/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
ViewVC logotype

Annotation of /branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1388 - (hide annotations)
Fri Jan 11 07:45:58 2008 UTC (11 years, 3 months ago) by trankine
Original Path: trunk/finley/src/CPPAdapter/MeshAdapter.cpp
File size: 86045 byte(s)
And get the *(&(*&(* name right
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     const escript::Data& A, const escript::Data& B, const escript::Data& C,const escript::Data& D,const escript::Data& X,const escript::Data& Y,
818     const escript::Data& d, const escript::Data& y,
819     const escript::Data& d_contact,const escript::Data& y_contact) const
820     {
821     DataArrayView::ShapeType shape;
822 gross 1370 source.expand();
823 gross 1367 escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true);
824     escriptDataC _source=source.getDataC();
825     escriptDataC _tmp=tmp.getDataC();
826     escriptDataC _M=M.getDataC();
827     escriptDataC _A=A.getDataC();
828     escriptDataC _B=B.getDataC();
829     escriptDataC _C=C.getDataC();
830     escriptDataC _D=D.getDataC();
831     escriptDataC _X=X.getDataC();
832     escriptDataC _Y=Y.getDataC();
833     escriptDataC _d=d.getDataC();
834     escriptDataC _y=y.getDataC();
835     escriptDataC _d_contact=d_contact.getDataC();
836     escriptDataC _y_contact=y_contact.getDataC();
837 jgs 149
838 gross 1367 Finley_Mesh* mesh=m_finleyMesh.get();
839     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
840    
841    
842     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_tmp, &_M);
843     checkFinleyError();
844     /* add mass matix to lumped mass matrix of transport problem */
845     double* tmp_prt=getSampleData(&_tmp,0);
846     int i;
847     int n=Paso_FCTransportProblem_getTotalNumRows(_tp);
848     #pragma omp parallel for private(i) schedule(static)
849     for (i=0;i<n ;++i) _tp->lumped_mass_matrix[i]+=tmp_prt[i];
850    
851     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, 0, 0, &_D, &_X, &_Y );
852     checkFinleyError();
853    
854     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->flux_matrix, &_source, 0, &_B, &_C, 0, 0, 0 );
855     checkFinleyError();
856    
857     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
858     checkFinleyError();
859    
860     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
861     checkFinleyError();
862     }
863    
864 jgs 102 //
865 jgs 82 // interpolates data between different function spaces:
866     //
867 jgs 480 void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
868 jgs 82 {
869     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
870     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
871 bcumming 751 if (inDomain!=*this)
872     throw FinleyAdapterException("Error - Illegal domain of interpolant.");
873 jgs 82 if (targetDomain!=*this)
874 bcumming 751 throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
875 jgs 82
876     Finley_Mesh* mesh=m_finleyMesh.get();
877 gross 1062 escriptDataC _target=target.getDataC();
878     escriptDataC _in=in.getDataC();
879 jgs 82 switch(in.getFunctionSpace().getTypeCode()) {
880     case(Nodes):
881     switch(target.getFunctionSpace().getTypeCode()) {
882     case(Nodes):
883 gross 1062 case(ReducedNodes):
884     case(DegreesOfFreedom):
885 jgs 82 case(ReducedDegreesOfFreedom):
886 gross 1062 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
887     break;
888     case(Elements):
889     case(ReducedElements):
890     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
891     break;
892     case(FaceElements):
893     case(ReducedFaceElements):
894     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
895     break;
896     case(Points):
897     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
898     break;
899     case(ContactElementsZero):
900     case(ReducedContactElementsZero):
901     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
902     break;
903     case(ContactElementsOne):
904     case(ReducedContactElementsOne):
905     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
906     break;
907     default:
908     stringstream temp;
909     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
910     throw FinleyAdapterException(temp.str());
911     break;
912     }
913     break;
914     case(ReducedNodes):
915     switch(target.getFunctionSpace().getTypeCode()) {
916     case(Nodes):
917     case(ReducedNodes):
918 jgs 82 case(DegreesOfFreedom):
919 gross 1062 case(ReducedDegreesOfFreedom):
920     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
921 jgs 82 break;
922     case(Elements):
923 gross 1062 case(ReducedElements):
924     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
925 jgs 82 break;
926     case(FaceElements):
927 gross 1062 case(ReducedFaceElements):
928     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
