Line 1397  void MeshAdapter::setToSize(escript::Dat
1397         case(Nodes):         case(Nodes):
1398            throw FinleyAdapterException("Error - Size of nodes is not supported.");            throw FinleyAdapterException("Error - Size of nodes is not supported.");
1399            break;            break;
1400           case(ReducedNodes):
1401              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1402              break;
1403         case(Elements):         case(Elements):
1404            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1405            break;            break;
1406           case(ReducedElements):
1407              Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1408              break;
1409         case(FaceElements):         case(FaceElements):
1410            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1411            break;            break;
1412           case(ReducedFaceElements):
1413              Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1414              break;
1415         case(Points):         case(Points):
1416            throw FinleyAdapterException("Error - Size of point elements is not supported.");            throw FinleyAdapterException("Error - Size of point elements is not supported.");
1417            break;            break;
# Line 613  void MeshAdapter::setToSize(escript::Dat Line 1419  void MeshAdapter::setToSize(escript::Dat
1419         case(ContactElementsOne):         case(ContactElementsOne):
1420            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1421            break;            break;
1422           case(ReducedContactElementsZero):
1423           case(ReducedContactElementsOne):
1424              Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1425              break;
1426         case(DegreesOfFreedom):         case(DegreesOfFreedom):
1427            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1428            break;            break;
# Line 632  void MeshAdapter::setToSize(escript::Dat Line 1442  void MeshAdapter::setToSize(escript::Dat
1442  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1443  {  {
1444    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
1445      escriptDataC tmp;
1446    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1447    if (newDomain!=*this)    if (newDomain!=*this)
1448       throw FinleyAdapterException("Error - Illegal domain of new point locations");       throw FinleyAdapterException("Error - Illegal domain of new point locations");
1449    Finley_Mesh_setCoordinates(mesh,&(new_x.getDataC()));    tmp = new_x.getDataC();
1450      Finley_Mesh_setCoordinates(mesh,&tmp);
1451    checkFinleyError();    checkFinleyError();
1452  }  }
1453    
# Line 644  void MeshAdapter::saveDX(const std::stri Line 1456  void MeshAdapter::saveDX(const std::stri
1456  {  {
1457      int MAX_namelength=256;      int MAX_namelength=256;
1458      const int num_data=boost::python::extract<int>(arg.attr("__len__")());      const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1459      char names[num_data][MAX_namelength];    /* win32 refactor */
1460      char* c_names[num_data];    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1461      escriptDataC data[num_data];    for(int i=0;i<num_data;i++)
1462      escriptDataC* ptr_data[num_data];    {
1463        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1464      }
1465    
1466      boost::python::list keys=arg.keys();    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1467      for (int i=0;i<num_data;++i) {    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1468      escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1469    
1470      boost::python::list keys=arg.keys();
1471      for (int i=0;i<num_data;++i) {
1472             std::string n=boost::python::extract<std::string>(keys[i]);
1473           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1474           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1475               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1476           data[i]=d.getDataC();           data[i]=d.getDataC();
1477           ptr_data[i]=&(data[i]);           ptr_data[i]=&(data[i]);
          std::string n=boost::python::extract<std::string>(keys[i]);  
1478           c_names[i]=&(names[i][0]);           c_names[i]=&(names[i][0]);
1479           if (n.length()>MAX_namelength-1) {           if (n.length()>MAX_namelength-1) {
1480              strncpy(c_names[i],n.c_str(),MAX_namelength-1);              strncpy(c_names[i],n.c_str(),MAX_namelength-1);
# Line 667  void MeshAdapter::saveDX(const std::stri Line 1485  void MeshAdapter::saveDX(const std::stri
1485      }      }
1486      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);
1487      checkFinleyError();      checkFinleyError();
1488        
1489          /* win32 refactor */
1490      TMPMEMFREE(c_names);
1491      TMPMEMFREE(data);
1492      TMPMEMFREE(ptr_data);
1493      for(int i=0;i<num_data;i++)
1494      {
1495        TMPMEMFREE(names[i]);
1496      }
1497      TMPMEMFREE(names);
1498    
1499      return;      return;
1500  }  }
1501    
# Line 675  void MeshAdapter::saveVTK(const std::str Line 1504  void MeshAdapter::saveVTK(const std::str
1504  {  {
1505      int MAX_namelength=256;      int MAX_namelength=256;
