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

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Revision 1407 - (hide annotations)
Mon Feb 4 06:45:48 2008 UTC (11 years, 4 months ago) by gross
File size: 85508 byte(s)
new upwinding algorithm (still fails)
1 jgs 472
2 ksteube 1312 /* $Id$ */
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 jgs 203 #include "MeshAdapter.h"
17 robwdcock 682 #include "escript/Data.h"
18     #include "escript/DataFactory.h"
19 ksteube 1343 #ifdef USE_NETCDF
20     #include <netcdfcpp.h>
21     #endif
22 ksteube 1312 extern "C" {
23     #include "escript/blocktimer.h"
24     }
25     #include <vector>
26 jgs 480
27 jgs 82 using namespace std;
28     using namespace escript;
29    
30     namespace finley {
31 jgs 149
32 jgs 82 //
33 jgs 149 // define the static constants
34 jgs 82 MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
35     const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
36     const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
37     const int MeshAdapter::Nodes=FINLEY_NODES;
38 gross 1062 const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
39 jgs 82 const int MeshAdapter::Elements=FINLEY_ELEMENTS;
40 gross 1059 const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
41 jgs 82 const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
42 gross 1059 const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
43 jgs 82 const int MeshAdapter::Points=FINLEY_POINTS;
44     const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
45 gross 1059 const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
46 jgs 82 const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
47 gross 1059 const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
48 jgs 82
49     MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
50     {
51     setFunctionSpaceTypeNames();
52     //
53 ksteube 1312 // need to use a null_deleter as Finley_Mesh_free deletes the pointer
54 jgs 82 // for us.
55     m_finleyMesh.reset(finleyMesh,null_deleter());
56     }
57 jgs 149
58 jgs 82 //
59     // The copy constructor should just increment the use count
60     MeshAdapter::MeshAdapter(const MeshAdapter& in):
61     m_finleyMesh(in.m_finleyMesh)
62     {
63     setFunctionSpaceTypeNames();
64     }
65    
66     MeshAdapter::~MeshAdapter()
67     {
68     //
69     // I hope the case for the pointer being zero has been taken care of.
70     // cout << "In MeshAdapter destructor." << endl;
71     if (m_finleyMesh.unique()) {
72 ksteube 1312 Finley_Mesh_free(m_finleyMesh.get());
73 jgs 82 }
74     }
75    
76 ksteube 1312 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 jgs 82 Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
87     return m_finleyMesh.get();
88     }
89    
90     void MeshAdapter::write(const std::string& fileName) const
91     {
92 woo409 757 char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
93 jgs 82 strcpy(fName,fileName.c_str());
94     Finley_Mesh_write(m_finleyMesh.get(),fName);
95     checkFinleyError();
96 woo409 757 TMPMEMFREE(fName);
97 jgs 82 }
98    
99 ksteube 1339 void MeshAdapter::Print_Mesh_Info(const bool full=false) const
100 ksteube 1326 {
101 ksteube 1339 Finley_PrintMesh_Info(m_finleyMesh.get(), full);
102 ksteube 1326 }
103    
104 ksteube 1312 void MeshAdapter::dump(const std::string& fileName) const
105     {
106 ksteube 1343 #ifdef USE_NETCDF
107 ksteube 1347 const NcDim* ncdims[12];
108 ksteube 1343 NcVar *ids, *data;
109     int *int_ptr;
110     Finley_Mesh *mesh = m_finleyMesh.get();
111 ksteube 1347 Finley_TagMap* tag_map;
112     int num_Tags = 0;
113 ksteube 1343 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 ksteube 1347 /* 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 ksteube 1343 // 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 ksteube 1347 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 ksteube 1343
175 ksteube 1345 // Attributes: MPI size, MPI rank, Name, order, reduced_order
176 ksteube 1343 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 ksteube 1345 if (!dataFile.add_att("numDim",numDim) )
183     throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
184 ksteube 1343 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 ksteube 1345 if (!dataFile.add_att("numNodes",numNodes) )
189     throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
190 ksteube 1343 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 ksteube 1346 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 ksteube 1347 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 ksteube 1343
215     // // // // // Nodes // // // // //
216    
217 ksteube 1345 // 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 ksteube 1343 // 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 ksteube 1345 }
276    
277 ksteube 1343 // // // // // 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 ksteube 1344 TMPMEMFREE(Elements_Nodes);
322    
323 ksteube 1343 }
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 ksteube 1344 TMPMEMFREE(FaceElements_Nodes);
370    
371 ksteube 1343 }
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 ksteube 1344 TMPMEMFREE(ContactElements_Nodes);
418    
419 ksteube 1343 }
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 ksteube 1344 TMPMEMFREE(Points_Nodes);
468    
469 ksteube 1343 }
470    
471     // // // // // TagMap // // // // //
472    
473 ksteube 1347 if (num_Tags>0) {
474 ksteube 1343
475 ksteube 1347 // 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 ksteube 1343 // 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 ksteube 1312 }
522    
523 jgs 82 string MeshAdapter::getDescription() const
524     {
525 ksteube 1312 return "FinleyMesh";
526 jgs 82 }
527    
528     string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
529     {
530     FunctionSpaceNamesMapType::iterator loc;
531     loc=m_functionSpaceTypeNames.find(functionSpaceType);
532     if (loc==m_functionSpaceTypeNames.end()) {
533     return "Invalid function space type code.";
534     } else {
535 ksteube 1312 return loc->second;
536 jgs 82 }
537     }
538    
539     bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
540     {
541     FunctionSpaceNamesMapType::iterator loc;
542     loc=m_functionSpaceTypeNames.find(functionSpaceType);
543     return (loc!=m_functionSpaceTypeNames.end());
544     }
545    
546     void MeshAdapter::setFunctionSpaceTypeNames()
547     {
548     m_functionSpaceTypeNames.insert
549     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
550     m_functionSpaceTypeNames.insert
551     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
552     m_functionSpaceTypeNames.insert
553     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
554     m_functionSpaceTypeNames.insert
555 gross 1062 (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
556     m_functionSpaceTypeNames.insert
557 jgs 82 (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
558     m_functionSpaceTypeNames.insert
559 gross 1059 (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
560     m_functionSpaceTypeNames.insert
561 jgs 82 (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
562     m_functionSpaceTypeNames.insert
563 gross 1059 (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
564     m_functionSpaceTypeNames.insert
565 jgs 82 (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
566     m_functionSpaceTypeNames.insert
567     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
568     m_functionSpaceTypeNames.insert
569 gross 1059 (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