929 jgs 82 break;
930     case(Points):
931 gross 1062 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
932 jgs 82 break;
933     case(ContactElementsZero):
934 gross 1062 case(ReducedContactElementsZero):
935     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
936 jgs 82 break;
937     case(ContactElementsOne):
938 gross 1062 case(ReducedContactElementsOne):
939     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
940 jgs 82 break;
941     default:
942 jgs 150 stringstream temp;
943     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
944     throw FinleyAdapterException(temp.str());
945 jgs 82 break;
946     }
947     break;
948     case(Elements):
949     if (target.getFunctionSpace().getTypeCode()==Elements) {
950 gross 1062 Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
951 gross 1116 } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
952     Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
953 jgs 82 } else {
954 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
955 jgs 82 }
956     break;
957 gross 1062 case(ReducedElements):
958     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
959     Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
960     } else {
961     throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
962     }
963     break;
964 jgs 82 case(FaceElements):
965     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
966 gross 1062 Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
967 gross 1116 } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
968     Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
969 jgs 82 } else {
970 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
971 gross 1361 }
972     break;
973 gross 1062 case(ReducedFaceElements):
974 gross 1375 if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
975 gross 1062 Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
976     } else {
977     throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
978     }
979     break;
980 jgs 82 case(Points):
981     if (target.getFunctionSpace().getTypeCode()==Points) {
982 gross 1062 Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
983 jgs 82 } else {
984 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on points possible.");
985 jgs 82 }
986     break;
987     case(ContactElementsZero):
988     case(ContactElementsOne):
989     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
990 gross 1062 Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
991 gross 1116 } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
992     Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
993 jgs 82 } else {
994 jgs 150 throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
995 jgs 82 }
996     break;
997 gross 1062 case(ReducedContactElementsZero):
998     case(ReducedContactElementsOne):
999     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1000     Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1001     } else {
1002     throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1003     }
1004     break;
1005 bcumming 751 case(DegreesOfFreedom):
1006 jgs 82 switch(target.getFunctionSpace().getTypeCode()) {
1007     case(ReducedDegreesOfFreedom):
1008     case(DegreesOfFreedom):
1009 ksteube 1312 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1010     break;
1011    
1012 jgs 82 case(Nodes):
1013 gross 1062 case(ReducedNodes):
1014 ksteube 1312 if (getMPISize()>1) {
1015     escript::Data temp=escript::Data(in);
1016     temp.expand();
1017     escriptDataC _in2 = temp.getDataC();
1018     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1019     } else {
1020     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1021     }
1022 jgs 82 break;
1023     case(Elements):
1024 gross 1062 case(ReducedElements):
1025 ksteube 1312 if (getMPISize()>1) {
1026     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1027     escriptDataC _in2 = temp.getDataC();
1028     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1029     } else {
1030     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1031     }
1032 jgs 82 break;
1033     case(FaceElements):
1034 gross 1062 case(ReducedFaceElements):
1035 ksteube 1312 if (getMPISize()>1) {
1036     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1037     escriptDataC _in2 = temp.getDataC();
1038     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1039    
1040     } else {
1041     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1042     }
1043 jgs 82 break;
1044     case(Points):
1045 ksteube 1312 if (getMPISize()>1) {
1046     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1047     escriptDataC _in2 = temp.getDataC();
1048     } else {
1049     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1050     }
1051 jgs 82 break;
1052     case(ContactElementsZero):
1053     case(ContactElementsOne):