1506      const int num_data=boost::python::extract<int>(arg.attr("__len__")());      const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1507      char names[num_data][MAX_namelength];    /* win32 refactor */
1508      char* c_names[num_data];    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1509      escriptDataC data[num_data];    for(int i=0;i<num_data;i++)
1510      escriptDataC* ptr_data[num_data];    {
1511        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1512      }
1513    
1514      char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1515      escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1516      escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1517    
1518      boost::python::list keys=arg.keys();      boost::python::list keys=arg.keys();
1519      for (int i=0;i<num_data;++i) {      for (int i=0;i<num_data;++i) {
1520             std::string n=boost::python::extract<std::string>(keys[i]);
1521           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1522           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1523               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1524           data[i]=d.getDataC();           data[i]=d.getDataC();
1525           ptr_data[i]=&(data[i]);           ptr_data[i]=&(data[i]);
          std::string n=boost::python::extract<std::string>(keys[i]);  
1526           c_names[i]=&(names[i][0]);           c_names[i]=&(names[i][0]);
1527           if (n.length()>MAX_namelength-1) {           if (n.length()>MAX_namelength-1) {
1528              strncpy(c_names[i],n.c_str(),MAX_namelength-1);              strncpy(c_names[i],n.c_str(),MAX_namelength-1);
# Line 697  void MeshAdapter::saveVTK(const std::str Line 1532  void MeshAdapter::saveVTK(const std::str
1532           }           }
1533      }      }
1534      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);
1535      checkFinleyError();  
1536      checkFinleyError();
1537      /* win32 refactor */
1538      TMPMEMFREE(c_names);
1539      TMPMEMFREE(data);
1540      TMPMEMFREE(ptr_data);
1541      for(int i=0;i<num_data;i++)
1542      {
1543        TMPMEMFREE(names[i]);
1544      }
1545      TMPMEMFREE(names);
1546    
1547      return;      return;
1548  }  }
1549                                                                                                                                                                                                                                                                                                                                                    
# Line 738  SystemMatrixAdapter MeshAdapter::newSyst Line 1584  SystemMatrixAdapter MeshAdapter::newSyst
1584            
1585      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1586      checkFinleyError();      checkFinleyError();
1587      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);      Paso_SystemMatrix* fsystemMatrix;
1588        int trilinos = 0;
1589        if (trilinos) {
1590    #ifdef TRILINOS
1591          /* Allocation Epetra_VrbMatrix here */
1592    #endif
1593        }
1594        else {
1595          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1596        }
1597      checkPasoError();      checkPasoError();
1598      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1599      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1600  }  }
1601    // creates a TransportProblemAdapter
1602    TransportProblemAdapter MeshAdapter::newTransportProblem(
1603                          const double theta,
1604                          const double dt_max,
1605                          const int blocksize,
1606                          const escript::FunctionSpace& functionspace,
1607                          const int type) const
1608    {
1609        int reduceOrder=0;
1610        // is the domain right?
1611        const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1612        if (domain!=*this)
1613              throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1614        // is the function space type right
1615        if (functionspace.getTypeCode()==DegreesOfFreedom) {
1616            reduceOrder=0;
1617        } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1618            reduceOrder=1;
1619        } else {
1620            throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1621        }
1622        // generate matrix:
1623        
1624        Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1625        checkFinleyError();
1626        Paso_FCTransportProblem* transportProblem;
1627        transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize);
1628        checkPasoError();
1629        Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1630        return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace);
1631    }
1632    
1633  //  //
1634  // vtkObject MeshAdapter::createVtkObject() const  // vtkObject MeshAdapter::createVtkObject() const
# Line 764  bool MeshAdapter::isCellOriented(int fun Line 1650  bool MeshAdapter::isCellOriented(int fun
1650         case(Points):         case(Points):
1651         case(ContactElementsZero):         case(ContactElementsZero):
1652         case(ContactElementsOne):         case(ContactElementsOne):
1653           case(ReducedElements):
1654           case(ReducedFaceElements):
1655           case(ReducedContactElementsZero):