570     m_functionSpaceTypeNames.insert
571 jgs 82 (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
572 gross 1059 m_functionSpaceTypeNames.insert
573     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
574 jgs 82 }
575    
576     int MeshAdapter::getContinuousFunctionCode() const
577     {
578     return Nodes;
579     }
580 gross 1062 int MeshAdapter::getReducedContinuousFunctionCode() const
581     {
582     return ReducedNodes;
583     }
584 jgs 149
585 jgs 82 int MeshAdapter::getFunctionCode() const
586     {
587     return Elements;
588     }
589 gross 1059 int MeshAdapter::getReducedFunctionCode() const
590     {
591     return ReducedElements;
592     }
593 jgs 149
594 jgs 82 int MeshAdapter::getFunctionOnBoundaryCode() const
595     {
596     return FaceElements;
597     }
598 gross 1059 int MeshAdapter::getReducedFunctionOnBoundaryCode() const
599     {
600     return ReducedFaceElements;
601     }
602 jgs 149
603 jgs 82 int MeshAdapter::getFunctionOnContactZeroCode() const
604     {
605     return ContactElementsZero;
606     }
607 gross 1059 int MeshAdapter::getReducedFunctionOnContactZeroCode() const
608     {
609     return ReducedContactElementsZero;
610     }
611 jgs 149
612 jgs 82 int MeshAdapter::getFunctionOnContactOneCode() const
613     {
614     return ContactElementsOne;
615     }
616 gross 1059 int MeshAdapter::getReducedFunctionOnContactOneCode() const
617     {
618     return ReducedContactElementsOne;
619     }
620 jgs 82
621     int MeshAdapter::getSolutionCode() const
622     {
623     return DegreesOfFreedom;
624     }
625 jgs 149
626 jgs 82 int MeshAdapter::getReducedSolutionCode() const
627     {
628     return ReducedDegreesOfFreedom;
629     }
630 jgs 149
631 jgs 82 int MeshAdapter::getDiracDeltaFunctionCode() const
632     {
633     return Points;
634     }
635 jgs 149
636 jgs 82 //
637     // return the spatial dimension of the Mesh:
638     //
639     int MeshAdapter::getDim() const
640     {
641     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
642     checkFinleyError();
643     return numDim;
644     }
645 jgs 149
646 jgs 82 //
647     // return the number of data points per sample and the number of samples
648     // needed to represent data on a parts of the mesh.
649     //
650     pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
651     {
652     int numDataPointsPerSample=0;
653     int numSamples=0;
654     Finley_Mesh* mesh=m_finleyMesh.get();
655     switch (functionSpaceCode) {
656     case(Nodes):
657     numDataPointsPerSample=1;
658 ksteube 1312 numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
659 jgs 82 break;
660 gross 1062 case(ReducedNodes):
661     numDataPointsPerSample=1;
662 ksteube 1312 numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
663 gross 1062 break;
664 jgs 82 case(Elements):
665     if (mesh->Elements!=NULL) {
666     numSamples=mesh->Elements->numElements;
667     numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
668     }
669     break;
670 gross 1062 case(ReducedElements):
671     if (mesh->Elements!=NULL) {
672     numSamples=mesh->Elements->numElements;
673     numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
674     }
675     break;
676 jgs 82 case(FaceElements):
677     if (mesh->FaceElements!=NULL) {
678     numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
679     numSamples=mesh->FaceElements->numElements;
680     }
681     break;
682 gross 1062 case(ReducedFaceElements):
683     if (mesh->FaceElements!=NULL) {
684     numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
685     numSamples=mesh->FaceElements->numElements;
686     }
687     break;
688 jgs 82 case(Points):
689     if (mesh->Points!=NULL) {
690     numDataPointsPerSample=1;
691     numSamples=mesh->Points->numElements;
692     }
693     break;
694     case(ContactElementsZero):
695     if (mesh->ContactElements!=NULL) {
696     numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
697     numSamples=mesh->ContactElements->numElements;
698     }
699     break;
700 gross 1062 case(ReducedContactElementsZero):
701     if (mesh->ContactElements!=NULL) {
702     numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
703     numSamples=mesh->ContactElements->numElements;
704     }
705     break;
706 jgs 82 case(ContactElementsOne):
707     if (mesh->ContactElements!=NULL) {
708     numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
709     numSamples=mesh->ContactElements->numElements;
710     }
711     break;
712 gross 1062 case(ReducedContactElementsOne):
713     if (mesh->ContactElements!=NULL) {
714     numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
715     numSamples=mesh->ContactElements->numElements;
716     }
717     break;
718 jgs 82 case(DegreesOfFreedom):
719     if (mesh->Nodes!=NULL) {
720     numDataPointsPerSample=1;
721 ksteube 1312 numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
722 jgs 82 }
723     break;
724     case(ReducedDegreesOfFreedom):
725     if (mesh->Nodes!=NULL) {
726     numDataPointsPerSample=1;
727 ksteube 1312 numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
728 jgs 82 }
729     break;
730     default:
731     stringstream temp;
732 jgs 150 temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
733 jgs 82 throw FinleyAdapterException(temp.str());
734     break;
735     }
736     return pair<int,int>(numDataPointsPerSample,numSamples);
737     }
738 jgs 149
739 jgs 82 //
740     // adds linear PDE of second order into a given stiffness matrix and right hand side:
741     //
742     void MeshAdapter::addPDEToSystem(
743 jgs 480 SystemMatrixAdapter& mat, escript::Data& rhs,
744     const escript::Data& A, const escript::Data& B, const escript::Data& C,const escript::Data& D,const escript::Data& X,const escript::Data& Y,
745     const escript::Data& d, const escript::Data& y,
746     const escript::Data& d_contact,const escript::Data& y_contact) const
747 jgs 82 {
748 gross 798 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 bcumming 751
760 jgs 82 Finley_Mesh* mesh=m_finleyMesh.get();
761 gross 798
762 bcumming 751 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
763 jgs 82 checkFinleyError();
764 bcumming 751
765 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
766 jgs 82 checkFinleyError();
767 bcumming 751
768 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
769 jgs 82 checkFinleyError();
770     }
771 jgs 149
772 gross 1204 void MeshAdapter::addPDEToLumpedSystem(
773     escript::Data& mat,
774 ksteube 1312 const escript::Data& D,
775 gross 1204 const escript::Data& d) const
776     {
777     escriptDataC _mat=mat.getDataC();
778     escriptDataC _D=D.getDataC();
779     escriptDataC _d=d.getDataC();
780    
781     Finley_Mesh* mesh=m_finleyMesh.get();
782 ksteube 1312
783 gross 1204 Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
784     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
785    
786     checkFinleyError();
787     }
788    
789    
790 jgs 82 //
791 jgs 102 // adds linear PDE of second order into the right hand side only
792     //
793 bcumming 751 void MeshAdapter::addPDEToRHS( escript::Data& rhs, const escript::Data& X,const escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const
794 jgs 102 {
795     Finley_Mesh* mesh=m_finleyMesh.get();
796 jgs 147
797 gross 798 escriptDataC _rhs=rhs.getDataC();
798     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 jgs 102 checkFinleyError();
805 jgs 147
806 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
807     checkFinleyError();