1054 gross 1062 case(ReducedContactElementsZero):
1055     case(ReducedContactElementsOne):
1056 ksteube 1312 if (getMPISize()>1) {
1057     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1058     escriptDataC _in2 = temp.getDataC();
1059     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1060     } else {
1061     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1062     }
1063 jgs 82 break;
1064     default:
1065 jgs 150 stringstream temp;
1066     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1067     throw FinleyAdapterException(temp.str());
1068 jgs 82 break;
1069     }
1070     break;
1071     case(ReducedDegreesOfFreedom):
1072     switch(target.getFunctionSpace().getTypeCode()) {
1073 gross 1062 case(Nodes):
1074     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1075     break;
1076     case(ReducedNodes):
1077 ksteube 1312 if (getMPISize()>1) {
1078     escript::Data temp=escript::Data(in);
1079     temp.expand();
1080     escriptDataC _in2 = temp.getDataC();
1081     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1082     } else {
1083     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1084     }
1085     break;
1086 gross 1062 case(DegreesOfFreedom):
1087     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1088     break;
1089 jgs 82 case(ReducedDegreesOfFreedom):
1090 gross 1062 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1091 jgs 82 break;
1092     case(Elements):
1093 gross 1062 case(ReducedElements):
1094 ksteube 1312 if (getMPISize()>1) {
1095     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1096     escriptDataC _in2 = temp.getDataC();
1097     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1098     } else {
1099     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1100     }
1101 jgs 82 break;
1102     case(FaceElements):
1103 gross 1062 case(ReducedFaceElements):
1104 ksteube 1312 if (getMPISize()>1) {
1105     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1106     escriptDataC _in2 = temp.getDataC();
1107     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1108     } else {
1109     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1110     }
1111 jgs 82 break;
1112     case(Points):
1113 ksteube 1312 if (getMPISize()>1) {
1114     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1115     escriptDataC _in2 = temp.getDataC();
1116     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1117     } else {
1118     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1119     }
1120 jgs 82 break;
1121     case(ContactElementsZero):
1122     case(ContactElementsOne):
1123 gross 1062 case(ReducedContactElementsZero):
1124     case(ReducedContactElementsOne):
1125 ksteube 1312 if (getMPISize()>1) {
1126     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1127     escriptDataC _in2 = temp.getDataC();
1128     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1129     } else {
1130     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1131     }
1132 jgs 82 break;
1133     default:
1134 jgs 150 stringstream temp;
1135     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1136     throw FinleyAdapterException(temp.str());
1137 jgs 82 break;
1138     }
1139     break;
1140     default:
1141 jgs 150 stringstream temp;
1142     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1143     throw FinleyAdapterException(temp.str());
1144 jgs 82 break;
1145     }
1146     checkFinleyError();
1147     }
1148    
1149     //
1150     // copies the locations of sample points into x:
1151     //
1152 jgs 480 void MeshAdapter::setToX(escript::Data& arg) const
1153 jgs 82 {
1154     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1155     if (argDomain!=*this)
1156     throw FinleyAdapterException("Error - Illegal domain of data point locations");
1157     Finley_Mesh* mesh=m_finleyMesh.get();
1158     // in case of values node coordinates we can do the job directly:
1159     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1160 gross 1062 escriptDataC _arg=arg.getDataC();
1161     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1162 jgs 82 } else {
1163 jgs 480 escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1164 gross 1062 escriptDataC _tmp_data=tmp_data.getDataC();
1165     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1166 jgs 82 // this is then interpolated onto arg:
1167     interpolateOnDomain(arg,tmp_data);
1168     }
1169     checkFinleyError();
1170     }
1171 jgs 149
1172 jgs 82 //
1173     // return the normal vectors at the location of data points as a Data object:
1174     //
1175 jgs 480 void MeshAdapter::setToNormal(escript::Data& normal) const
1176 jgs 82 {
1177     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());
1178     if (normalDomain!=*this)
1179     throw FinleyAdapterException("Error - Illegal domain of normal locations");