1656           case(ReducedContactElementsOne):
1657            return true;            return true;
1658            break;            break;
1659         default:         default:
# Line 782  bool MeshAdapter::probeInterpolationOnDo Line 1672  bool MeshAdapter::probeInterpolationOnDo
1672       case(Nodes):       case(Nodes):
1673          switch(functionSpaceType_target) {          switch(functionSpaceType_target) {
1674             case(Nodes):             case(Nodes):
1675               case(ReducedNodes):
1676             case(ReducedDegreesOfFreedom):             case(ReducedDegreesOfFreedom):
1677             case(DegreesOfFreedom):             case(DegreesOfFreedom):
1678             case(Elements):             case(Elements):
1679               case(ReducedElements):
1680             case(FaceElements):             case(FaceElements):
1681               case(ReducedFaceElements):
1682             case(Points):             case(Points):
1683             case(ContactElementsZero):             case(ContactElementsZero):
1684               case(ReducedContactElementsZero):
1685             case(ContactElementsOne):             case(ContactElementsOne):
1686               case(ReducedContactElementsOne):
1687                 return true;                 return true;
1688             default:             default:
1689                 stringstream temp;                 stringstream temp;
# Line 796  bool MeshAdapter::probeInterpolationOnDo Line 1691  bool MeshAdapter::probeInterpolationOnDo
1691                 throw FinleyAdapterException(temp.str());                 throw FinleyAdapterException(temp.str());
1692          }          }
1693          break;          break;
1694         case(ReducedNodes):
1695            switch(functionSpaceType_target) {
1696               case(ReducedNodes):
1697               case(ReducedDegreesOfFreedom):
1698               case(Elements):
1699               case(ReducedElements):
1700               case(FaceElements):
1701               case(ReducedFaceElements):
1702               case(Points):
1703               case(ContactElementsZero):
1704               case(ReducedContactElementsZero):
1705               case(ContactElementsOne):
1706               case(ReducedContactElementsOne):
1707                   return true;
1708              case(Nodes):
1709              case(DegreesOfFreedom):
1710                 return false;
1711               default:
1712                   stringstream temp;
1713                   temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1714                   throw FinleyAdapterException(temp.str());
1715            }
1716            break;
1717       case(Elements):       case(Elements):
1718          if (functionSpaceType_target==Elements) {          if (functionSpaceType_target==Elements) {
1719             return true;             return true;
1720            } else if (functionSpaceType_target==ReducedElements) {
1721               return true;
1722            } else {
1723               return false;
1724            }
1725         case(ReducedElements):
1726            if (functionSpaceType_target==ReducedElements) {
1727               return true;
1728          } else {          } else {
1729             return false;             return false;
1730          }          }
1731       case(FaceElements):       case(FaceElements):
1732          if (functionSpaceType_target==FaceElements) {          if (functionSpaceType_target==FaceElements) {
1733             return true;             return true;
1734            } else if (functionSpaceType_target==ReducedFaceElements) {
1735               return true;
1736            } else {
1737               return false;
1738            }
1739         case(ReducedFaceElements):
1740            if (functionSpaceType_target==ReducedFaceElements) {
1741               return true;
1742          } else {          } else {
1743             return false;             return false;
1744          }          }
# Line 818  bool MeshAdapter::probeInterpolationOnDo Line 1752  bool MeshAdapter::probeInterpolationOnDo
1752       case(ContactElementsOne):       case(ContactElementsOne):
1753          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1754             return true;             return true;
1755            } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1756               return true;
1757            } else {
1758               return false;
1759            }
1760         case(ReducedContactElementsZero):
1761         case(ReducedContactElementsOne):
1762            if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1763               return true;
1764          } else {          } else {
1765             return false;             return false;
1766          }          }
# Line 826  bool MeshAdapter::probeInterpolationOnDo Line 1769  bool MeshAdapter::probeInterpolationOnDo
1769             case(ReducedDegreesOfFreedom):             case(ReducedDegreesOfFreedom):
1770             case(DegreesOfFreedom):             case(DegreesOfFreedom):
1771             case(Nodes):             case(Nodes):
1772               case(ReducedNodes):
1773             case(Elements):             case(Elements):
1774             case(FaceElements):             case(ReducedElements):
1775             case(Points):             case(Points):