808 jgs 147
809 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
810 jgs 102 checkFinleyError();
811     }
812 gross 1367 //
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 gross 1407 const escript::Data& A, const escript::Data& B, const escript::Data& C,
818     const escript::Data& D,const escript::Data& X,const escript::Data& Y,
819 gross 1367 const escript::Data& d, const escript::Data& y,
820     const escript::Data& d_contact,const escript::Data& y_contact) const
821     {
822     DataArrayView::ShapeType shape;
823 gross 1370 source.expand();
824 gross 1367 escriptDataC _source=source.getDataC();
825     escriptDataC _M=M.getDataC();
826     escriptDataC _A=A.getDataC();
827     escriptDataC _B=B.getDataC();
828     escriptDataC _C=C.getDataC();
829     escriptDataC _D=D.getDataC();
830     escriptDataC _X=X.getDataC();
831     escriptDataC _Y=Y.getDataC();
832     escriptDataC _d=d.getDataC();
833     escriptDataC _y=y.getDataC();
834     escriptDataC _d_contact=d_contact.getDataC();
835     escriptDataC _y_contact=y_contact.getDataC();
836 jgs 149
837 gross 1367 Finley_Mesh* mesh=m_finleyMesh.get();
838     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
839    
840 gross 1407 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
841 gross 1367 checkFinleyError();
842    
843 gross 1407 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
844 gross 1367 checkFinleyError();
845    
846     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
847     checkFinleyError();
848    
849     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
850     checkFinleyError();
851     }
852    
853 jgs 102 //
854 jgs 82 // interpolates data between different function spaces:
855     //
856 jgs 480 void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
857 jgs 82 {
858     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
859     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
860 bcumming 751 if (inDomain!=*this)
861     throw FinleyAdapterException("Error - Illegal domain of interpolant.");
862 jgs 82 if (targetDomain!=*this)
863 bcumming 751 throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
864 jgs 82
865     Finley_Mesh* mesh=m_finleyMesh.get();
866 gross 1062 escriptDataC _target=target.getDataC();
867     escriptDataC _in=in.getDataC();
868 jgs 82 switch(in.getFunctionSpace().getTypeCode()) {
869     case(Nodes):
870     switch(target.getFunctionSpace().getTypeCode()) {
871     case(Nodes):
872 gross 1062 case(ReducedNodes):
873     case(DegreesOfFreedom):
874 jgs 82 case(ReducedDegreesOfFreedom):
875 gross 1062 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
876     break;
877     case(Elements):
878     case(ReducedElements):
879     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
880     break;
881     case(FaceElements):
882     case(ReducedFaceElements):
883     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
884     break;
885     case(Points):
886     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
887     break;
888     case(ContactElementsZero):
889     case(ReducedContactElementsZero):
890     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
891     break;
892     case(ContactElementsOne):
893     case(ReducedContactElementsOne):
894     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
895     break;
896     default:
897     stringstream temp;
898     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
899     throw FinleyAdapterException(temp.str());
900     break;
901     }
902     break;
903     case(ReducedNodes):
904     switch(target.getFunctionSpace().getTypeCode()) {
905     case(Nodes):
906     case(ReducedNodes):
907 jgs 82 case(DegreesOfFreedom):
908 gross 1062 case(ReducedDegreesOfFreedom):
909     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
910 jgs 82 break;
911     case(Elements):
912 gross 1062 case(ReducedElements):
913     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
914 jgs 82 break;
915     case(FaceElements):
916 gross 1062 case(ReducedFaceElements):
917     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
918 jgs 82 break;
919     case(Points):
920 gross 1062 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
921 jgs 82 break;
922     case(ContactElementsZero):
923 gross 1062 case(ReducedContactElementsZero):
924     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
925 jgs 82 break;
926     case(ContactElementsOne):
927 gross 1062 case(ReducedContactElementsOne):
928     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
929 jgs 82 break;
930     default:
931 jgs 150 stringstream temp;
932     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
933     throw FinleyAdapterException(temp.str());
934 jgs 82 break;
935     }
936     break;
937     case(Elements):
938     if (target.getFunctionSpace().getTypeCode()==Elements) {
939 gross 1062 Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
940 gross 1116 } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
941     Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
942 jgs 82 } else {
943 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
944 jgs 82 }
945     break;
946 gross 1062 case(ReducedElements):
947     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
948     Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
949     } else {
950     throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
951     }
952     break;
953 jgs 82 case(FaceElements):
954     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
955 gross 1062 Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
956 gross 1116 } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
957     Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
958 jgs 82 } else {
959 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
960 gross 1361 }
961     break;
962 gross 1062 case(ReducedFaceElements):
963 gross 1375 if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
964 gross 1062 Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
965     } else {
966     throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
967     }
968     break;
969 jgs 82 case(Points):
970     if (target.getFunctionSpace().getTypeCode()==Points) {
971 gross 1062 Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
972 jgs 82 } else {
973 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on points possible.");
974 jgs 82 }
975     break;
976     case(ContactElementsZero):
977     case(ContactElementsOne):
978     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
979 gross 1062 Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
980 gross 1116 } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
981     Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
982 jgs 82 } else {
983 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
984 jgs 82 }
985     break;
986 gross 1062 case(ReducedContactElementsZero):
987     case(ReducedContactElementsOne):
988     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
989     Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
990     } else {
991     throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
992     }
993     break;
994 bcumming 751 case(DegreesOfFreedom):
995 jgs 82 switch(target.getFunctionSpace().getTypeCode()) {
996     case(ReducedDegreesOfFreedom):
997     case(DegreesOfFreedom):
998 ksteube 1312 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
999     break;
1000    
1001 jgs 82 case(Nodes):
1002 gross 1062 case(ReducedNodes):
1003 ksteube 1312 if (getMPISize()>1) {
1004     escript::Data temp=escript::Data(in);