1180     Finley_Mesh* mesh=m_finleyMesh.get();
1181 gross 1062 escriptDataC _normal=normal.getDataC();
1182 jgs 82 switch(normal.getFunctionSpace().getTypeCode()) {
1183     case(Nodes):
1184 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1185 jgs 82 break;
1186 gross 1062 case(ReducedNodes):
1187     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1188     break;
1189 jgs 82 case(Elements):
1190 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1191 jgs 82 break;
1192 gross 1062 case(ReducedElements):
1193     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1194     break;
1195 jgs 82 case (FaceElements):
1196 gross 1062 Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1197 jgs 82 break;
1198 gross 1062 case (ReducedFaceElements):
1199     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1200     break;
1201 jgs 82 case(Points):
1202 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1203 jgs 82 break;
1204     case (ContactElementsOne):
1205     case (ContactElementsZero):
1206 gross 1062 Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1207 jgs 82 break;
1208 gross 1062 case (ReducedContactElementsOne):
1209     case (ReducedContactElementsZero):
1210     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1211     break;
1212 jgs 82 case(DegreesOfFreedom):
1213 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1214 jgs 82 break;
1215     case(ReducedDegreesOfFreedom):
1216 jgs 150 throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1217 jgs 82 break;
1218     default:
1219 jgs 150 stringstream temp;
1220     temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1221     throw FinleyAdapterException(temp.str());
1222 jgs 82 break;
1223     }
1224     checkFinleyError();
1225     }
1226 jgs 149
1227 jgs 82 //
1228     // interpolates data to other domain:
1229     //
1230 jgs 480 void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1231 jgs 82 {
1232     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
1233     if (targetDomain!=*this)
1234     throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1235    
1236 jgs 150 throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1237 jgs 82 }
1238 jgs 149
1239 jgs 82 //
1240     // calculates the integral of a function defined of arg:
1241     //
1242 jgs 480 void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1243 jgs 82 {
1244     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1245     if (argDomain!=*this)
1246     throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1247    
1248 ksteube 1312 double blocktimer_start = blocktimer_time();
1249 jgs 82 Finley_Mesh* mesh=m_finleyMesh.get();
1250 ksteube 1312 escriptDataC _temp;
1251     escript::Data temp;
1252 gross 1062 escriptDataC _arg=arg.getDataC();
1253 jgs 82 switch(arg.getFunctionSpace().getTypeCode()) {
1254     case(Nodes):
1255 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1256     _temp=temp.getDataC();
1257     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1258 jgs 82 break;
1259 gross 1062 case(ReducedNodes):
1260 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1261     _temp=temp.getDataC();
1262     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1263 gross 1062 break;
1264 jgs 82 case(Elements):
1265 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1266 jgs 82 break;
1267 gross 1062 case(ReducedElements):
1268     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1269 gross 1064 break;
1270 jgs 82 case(FaceElements):
1271 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1272 jgs 82 break;
1273 gross 1062 case(ReducedFaceElements):
1274     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1275     break;
1276 jgs 82 case(Points):
1277 jgs 150 throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1278 jgs 82 break;
1279     case(ContactElementsZero):
1280 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1281 jgs 82 break;
1282 gross 1062 case(ReducedContactElementsZero):
1283     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1284     break;
1285 jgs 82 case(ContactElementsOne):
1286 gross 1062 Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287 jgs 82 break;
1288 gross 1062 case(ReducedContactElementsOne):
1289     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1290     break;
1291 jgs 82 case(DegreesOfFreedom):
1292 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1293     _temp=temp.getDataC();
1294     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1295 jgs 82 break;
1296     case(ReducedDegreesOfFreedom):
1297 ksteube 1312 temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1298     _temp=temp.getDataC();
1299     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1300 jgs 82 break;
1301     default:
1302 jgs 150 stringstream temp;
1303     temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1304     throw FinleyAdapterException(temp.str());