1776               case(FaceElements):
1777               case(ReducedFaceElements):
1778             case(ContactElementsZero):             case(ContactElementsZero):
1779               case(ReducedContactElementsZero):
1780             case(ContactElementsOne):             case(ContactElementsOne):
1781               case(ReducedContactElementsOne):
1782                return true;                return true;
1783             default:             default:
1784               stringstream temp;               stringstream temp;
# Line 841  bool MeshAdapter::probeInterpolationOnDo Line 1789  bool MeshAdapter::probeInterpolationOnDo
1789       case(ReducedDegreesOfFreedom):       case(ReducedDegreesOfFreedom):
1790         switch(functionSpaceType_target) {         switch(functionSpaceType_target) {
1791            case(ReducedDegreesOfFreedom):            case(ReducedDegreesOfFreedom):
1792              case(ReducedNodes):
1793            case(Elements):            case(Elements):
1794              case(ReducedElements):
1795            case(FaceElements):            case(FaceElements):
1796              case(ReducedFaceElements):
1797            case(Points):            case(Points):
1798            case(ContactElementsZero):            case(ContactElementsZero):
1799              case(ReducedContactElementsZero):
1800            case(ContactElementsOne):            case(ContactElementsOne):
1801              case(ReducedContactElementsOne):
1802                return true;                return true;
1803            case(Nodes):            case(Nodes):
1804            case(DegreesOfFreedom):            case(DegreesOfFreedom):
# Line 908  escript::Data MeshAdapter::getSize() con Line 1861  escript::Data MeshAdapter::getSize() con
1861    return function(asAbstractContinuousDomain()).getSize();    return function(asAbstractContinuousDomain()).getSize();
1862  }  }
1863    
1864    int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1865    {
1866      int *out=0,i;
1867      Finley_Mesh* mesh=m_finleyMesh.get();
1868      switch (functionSpaceType) {
1869        case(Nodes):
1870          out=mesh->Nodes->Id;
1871          break;
1872        case(ReducedNodes):
1873          out=mesh->Nodes->reducedNodesId;
1874          break;
1875        case(Elements):
1876          out=mesh->Elements->Id;
1877          break;
1878        case(ReducedElements):
1879          out=mesh->Elements->Id;
1880          break;
1881        case(FaceElements):
1882          out=mesh->FaceElements->Id;
1883          break;
1884        case(ReducedFaceElements):
1885          out=mesh->FaceElements->Id;
1886          break;
1887        case(Points):
1888          out=mesh->Points->Id;
1889          break;
1890        case(ContactElementsZero):
1891          out=mesh->ContactElements->Id;
1892          break;
1893        case(ReducedContactElementsZero):
1894          out=mesh->ContactElements->Id;
1895          break;
1896        case(ContactElementsOne):
1897          out=mesh->ContactElements->Id;
1898          break;
1899        case(ReducedContactElementsOne):
1900          out=mesh->ContactElements->Id;
1901          break;
1902        case(DegreesOfFreedom):
1903          out=mesh->Nodes->degreesOfFreedomId;
1904          break;
1905        case(ReducedDegreesOfFreedom):
1906          out=mesh->Nodes->reducedDegreesOfFreedomId;
1907          break;
1908        default:
1909          stringstream temp;
1910          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1911          throw FinleyAdapterException(temp.str());
1912          break;
1913      }
1914      return out;
1915    }
1916  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1917  {  {
1918    int out=0;    int out=0;
# Line 916  int MeshAdapter::getTagFromSampleNo(int Line 1921  int MeshAdapter::getTagFromSampleNo(int
1921    case(Nodes):    case(Nodes):
1922      out=mesh->Nodes->Tag[sampleNo];      out=mesh->Nodes->Tag[sampleNo];
1923      break;      break;
1924      case(ReducedNodes):
1925        throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1926        break;
1927    case(Elements):    case(Elements):
1928      out=mesh->Elements->Tag[sampleNo];      out=mesh->Elements->Tag[sampleNo];
1929      break;      break;
1930      case(ReducedElements):
1931        out=mesh->Elements->Tag[sampleNo];
1932        break;
1933    case(FaceElements):    case(FaceElements):
1934      out=mesh->FaceElements->Tag[sampleNo];      out=mesh->FaceElements->Tag[sampleNo];
1935      break;      break;
1936      case(ReducedFaceElements):
1937        out=mesh->FaceElements->Tag[sampleNo];
1938        break;
1939    case(Points):    case(Points):
1940      out=mesh->Points->Tag[sampleNo];      out=mesh->Points->Tag[sampleNo];
1941      break;      break;
1942    case(ContactElementsZero):    case(ContactElementsZero):
1943      out=mesh->ContactElements->Tag[sampleNo];      out=mesh->ContactElements->Tag[sampleNo];
1944      break;      break;
1945      case(ReducedContactElementsZero):
1946        out=mesh->ContactElements->Tag[sampleNo];
1947        break;
1948    case(ContactElementsOne):    case(ContactElementsOne):
1949      out=mesh->ContactElements->Tag[sampleNo];      out=mesh->ContactElements->Tag[sampleNo];
1950      break;      break;
1951      case(ReducedContactElementsOne):
1952        out=mesh->ContactElements->Tag[sampleNo];