1005     temp.expand();
1006     escriptDataC _in2 = temp.getDataC();
1007     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1008     } else {
1009     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1010     }
1011 jgs 82 break;
1012     case(Elements):
1013 gross 1062 case(ReducedElements):
1014 ksteube 1312 if (getMPISize()>1) {
1015     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1016     escriptDataC _in2 = temp.getDataC();
1017     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1018     } else {
1019     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1020     }
1021 jgs 82 break;
1022     case(FaceElements):
1023 gross 1062 case(ReducedFaceElements):
1024 ksteube 1312 if (getMPISize()>1) {
1025     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1026     escriptDataC _in2 = temp.getDataC();
1027     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1028    
1029     } else {
1030     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1031     }
1032 jgs 82 break;
1033     case(Points):
1034 ksteube 1312 if (getMPISize()>1) {
1035     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1036     escriptDataC _in2 = temp.getDataC();
1037     } else {
1038     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1039     }
1040 jgs 82 break;
1041     case(ContactElementsZero):
1042     case(ContactElementsOne):
1043 gross 1062 case(ReducedContactElementsZero):
1044     case(ReducedContactElementsOne):
1045 ksteube 1312 if (getMPISize()>1) {
1046     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1047     escriptDataC _in2 = temp.getDataC();
1048     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1049     } else {
1050     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1051     }
1052 jgs 82 break;
1053     default:
1054 jgs 150 stringstream temp;
1055     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1056     throw FinleyAdapterException(temp.str());
1057 jgs 82 break;
1058     }
1059     break;
1060     case(ReducedDegreesOfFreedom):
1061     switch(target.getFunctionSpace().getTypeCode()) {
1062 gross 1062 case(Nodes):
1063     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1064     break;
1065     case(ReducedNodes):
1066 ksteube 1312 if (getMPISize()>1) {
1067     escript::Data temp=escript::Data(in);
1068     temp.expand();
1069     escriptDataC _in2 = temp.getDataC();
1070     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1071     } else {
1072     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1073     }
1074     break;
1075 gross 1062 case(DegreesOfFreedom):
1076     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1077     break;
1078 jgs 82 case(ReducedDegreesOfFreedom):
1079 gross 1062 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1080 jgs 82 break;
1081     case(Elements):
1082 gross 1062 case(ReducedElements):
1083 ksteube 1312 if (getMPISize()>1) {
1084     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1085     escriptDataC _in2 = temp.getDataC();
1086     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1087     } else {
1088     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1089     }
1090 jgs 82 break;
1091     case(FaceElements):
1092 gross 1062 case(ReducedFaceElements):
1093 ksteube 1312 if (getMPISize()>1) {
1094     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1095     escriptDataC _in2 = temp.getDataC();
1096     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1097     } else {
1098     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1099     }
1100 jgs 82 break;
1101     case(Points):
1102 ksteube 1312 if (getMPISize()>1) {
1103     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1104     escriptDataC _in2 = temp.getDataC();
1105     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1106     } else {
1107     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1108     }
1109 jgs 82 break;
1110     case(ContactElementsZero):
1111     case(ContactElementsOne):
1112 gross 1062 case(ReducedContactElementsZero):
1113     case(ReducedContactElementsOne):
1114 ksteube 1312 if (getMPISize()>1) {
1115     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1116     escriptDataC _in2 = temp.getDataC();
1117     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1118     } else {
1119     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1120     }
1121 jgs 82 break;
1122     default:
1123 jgs 150 stringstream temp;
1124     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1125     throw FinleyAdapterException(temp.str());
1126 jgs 82 break;
1127     }
1128     break;
1129     default:
1130 jgs 150 stringstream temp;
1131     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1132     throw FinleyAdapterException(temp.str());
1133 jgs 82 break;
1134     }
1135     checkFinleyError();
1136     }
1137    
1138     //
1139     // copies the locations of sample points into x:
1140     //
1141 jgs 480 void MeshAdapter::setToX(escript::Data& arg) const
1142 jgs 82 {
1143     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1144     if (argDomain!=*this)
1145     throw FinleyAdapterException("Error - Illegal domain of data point locations");
1146     Finley_Mesh* mesh=m_finleyMesh.get();
1147     // in case of values node coordinates we can do the job directly:
1148     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1149 gross 1062 escriptDataC _arg=arg.getDataC();
1150     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1151 jgs 82 } else {
1152 jgs 480 escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1153 gross 1062 escriptDataC _tmp_data=tmp_data.getDataC();
1154     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1155 jgs 82 // this is then interpolated onto arg:
1156     interpolateOnDomain(arg,tmp_data);
1157     }
1158     checkFinleyError();
1159     }
1160 jgs 149
1161 jgs 82 //
1162     // return the normal vectors at the location of data points as a Data object:
1163     //
1164 jgs 480 void MeshAdapter::setToNormal(escript::Data& normal) const
1165 jgs 82 {
1166     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());
1167     if (normalDomain!=*this)
1168     throw FinleyAdapterException("Error - Illegal domain of normal locations");
1169     Finley_Mesh* mesh=m_finleyMesh.get();
1170 gross 1062 escriptDataC _normal=normal.getDataC();
1171 jgs 82 switch(normal.getFunctionSpace().getTypeCode()) {
1172     case(Nodes):
1173 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1174 jgs 82 break;
1175 gross 1062 case(ReducedNodes):
1176     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1177     break;
1178 jgs 82 case(Elements):
1179 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1180 jgs 82 break;
1181 gross 1062 case(ReducedElements):
1182     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1183     break;
1184 jgs 82 case (FaceElements):
1185 gross 1062 Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1186 jgs 82 break;
1187 gross 1062 case (ReducedFaceElements):
1188     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1189     break;
1190 jgs 82 case(Points):
1191 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1192 jgs 82 break;
1193     case (ContactElementsOne):
1194     case (ContactElementsZero):
1195 gross 1062 Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1196 jgs 82 break;
1197 gross 1062 case (ReducedContactElementsOne):
1198     case (ReducedContactElementsZero):
1199     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1200     break;
1201 jgs 82 case(DegreesOfFreedom):