1305 jgs 82 break;
1306     }
1307     checkFinleyError();
1308 ksteube 1312 blocktimer_increment("integrate()", blocktimer_start);
1309 jgs 82 }
1310 jgs 149
1311 jgs 82 //
1312     // calculates the gradient of arg:
1313     //
1314 jgs 480 void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1315 jgs 82 {
1316     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1317     if (argDomain!=*this)
1318     throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1319     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());
1320     if (gradDomain!=*this)
1321     throw FinleyAdapterException("Error - Illegal domain of gradient");
1322    
1323     Finley_Mesh* mesh=m_finleyMesh.get();
1324 gross 1062 escriptDataC _grad=grad.getDataC();
1325 bcumming 751 escriptDataC nodeDataC;
1326 ksteube 1312 escript::Data temp;
1327     if (getMPISize()>1) {
1328     if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1329     temp=escript::Data( arg, continuousFunction(asAbstractContinuousDomain()) );
1330     nodeDataC = temp.getDataC();
1331     } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1332     temp=escript::Data( arg, reducedContinuousFunction(asAbstractContinuousDomain()) );
1333     nodeDataC = temp.getDataC();
1334     } else {
1335     nodeDataC = arg.getDataC();
1336     }
1337     } else {
1338     nodeDataC = arg.getDataC();
1339 bcumming 751 }
1340 jgs 82 switch(grad.getFunctionSpace().getTypeCode()) {
1341     case(Nodes):
1342 jgs 150 throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1343 jgs 82 break;
1344 gross 1062 case(ReducedNodes):
1345     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1346     break;
1347 jgs 82 case(Elements):
1348 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1349 jgs 82 break;
1350 gross 1062 case(ReducedElements):
1351     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1352     break;
1353 jgs 82 case(FaceElements):
1354 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1355 jgs 82 break;
1356 gross 1062 case(ReducedFaceElements):
1357     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1358     break;
1359 jgs 82 case(Points):
1360 jgs 150 throw FinleyAdapterException("Error - Gradient at points is not supported.");
1361 jgs 82 break;
1362     case(ContactElementsZero):
1363 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1364 jgs 82 break;
1365 gross 1062 case(ReducedContactElementsZero):
1366     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1367     break;
1368 jgs 82 case(ContactElementsOne):
1369 gross 1062 Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370 jgs 82 break;
1371 gross 1062 case(ReducedContactElementsOne):
1372     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1373     break;
1374 jgs 82 case(DegreesOfFreedom):
1375 jgs 150 throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1376 jgs 82 break;
1377     case(ReducedDegreesOfFreedom):
1378 jgs 150 throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1379 jgs 82 break;
1380     default:
1381 jgs 150 stringstream temp;
1382     temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1383     throw FinleyAdapterException(temp.str());
1384 jgs 82 break;
1385     }
1386     checkFinleyError();
1387     }
1388 jgs 149
1389 jgs 82 //
1390     // returns the size of elements:
1391     //
1392 jgs 480 void MeshAdapter::setToSize(escript::Data& size) const
1393 jgs 82 {
1394     Finley_Mesh* mesh=m_finleyMesh.get();
1395     escriptDataC tmp=size.getDataC();
1396     switch(size.getFunctionSpace().getTypeCode()) {
1397     case(Nodes):
1398 jgs 150 throw FinleyAdapterException("Error - Size of nodes is not supported.");
1399 jgs 82 break;
1400 gross 1062 case(ReducedNodes):
1401     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1402     break;
1403 jgs 82 case(Elements):
1404     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1405     break;
1406 gross 1062 case(ReducedElements):
1407     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1408     break;
1409 jgs 82 case(FaceElements):
1410     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1411     break;
1412 gross 1062 case(ReducedFaceElements):
1413     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1414     break;
1415 jgs 82 case(Points):
1416 jgs 150 throw FinleyAdapterException("Error - Size of point elements is not supported.");
1417 jgs 82 break;
1418     case(ContactElementsZero):
1419     case(ContactElementsOne):
1420     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1421     break;
1422 gross 1062 case(ReducedContactElementsZero):
1423     case(ReducedContactElementsOne):
1424     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1425     break;
1426 jgs 82 case(DegreesOfFreedom):
1427 jgs 150 throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1428 jgs 82 break;
1429     case(ReducedDegreesOfFreedom):