1953        break;
1954    case(DegreesOfFreedom):    case(DegreesOfFreedom):
1955        throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1956      break;      break;
1957    case(ReducedDegreesOfFreedom):    case(ReducedDegreesOfFreedom):
1958        throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1959      break;      break;
1960    default:    default:
1961      stringstream temp;      stringstream temp;
# Line 943  int MeshAdapter::getTagFromSampleNo(int Line 1965  int MeshAdapter::getTagFromSampleNo(int
1965    }    }
1966    return out;    return out;
1967  }  }
1968  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  
1969    
1970    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1971  {  {
   int out=0,i;  
1972    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
1973    switch (functionSpaceType) {    escriptDataC tmp=mask.getDataC();
1974    case(Nodes):    switch(functionSpaceType) {
1975      if (mesh->Nodes!=NULL) {         case(Nodes):
1976        out=mesh->Nodes->Id[sampleNo];            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
       break;  
     }  
   case(Elements):  
     out=mesh->Elements->Id[sampleNo];  
     break;  
   case(FaceElements):  
     out=mesh->FaceElements->Id[sampleNo];  
     break;  
   case(Points):  
     out=mesh->Points->Id[sampleNo];  
     break;  
   case(ContactElementsZero):  
     out=mesh->ContactElements->Id[sampleNo];  
     break;  
   case(ContactElementsOne):  
     out=mesh->ContactElements->Id[sampleNo];  
     break;  
   case(DegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->degreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
1977            break;            break;
1978         }         case(ReducedNodes):
1979      }            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
     break;  
   case(ReducedDegreesOfFreedom):  
     for (i=0;i<mesh->Nodes->numNodes; ++i) {  
        if (mesh->Nodes->reducedDegreeOfFreedom[i]==sampleNo) {  
           out=mesh->Nodes->Id[i];  
1980            break;            break;
1981         }         case(DegreesOfFreedom):
1982      }            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1983      break;            break;
1984    default:         case(ReducedDegreesOfFreedom):
1985      stringstream temp;            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1986      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();            break;
1987      throw FinleyAdapterException(temp.str());         case(Elements):
1988      break;            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1989              break;
1990           case(ReducedElements):
1991              Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1992              break;
1993           case(FaceElements):
1994              Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1995              break;
1996           case(ReducedFaceElements):
1997              Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1998              break;
1999           case(Points):
2000              Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2001              break;
2002           case(ContactElementsZero):
2003              Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2004              break;
2005           case(ReducedContactElementsZero):
2006              Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2007              break;
2008           case(ContactElementsOne):
2009              Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2010              break;
2011           case(ReducedContactElementsOne):
2012              Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2013              break;
2014           default:
2015              stringstream temp;
2016              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2017              throw FinleyAdapterException(temp.str());
2018    }    }
2019    return out;    checkFinleyError();
2020      return;
2021    }
2022    
2023    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2024    {
2025      Finley_Mesh* mesh=m_finleyMesh.get();
2026      Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2027      checkPasoError();
2028      // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2029    }
2030    
2031    int MeshAdapter::getTag(const std::string& name) const
2032    {
2033      Finley_Mesh* mesh=m_finleyMesh.get();
2034      int tag=0;
2035      tag=Finley_Mesh_getTag(mesh, name.c_str());
2036      checkPasoError();
2037      // throwStandardException("MeshAdapter::getTag is not implemented.");
2038      return tag;
2039    }
2040    
2041    bool MeshAdapter::isValidTagName(const std::string& name) const
2042    {
2043      Finley_Mesh* mesh=m_finleyMesh.get();
2044      return Finley_Mesh_isValidTagName(mesh,name.c_str());
2045    }
2046    
2047    std::string MeshAdapter::showTagNames() const
2048    {
2049      stringstream temp;
2050      Finley_Mesh* mesh=m_finleyMesh.get();
2051      Finley_TagMap* tag_map=mesh->TagMap;
2052      while (tag_map) {
2053         temp << tag_map->name;
2054         tag_map=tag_map->next;
2055         if (tag_map) temp << ", ";
2056      }
2057      return temp.str();
2058  }  }
2059    
2060  }  // end of namespace  }  // end of namespace

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