1202 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1203 jgs 82 break;
1204     case(ReducedDegreesOfFreedom):
1205 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1206 jgs 82 break;
1207     default:
1208 jgs 150 stringstream temp;
1209     temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1210     throw FinleyAdapterException(temp.str());
1211 jgs 82 break;
1212     }
1213     checkFinleyError();
1214     }
1215 jgs 149
1216 jgs 82 //
1217     // interpolates data to other domain:
1218     //
1219 jgs 480 void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1220 jgs 82 {
1221     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
1222     if (targetDomain!=*this)
1223     throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1224    
1225 jgs 150 throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1226 jgs 82 }
1227 jgs 149
1228 jgs 82 //
1229     // calculates the integral of a function defined of arg:
1230     //
1231 jgs 480 void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1232 jgs 82 {
1233     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1234     if (argDomain!=*this)
1235     throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1236    
1237 ksteube 1312 double blocktimer_start = blocktimer_time();
1238 jgs 82 Finley_Mesh* mesh=m_finleyMesh.get();
1239 ksteube 1312 escriptDataC _temp;
1240     escript::Data temp;
1241 gross 1062 escriptDataC _arg=arg.getDataC();
1242 jgs 82 switch(arg.getFunctionSpace().getTypeCode()) {
1243     case(Nodes):
1244 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1245     _temp=temp.getDataC();
1246     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1247 jgs 82 break;
1248 gross 1062 case(ReducedNodes):
1249 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1250     _temp=temp.getDataC();
1251     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1252 gross 1062 break;
1253 jgs 82 case(Elements):
1254 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1255 jgs 82 break;
1256 gross 1062 case(ReducedElements):
1257     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1258 gross 1064 break;
1259 jgs 82 case(FaceElements):
1260 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1261 jgs 82 break;
1262 gross 1062 case(ReducedFaceElements):
1263     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1264     break;
1265 jgs 82 case(Points):
1266 jgs 150 throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1267 jgs 82 break;
1268     case(ContactElementsZero):
1269 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1270 jgs 82 break;
1271 gross 1062 case(ReducedContactElementsZero):
1272     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1273     break;
1274 jgs 82 case(ContactElementsOne):
1275 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1276 jgs 82 break;
1277 gross 1062 case(ReducedContactElementsOne):
1278     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1279     break;
1280 jgs 82 case(DegreesOfFreedom):
1281 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1282     _temp=temp.getDataC();
1283     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1284 jgs 82 break;
1285     case(ReducedDegreesOfFreedom):
1286 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1287     _temp=temp.getDataC();
1288     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1289 jgs 82 break;
1290     default:
1291 jgs 150 stringstream temp;
1292     temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1293     throw FinleyAdapterException(temp.str());
1294 jgs 82 break;
1295     }
1296     checkFinleyError();
1297 ksteube 1312 blocktimer_increment("integrate()", blocktimer_start);
1298 jgs 82 }
1299 jgs 149
1300 jgs 82 //
1301     // calculates the gradient of arg:
1302     //
1303 jgs 480 void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1304 jgs 82 {
1305     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1306     if (argDomain!=*this)
1307     throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1308     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());
1309     if (gradDomain!=*this)
1310     throw FinleyAdapterException("Error - Illegal domain of gradient");
1311    
1312     Finley_Mesh* mesh=m_finleyMesh.get();
1313 gross 1062 escriptDataC _grad=grad.getDataC();
1314 bcumming 751 escriptDataC nodeDataC;
1315 ksteube 1312 escript::Data temp;
1316     if (getMPISize()>1) {
1317     if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1318     temp=escript::Data( arg, continuousFunction(asAbstractContinuousDomain()) );
1319     nodeDataC = temp.getDataC();
1320     } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1321     temp=escript::Data( arg, reducedContinuousFunction(asAbstractContinuousDomain()) );
1322     nodeDataC = temp.getDataC();
1323     } else {
1324     nodeDataC = arg.getDataC();
1325     }
1326     } else {
1327     nodeDataC = arg.getDataC();
1328 bcumming 751 }
1329 jgs 82 switch(grad.getFunctionSpace().getTypeCode()) {
1330     case(Nodes):
1331 jgs 150 throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1332 jgs 82 break;
1333 gross 1062 case(ReducedNodes):
1334     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1335     break;
1336 jgs 82 case(Elements):
1337 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1338 jgs 82 break;
1339 gross 1062 case(ReducedElements):
1340     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1341     break;
1342 jgs 82 case(FaceElements):
1343 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1344 jgs 82 break;
1345 gross 1062 case(ReducedFaceElements):
1346     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1347     break;
1348 jgs 82 case(Points):
1349 jgs 150 throw FinleyAdapterException("Error - Gradient at points is not supported.");
1350 jgs 82 break;
1351     case(ContactElementsZero):
1352 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1353 jgs 82 break;
1354 gross 1062 case(ReducedContactElementsZero):
1355     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1356     break;
1357 jgs 82 case(ContactElementsOne):
1358 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1359 jgs 82 break;
1360 gross 1062 case(ReducedContactElementsOne):
1361     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1362     break;
1363 jgs 82 case(DegreesOfFreedom):
1364 jgs 150 throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1365 jgs 82 break;
1366     case(ReducedDegreesOfFreedom):
1367 jgs 150 throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1368 jgs 82 break;
1369     default:
1370 jgs 150 stringstream temp;
1371     temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1372     throw FinleyAdapterException(temp.str());
1373 jgs 82 break;
1374     }
1375     checkFinleyError();
1376     }
1377 jgs 149
1378 jgs 82 //
1379     // returns the size of elements:
1380     //
1381 jgs 480 void MeshAdapter::setToSize(escript::Data& size) const
1382 jgs 82 {
1383     Finley_Mesh* mesh=m_finleyMesh.get();
1384     escriptDataC tmp=size.getDataC();
1385     switch(size.getFunctionSpace().getTypeCode()) {
1386     case(Nodes):
1387 jgs 150 throw FinleyAdapterException("Error - Size of nodes is not supported.");
1388 jgs 82 break;
1389 gross 1062 case(ReducedNodes):
1390     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1391     break;
1392 jgs 82 case(Elements):
1393     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1394     break;
1395 gross 1062 case(ReducedElements):
1396     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1397     break;
1398 jgs 82 case(FaceElements):