1430 jgs 150 throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1431 jgs 82 break;
1432     default:
1433 jgs 150 stringstream temp;
1434     temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1435     throw FinleyAdapterException(temp.str());
1436 jgs 82 break;
1437     }
1438     checkFinleyError();
1439     }
1440 jgs 149
1441 jgs 82 // sets the location of nodes:
1442 jgs 480 void MeshAdapter::setNewX(const escript::Data& new_x)
1443 jgs 82 {
1444     Finley_Mesh* mesh=m_finleyMesh.get();
1445 bcumming 751 escriptDataC tmp;
1446 jgs 82 const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1447     if (newDomain!=*this)
1448     throw FinleyAdapterException("Error - Illegal domain of new point locations");
1449 bcumming 751 tmp = new_x.getDataC();
1450     Finley_Mesh_setCoordinates(mesh,&tmp);
1451 jgs 82 checkFinleyError();
1452     }
1453 jgs 149
1454 jgs 82 // saves a data array in openDX format:
1455 jgs 153 void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1456     {
1457     int MAX_namelength=256;
1458     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1459 woo409 757 /* win32 refactor */
1460     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1461     for(int i=0;i<num_data;i++)
1462     {
1463     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1464     }
1465 jgs 153
1466 woo409 757 char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1467     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1468     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1469    
1470 ksteube 1312 boost::python::list keys=arg.keys();
1471     for (int i=0;i<num_data;++i) {
1472     std::string n=boost::python::extract<std::string>(keys[i]);
1473 jgs 480 escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1474 jgs 153 if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1475 ksteube 1312 throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1476 jgs 153 data[i]=d.getDataC();
1477     ptr_data[i]=&(data[i]);
1478     c_names[i]=&(names[i][0]);
1479     if (n.length()>MAX_namelength-1) {
1480     strncpy(c_names[i],n.c_str(),MAX_namelength-1);
1481     c_names[i][MAX_namelength-1]='\0';
1482     } else {
1483     strcpy(c_names[i],n.c_str());
1484     }
1485     }
1486     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);
1487     checkFinleyError();
1488 woo409 757
1489     /* win32 refactor */
1490     TMPMEMFREE(c_names);
1491     TMPMEMFREE(data);
1492     TMPMEMFREE(ptr_data);
1493     for(int i=0;i<num_data;i++)
1494     {
1495     TMPMEMFREE(names[i]);
1496     }
1497     TMPMEMFREE(names);
1498    
1499 jgs 153 return;
1500 jgs 82 }
1501 jgs 149
1502 jgs 110 // saves a data array in openVTK format:
1503 jgs 153 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1504     {
1505     int MAX_namelength=256;
1506     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1507 woo409 757 /* win32 refactor */
1508     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1509     for(int i=0;i<num_data;i++)
1510     {
1511     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1512     }
1513 jgs 153
1514 woo409 757 char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1515     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1516     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1517    
1518 jgs 153 boost::python::list keys=arg.keys();
1519     for (int i=0;i<num_data;++i) {
1520 ksteube 1312 std::string n=boost::python::extract<std::string>(keys[i]);
1521 jgs 480 escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1522 jgs 153 if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1523     throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1524     data[i]=d.getDataC();
1525     ptr_data[i]=&(data[i]);
1526     c_names[i]=&(names[i][0]);
1527     if (n.length()>MAX_namelength-1) {
1528     strncpy(c_names[i],n.c_str(),MAX_namelength-1);
1529     c_names[i][MAX_namelength-1]='\0';
1530     } else {
1531     strcpy(c_names[i],n.c_str());
1532     }
1533     }
1534     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);
1535 dhawcroft 793
1536 ksteube 1312 checkFinleyError();
1537 woo409 757 /* win32 refactor */
1538     TMPMEMFREE(c_names);
1539     TMPMEMFREE(data);
1540     TMPMEMFREE(ptr_data);
1541     for(int i=0;i<num_data;i++)
1542     {
1543     TMPMEMFREE(names[i]);
1544     }
1545     TMPMEMFREE(names);
1546    
1547 jgs 153 return;
1548 jgs 110 }
1549 jgs 153
1550    
1551 jgs 82 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1552     SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1553     const int row_blocksize,
1554     const escript::FunctionSpace& row_functionspace,
1555     const int column_blocksize,
1556     const escript::FunctionSpace& column_functionspace,
1557 jgs 102 const int type) const
1558 jgs 82 {
1559     int reduceRowOrder=0;
1560     int reduceColOrder=0;
1561     // is the domain right?