1399     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1400     break;
1401 gross 1062 case(ReducedFaceElements):
1402     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1403     break;
1404 jgs 82 case(Points):
1405 jgs 150 throw FinleyAdapterException("Error - Size of point elements is not supported.");
1406 jgs 82 break;
1407     case(ContactElementsZero):
1408     case(ContactElementsOne):
1409     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1410     break;
1411 gross 1062 case(ReducedContactElementsZero):
1412     case(ReducedContactElementsOne):
1413     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1414     break;
1415 jgs 82 case(DegreesOfFreedom):
1416 jgs 150 throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1417 jgs 82 break;
1418     case(ReducedDegreesOfFreedom):
1419 jgs 150 throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1420 jgs 82 break;
1421     default:
1422 jgs 150 stringstream temp;
1423     temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1424     throw FinleyAdapterException(temp.str());
1425 jgs 82 break;
1426     }
1427     checkFinleyError();
1428     }
1429 jgs 149
1430 jgs 82 // sets the location of nodes:
1431 jgs 480 void MeshAdapter::setNewX(const escript::Data& new_x)
1432 jgs 82 {
1433     Finley_Mesh* mesh=m_finleyMesh.get();
1434 bcumming 751 escriptDataC tmp;
1435 jgs 82 const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1436     if (newDomain!=*this)
1437     throw FinleyAdapterException("Error - Illegal domain of new point locations");
1438 bcumming 751 tmp = new_x.getDataC();
1439     Finley_Mesh_setCoordinates(mesh,&tmp);
1440 jgs 82 checkFinleyError();
1441     }
1442 jgs 149
1443 jgs 82 // saves a data array in openDX format:
1444 jgs 153 void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1445     {
1446     int MAX_namelength=256;
1447     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1448 woo409 757 /* win32 refactor */
1449     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1450     for(int i=0;i<num_data;i++)
1451     {
1452     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1453     }
1454 jgs 153
1455 woo409 757 char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1456     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1457     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1458    
1459 ksteube 1312 boost::python::list keys=arg.keys();
1460     for (int i=0;i<num_data;++i) {
1461     std::string n=boost::python::extract<std::string>(keys[i]);
1462 jgs 480 escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1463 jgs 153 if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1464 ksteube 1312 throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1465 jgs 153 data[i]=d.getDataC();
1466     ptr_data[i]=&(data[i]);
1467     c_names[i]=&(names[i][0]);
1468     if (n.length()>MAX_namelength-1) {
1469     strncpy(c_names[i],n.c_str(),MAX_namelength-1);
1470     c_names[i][MAX_namelength-1]='\0';
1471     } else {
1472     strcpy(c_names[i],n.c_str());
1473     }
1474     }
1475     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);
1476     checkFinleyError();
1477 woo409 757
1478     /* win32 refactor */
1479     TMPMEMFREE(c_names);
1480     TMPMEMFREE(data);
1481     TMPMEMFREE(ptr_data);
1482     for(int i=0;i<num_data;i++)
1483     {
1484     TMPMEMFREE(names[i]);
1485     }
1486     TMPMEMFREE(names);
1487    
1488 jgs 153 return;
1489 jgs 82 }
1490 jgs 149
1491 jgs 110 // saves a data array in openVTK format:
1492 jgs 153 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1493     {
1494     int MAX_namelength=256;
1495     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1496 woo409 757 /* win32 refactor */
1497     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1498     for(int i=0;i<num_data;i++)
1499     {
1500     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1501     }
1502 jgs 153
1503 woo409 757 char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1504     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1505     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1506    
1507 jgs 153 boost::python::list keys=arg.keys();
1508     for (int i=0;i<num_data;++i) {
1509 ksteube 1312 std::string n=boost::python::extract<std::string>(keys[i]);
1510 jgs 480 escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1511 jgs 153 if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1512     throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1513     data[i]=d.getDataC();
1514     ptr_data[i]=&(data[i]);
1515     c_names[i]=&(names[i][0]);
1516     if (n.length()>MAX_namelength-1) {
1517     strncpy(c_names[i],n.c_str(),MAX_namelength-1);
1518     c_names[i][MAX_namelength-1]='\0';
1519     } else {
1520     strcpy(c_names[i],n.c_str());
1521     }
1522     }
1523     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);
1524 dhawcroft 793
1525 ksteube 1312 checkFinleyError();
1526 woo409 757 /* win32 refactor */
1527     TMPMEMFREE(c_names);
1528     TMPMEMFREE(data);
1529     TMPMEMFREE(ptr_data);
1530     for(int i=0;i<num_data;i++)
1531     {
1532     TMPMEMFREE(names[i]);
1533     }
1534     TMPMEMFREE(names);
1535    
1536 jgs 153 return;
1537 jgs 110 }
1538 jgs 153
1539    
1540 jgs 82 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1541     SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1542     const int row_blocksize,
1543     const escript::FunctionSpace& row_functionspace,
1544     const int column_blocksize,
1545     const escript::FunctionSpace& column_functionspace,
1546 jgs 102 const int type) const
1547 jgs 82 {
1548     int reduceRowOrder=0;
1549     int reduceColOrder=0;
1550     // is the domain right?
1551     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());
1552     if (row_domain!=*this)
1553     throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1554     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());
1555     if (col_domain!=*this)
1556     throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1557     // is the function space type right
1558     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1559     reduceRowOrder=0;
1560     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1561     reduceRowOrder=1;
1562     } else {
1563     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1564     }
1565     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1566     reduceColOrder=0;
1567     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1568     reduceColOrder=1;
1569     } else {
1570     throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1571     }
1572     // generate matrix:
1573 jgs 102
1574 jgs 150 Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1575 jgs 82 checkFinleyError();
1576 ksteube 1312 Paso_SystemMatrix* fsystemMatrix;
1577     int trilinos = 0;
1578     if (trilinos) {
1579     #ifdef TRILINOS
1580     /* Allocation Epetra_VrbMatrix here */
1581     #endif
1582     }
1583     else {
1584     fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1585     }
1586 jgs 150 checkPasoError();
1587 ksteube 1312 Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1588 jgs 82 return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1589     }
1590 gross 1366 // creates a TransportProblemAdapter
1591     TransportProblemAdapter MeshAdapter::newTransportProblem(
1592     const double theta,
1593     const int blocksize,
1594     const escript::FunctionSpace& functionspace,
1595     const int type) const
1596     {
1597     int reduceOrder=0;
1598     // is the domain right?