1562     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());
1563     if (row_domain!=*this)
1564     throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1565     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());
1566     if (col_domain!=*this)
1567     throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1568     // is the function space type right
1569     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1570     reduceRowOrder=0;
1571     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1572     reduceRowOrder=1;
1573     } else {
1574     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1575     }
1576     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1577     reduceColOrder=0;
1578     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1579     reduceColOrder=1;
1580     } else {
1581     throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1582     }
1583     // generate matrix:
1584 jgs 102
1585 jgs 150 Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1586 jgs 82 checkFinleyError();
1587 ksteube 1312 Paso_SystemMatrix* fsystemMatrix;
1588     int trilinos = 0;
1589     if (trilinos) {
1590     #ifdef TRILINOS
1591     /* Allocation Epetra_VrbMatrix here */
1592     #endif
1593     }
1594     else {
1595     fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1596     }
1597 jgs 150 checkPasoError();
1598 ksteube 1312 Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1599 jgs 82 return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1600     }
1601 gross 1366 // creates a TransportProblemAdapter
1602     TransportProblemAdapter MeshAdapter::newTransportProblem(
1603     const double theta,
1604     const double dt_max,
1605     const int blocksize,
1606     const escript::FunctionSpace& functionspace,
1607     const int type) const
1608     {
1609     int reduceOrder=0;
1610     // is the domain right?
1611     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1612     if (domain!=*this)
1613     throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1614     // is the function space type right
1615     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1616     reduceOrder=0;
1617     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1618     reduceOrder=1;
1619     } else {
1620     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1621     }
1622     // generate matrix:
1623    
1624     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1625     checkFinleyError();
1626     Paso_FCTransportProblem* transportProblem;
1627     transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize);
1628     checkPasoError();
1629     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1630     return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace);
1631     }
1632 jgs 149
1633 jgs 82 //
1634     // vtkObject MeshAdapter::createVtkObject() const
1635     // TODO:
1636     //
1637 jgs 149
1638 jgs 82 //
1639     // returns true if data at the atom_type is considered as being cell centered:
1640     bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1641     {
1642     switch(functionSpaceCode) {
1643     case(Nodes):
1644     case(DegreesOfFreedom):
1645     case(ReducedDegreesOfFreedom):
1646     return false;
1647     break;
1648     case(Elements):
1649     case(FaceElements):
1650     case(Points):
1651     case(ContactElementsZero):
1652     case(ContactElementsOne):
1653 gross 1062 case(ReducedElements):
1654     case(ReducedFaceElements):
1655     case(ReducedContactElementsZero):
1656     case(ReducedContactElementsOne):
1657 jgs 82 return true;
1658     break;
1659     default:
1660 jgs 150 stringstream temp;
1661     temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1662     throw FinleyAdapterException(temp.str());
1663 jgs 82 break;
1664     }
1665     checkFinleyError();
1666     return false;
1667     }
1668 jgs 149
1669 jgs 82 bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1670     {
1671     switch(functionSpaceType_source) {
1672     case(Nodes):
1673     switch(functionSpaceType_target) {
1674     case(Nodes):
1675 gross 1062 case(ReducedNodes):
1676 jgs 82 case(ReducedDegreesOfFreedom):