1599     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1600     if (domain!=*this)
1601     throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1602     // is the function space type right
1603     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1604     reduceOrder=0;
1605     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1606     reduceOrder=1;
1607     } else {
1608     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1609     }
1610     // generate matrix:
1611    
1612     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1613     checkFinleyError();
1614     Paso_FCTransportProblem* transportProblem;
1615 gross 1407 transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1616 gross 1366 checkPasoError();
1617     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1618 gross 1407 return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1619 gross 1366 }
1620 jgs 149
1621 jgs 82 //
1622     // vtkObject MeshAdapter::createVtkObject() const
1623     // TODO:
1624     //
1625 jgs 149
1626 jgs 82 //
1627     // returns true if data at the atom_type is considered as being cell centered:
1628     bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1629     {
1630     switch(functionSpaceCode) {
1631     case(Nodes):
1632     case(DegreesOfFreedom):
1633     case(ReducedDegreesOfFreedom):
1634     return false;
1635     break;
1636     case(Elements):
1637     case(FaceElements):
1638     case(Points):
1639     case(ContactElementsZero):
1640     case(ContactElementsOne):
1641 gross 1062 case(ReducedElements):
1642     case(ReducedFaceElements):
1643     case(ReducedContactElementsZero):
1644     case(ReducedContactElementsOne):
1645 jgs 82 return true;
1646     break;
1647     default:
1648 jgs 150 stringstream temp;
1649     temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1650     throw FinleyAdapterException(temp.str());
1651 jgs 82 break;
1652     }
1653     checkFinleyError();
1654     return false;
1655     }
1656 jgs 149
1657 jgs 82 bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1658     {
1659     switch(functionSpaceType_source) {
1660     case(Nodes):
1661     switch(functionSpaceType_target) {
1662     case(Nodes):
1663 gross 1062 case(ReducedNodes):
1664 jgs 82 case(ReducedDegreesOfFreedom):
1665     case(DegreesOfFreedom):
1666     case(Elements):
1667 gross 1062 case(ReducedElements):
1668 jgs 82 case(FaceElements):
1669 gross 1062 case(ReducedFaceElements):
1670 jgs 82 case(Points):
1671     case(ContactElementsZero):
1672 gross 1062 case(ReducedContactElementsZero):
1673 jgs 82 case(ContactElementsOne):
1674 gross 1062 case(ReducedContactElementsOne):
1675 jgs 82 return true;
1676     default:
1677 jgs 150 stringstream temp;
1678     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1679     throw FinleyAdapterException(temp.str());
1680 jgs 82 }
1681     break;
1682 gross 1062 case(ReducedNodes):
1683     switch(functionSpaceType_target) {
1684     case(ReducedNodes):
1685     case(ReducedDegreesOfFreedom):
1686     case(Elements):
1687     case(ReducedElements):
1688     case(FaceElements):
1689     case(ReducedFaceElements):
1690     case(Points):
1691     case(ContactElementsZero):
1692     case(ReducedContactElementsZero):
1693     case(ContactElementsOne):
1694     case(ReducedContactElementsOne):
1695     return true;
1696     case(Nodes):
1697     case(DegreesOfFreedom):
1698     return false;
1699     default:
1700     stringstream temp;
1701     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1702     throw FinleyAdapterException(temp.str());
1703     }
1704     break;
1705 jgs 82 case(Elements):
1706     if (functionSpaceType_target==Elements) {
1707     return true;
1708 gross 1116 } else if (functionSpaceType_target==ReducedElements) {
1709     return true;
1710 jgs 82 } else {
1711     return false;
1712     }
1713 gross 1062 case(ReducedElements):
1714     if (functionSpaceType_target==ReducedElements) {
1715     return true;
1716     } else {
1717     return false;
1718     }
1719 jgs 82 case(FaceElements):
1720     if (functionSpaceType_target==FaceElements) {
1721     return true;
1722 gross 1116 } else if (functionSpaceType_target==ReducedFaceElements) {
1723     return true;
1724 jgs 82 } else {
1725     return false;
1726     }
1727 gross 1062 case(ReducedFaceElements):
1728     if (functionSpaceType_target==ReducedFaceElements) {
1729     return true;
1730     } else {
1731     return false;
1732     }
1733 jgs 82 case(Points):
1734     if (functionSpaceType_target==Points) {
1735     return true;
1736     } else {
1737     return false;
1738     }
1739     case(ContactElementsZero):
1740     case(ContactElementsOne):
1741     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1742     return true;
1743 gross 1116 } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1744     return true;
1745 jgs 82 } else {
1746     return false;
1747     }
1748 gross 1062 case(ReducedContactElementsZero):
1749     case(ReducedContactElementsOne):
1750     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1751     return true;
1752     } else {
1753     return false;
1754     }
1755 jgs 82 case(DegreesOfFreedom):
1756     switch(functionSpaceType_target) {
1757     case(ReducedDegreesOfFreedom):
1758     case(DegreesOfFreedom):
1759     case(Nodes):
1760 gross 1062 case(ReducedNodes):
1761 jgs 82 case(Elements):
1762 gross 1062 case(ReducedElements):
1763     case(Points):
1764 jgs 82 case(FaceElements):
1765 gross 1062 case(ReducedFaceElements):
1766 jgs 82 case(ContactElementsZero):
1767 gross 1062 case(ReducedContactElementsZero):
1768 jgs 82 case(ContactElementsOne):
1769 gross 1062 case(ReducedContactElementsOne):
1770 jgs 82 return true;
1771     default:
1772 jgs 150 stringstream temp;
1773     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1774     throw FinleyAdapterException(temp.str());
1775 jgs 82 }
1776     break;
1777     case(ReducedDegreesOfFreedom):
1778     switch(functionSpaceType_target) {
1779     case(ReducedDegreesOfFreedom):
1780 gross 1062 case(ReducedNodes):
1781 jgs 82 case(Elements):
1782 gross 1062 case(ReducedElements):
1783 jgs 82 case(FaceElements):
1784 gross 1062 case(ReducedFaceElements):
1785 jgs 82 case(Points):
1786     case(ContactElementsZero):
1787 gross 1062 case(ReducedContactElementsZero):
1788 jgs 82 case(ContactElementsOne):
1789 gross 1062 case(ReducedContactElementsOne):
1790 jgs 82 return true;
1791 jgs 147 case(Nodes):
1792 jgs 82 case(DegreesOfFreedom):
1793     return false;
1794     default:
1795 jgs 150 stringstream temp;
1796     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1797     throw FinleyAdapterException(temp.str());
1798 jgs 82 }
1799     break;
1800     default:
1801 jgs 150 stringstream temp;
1802     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1803     throw FinleyAdapterException(temp.str());
1804 jgs 82 break;
1805     }
1806     checkFinleyError();
1807     return false;
1808     }
1809 jgs 149
1810 jgs 82 bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
1811     {
1812     return false;
1813     }
1814 jgs 104
1815 jgs 121 bool MeshAdapter::operator==(const AbstractDomain& other) const
1816 jgs 82 {
1817 jgs 121 const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1818     if (temp!=0) {
1819     return (m_finleyMesh==temp->m_finleyMesh);
1820     } else {
1821     return false;
1822     }
1823 jgs 82 }
1824    
1825 jgs 121 bool MeshAdapter::operator!=(const AbstractDomain& other) const
1826 jgs 104 {
1827 jgs 121 return !(operator==(other));
1828 jgs 104 }
1829    
1830 jgs 150 int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const
1831 jgs 102 {
1832 jgs 150 int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1833     checkPasoError();
1834 jgs 102 return out;
1835     }
1836 jgs 149
1837 jgs 480 escript::Data MeshAdapter::getX() const
1838 jgs 102 {
1839     return continuousFunction(asAbstractContinuousDomain()).getX();
1840     }
1841 jgs 149
1842 jgs 480 escript::Data MeshAdapter::getNormal() const
1843 jgs 102 {
1844     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1845     }
1846 jgs 149
1847 jgs 480 escript::Data MeshAdapter::getSize() const
1848 jgs 102 {
1849     return function(asAbstractContinuousDomain()).getSize();
1850     }
1851    
1852 gross 1062 int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1853     {
1854     int *out=0,i;
1855     Finley_Mesh* mesh=m_finleyMesh.get();
1856     switch (functionSpaceType) {
1857     case(Nodes):
1858 ksteube 1312 out=mesh->Nodes->Id;
1859     break;
1860 gross 1062 case(ReducedNodes):
1861 ksteube 1312 out=mesh->Nodes->reducedNodesId;
1862 gross 1062 break;
1863     case(Elements):
1864 gross 1080 out=mesh->Elements->Id;
1865 gross 1062 break;
1866     case(ReducedElements):
1867     out=mesh->Elements->Id;
1868     break;
1869     case(FaceElements):
1870     out=mesh->FaceElements->Id;
1871     break;
1872     case(ReducedFaceElements):
1873     out=mesh->FaceElements->Id;
1874     break;
1875     case(Points):
1876     out=mesh->Points->Id;
1877     break;
1878     case(ContactElementsZero):
1879     out=mesh->ContactElements->Id;
1880     break;
1881     case(ReducedContactElementsZero):
1882     out=mesh->ContactElements->Id;
1883     break;
1884     case(ContactElementsOne):
1885     out=mesh->ContactElements->Id;
1886     break;
1887     case(ReducedContactElementsOne):
1888     out=mesh->ContactElements->Id;
1889     break;
1890     case(DegreesOfFreedom):
1891 ksteube 1312 out=mesh->Nodes->degreesOfFreedomId;
1892 gross 1062 break;
1893     case(ReducedDegreesOfFreedom):
1894 ksteube 1312 out=mesh->Nodes->reducedDegreesOfFreedomId;
1895 gross 1062 break;
1896     default:
1897     stringstream temp;
1898     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1899     throw FinleyAdapterException(temp.str());
1900     break;
1901     }
1902     return out;
1903     }
1904 jgs 110 int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1905     {
1906 gross 547 int out=0;
1907     Finley_Mesh* mesh=m_finleyMesh.get();
1908     switch (functionSpaceType) {
1909     case(Nodes):
1910     out=mesh->Nodes->Tag[sampleNo];
1911     break;
1912 gross 1062 case(ReducedNodes):
1913     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1914     break;
1915 gross 547 case(Elements):
1916     out=mesh->Elements->Tag[sampleNo];
1917     break;
1918 gross 1062 case(ReducedElements):
1919     out=mesh->Elements->Tag[sampleNo];
1920     break;
1921 gross 547 case(FaceElements):
1922     out=mesh->FaceElements->Tag[sampleNo];
1923     break;
1924 gross 1062 case(ReducedFaceElements):
1925     out=mesh->FaceElements->Tag[sampleNo];
1926     break;
1927 gross 547 case(Points):
1928     out=mesh->Points->Tag[sampleNo];
1929     break;
1930     case(ContactElementsZero):
1931     out=mesh->ContactElements->Tag[sampleNo];
1932     break;
1933 gross 1062 case(ReducedContactElementsZero):
1934     out=mesh->ContactElements->Tag[sampleNo];
1935     break;
1936 gross 547 case(ContactElementsOne):
1937     out=mesh->ContactElements->Tag[sampleNo];
1938     break;
1939 gross 1062 case(ReducedContactElementsOne):
1940     out=mesh->ContactElements->Tag[sampleNo];
1941 gross 547 break;
1942     case(DegreesOfFreedom):
1943 gross 1062 throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1944 gross 547 break;
1945     case(ReducedDegreesOfFreedom):
1946 gross 1062 throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1947 gross 547 break;
1948     default:
1949     stringstream temp;
1950     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1951     throw FinleyAdapterException(temp.str());
1952     break;
1953     }
1954     return out;
1955 jgs 110 }
1956    
1957 gross 1062
1958 gross 767 void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1959     {
1960     Finley_Mesh* mesh=m_finleyMesh.get();
1961     escriptDataC tmp=mask.getDataC();
1962     switch(functionSpaceType) {
1963     case(Nodes):
1964     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1965     break;
1966 gross 1062 case(ReducedNodes):
1967     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1968     break;
1969 gross 767 case(DegreesOfFreedom):
1970     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1971     break;
1972     case(ReducedDegreesOfFreedom):
1973     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1974     break;
1975     case(Elements):
1976     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1977     break;
1978 gross 1062 case(ReducedElements):
1979     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1980     break;
1981 gross 767 case(FaceElements):
1982     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1983     break;
1984 gross 1062 case(ReducedFaceElements):
1985     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1986     break;
1987 gross 767 case(Points):
1988     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1989     break;
1990     case(ContactElementsZero):
1991     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1992     break;
1993 gross 1062 case(ReducedContactElementsZero):
1994     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1995     break;
1996 gross 767 case(ContactElementsOne):
1997     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1998     break;
1999 gross 1062 case(ReducedContactElementsOne):
2000     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2001     break;
2002 gross 767 default:
2003     stringstream temp;
2004     temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2005     throw FinleyAdapterException(temp.str());
2006     }
2007     checkFinleyError();
2008     return;
2009     }
2010    
2011 gross 1044 void MeshAdapter::setTagMap(const std::string& name, int tag)
2012     {
2013     Finley_Mesh* mesh=m_finleyMesh.get();
2014     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2015     checkPasoError();
2016     // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2017     }
2018 gross 767
2019 gross 1044 int MeshAdapter::getTag(const std::string& name) const
2020     {
2021     Finley_Mesh* mesh=m_finleyMesh.get();
2022     int tag=0;
2023     tag=Finley_Mesh_getTag(mesh, name.c_str());
2024     checkPasoError();
2025     // throwStandardException("MeshAdapter::getTag is not implemented.");
2026     return tag;
2027     }
2028    
2029     bool MeshAdapter::isValidTagName(const std::string& name) const
2030     {
2031     Finley_Mesh* mesh=m_finleyMesh.get();
2032     return Finley_Mesh_isValidTagName(mesh,name.c_str());
2033     }
2034    
2035     std::string MeshAdapter::showTagNames() const
2036     {
2037     stringstream temp;
2038     Finley_Mesh* mesh=m_finleyMesh.get();
2039     Finley_TagMap* tag_map=mesh->TagMap;
2040     while (tag_map) {
2041     temp << tag_map->name;
2042     tag_map=tag_map->next;
2043     if (tag_map) temp << ", ";
2044     }
2045 ksteube 1312 return temp.str();
2046 gross 1044 }
2047    
2048 jgs 82 } // end of namespace

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