1677     case(DegreesOfFreedom):
1678     case(Elements):
1679 gross 1062 case(ReducedElements):
1680 jgs 82 case(FaceElements):
1681 gross 1062 case(ReducedFaceElements):
1682 jgs 82 case(Points):
1683     case(ContactElementsZero):
1684 gross 1062 case(ReducedContactElementsZero):
1685 jgs 82 case(ContactElementsOne):
1686 gross 1062 case(ReducedContactElementsOne):
1687 jgs 82 return true;
1688     default:
1689 jgs 150 stringstream temp;
1690     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1691     throw FinleyAdapterException(temp.str());
1692 jgs 82 }
1693     break;
1694 gross 1062 case(ReducedNodes):
1695     switch(functionSpaceType_target) {
1696     case(ReducedNodes):
1697     case(ReducedDegreesOfFreedom):
1698     case(Elements):
1699     case(ReducedElements):
1700     case(FaceElements):
1701     case(ReducedFaceElements):
1702     case(Points):
1703     case(ContactElementsZero):
1704     case(ReducedContactElementsZero):
1705     case(ContactElementsOne):
1706     case(ReducedContactElementsOne):
1707     return true;
1708     case(Nodes):
1709     case(DegreesOfFreedom):
1710     return false;
1711     default:
1712     stringstream temp;
1713     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1714     throw FinleyAdapterException(temp.str());
1715     }
1716     break;
1717 jgs 82 case(Elements):
1718     if (functionSpaceType_target==Elements) {
1719     return true;
1720 gross 1116 } else if (functionSpaceType_target==ReducedElements) {
1721     return true;
1722 jgs 82 } else {
1723     return false;
1724     }
1725 gross 1062 case(ReducedElements):
1726     if (functionSpaceType_target==ReducedElements) {
1727     return true;
1728     } else {
1729     return false;
1730     }
1731 jgs 82 case(FaceElements):
1732     if (functionSpaceType_target==FaceElements) {
1733     return true;
1734 gross 1116 } else if (functionSpaceType_target==ReducedFaceElements) {
1735     return true;
1736 jgs 82 } else {
1737     return false;
1738     }
1739 gross 1062 case(ReducedFaceElements):
1740     if (functionSpaceType_target==ReducedFaceElements) {
1741     return true;
1742     } else {
1743     return false;
1744     }
1745 jgs 82 case(Points):
1746     if (functionSpaceType_target==Points) {
1747     return true;
1748     } else {
1749     return false;
1750     }
1751     case(ContactElementsZero):
1752     case(ContactElementsOne):
1753     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1754     return true;
1755 gross 1116 } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1756     return true;
1757 jgs 82 } else {
1758     return false;
1759     }
1760 gross 1062 case(ReducedContactElementsZero):
1761     case(ReducedContactElementsOne):
1762     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1763     return true;
1764     } else {
1765     return false;
1766     }
1767 jgs 82 case(DegreesOfFreedom):
1768     switch(functionSpaceType_target) {
1769     case(ReducedDegreesOfFreedom):
1770     case(DegreesOfFreedom):
1771     case(Nodes):
1772 gross 1062 case(ReducedNodes):
1773 jgs 82 case(Elements):
1774 gross 1062 case(ReducedElements):
1775     case(Points):
1776 jgs 82 case(FaceElements):
1777 gross 1062 case(ReducedFaceElements):
1778 jgs 82 case(ContactElementsZero):
1779 gross 1062 case(ReducedContactElementsZero):
1780 jgs 82 case(ContactElementsOne):
1781 gross 1062 case(ReducedContactElementsOne):
1782 jgs 82 return true;
1783     default:
1784 jgs 150 stringstream temp;
1785     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1786     throw FinleyAdapterException(temp.str());
1787 jgs 82 }
1788     break;
1789     case(ReducedDegreesOfFreedom):
1790     switch(functionSpaceType_target) {
1791     case(ReducedDegreesOfFreedom):
1792 gross 1062 case(ReducedNodes):
1793 jgs 82 case(Elements):
1794 gross 1062 case(ReducedElements):
1795 jgs 82 case(FaceElements):
1796 gross 1062 case(ReducedFaceElements):
1797 jgs 82 case(Points):
1798     case(ContactElementsZero):
1799 gross 1062 case(ReducedContactElementsZero):
1800 jgs 82 case(ContactElementsOne):
1801 gross 1062 case(ReducedContactElementsOne):
1802 jgs 82 return true;
1803 jgs 147 case(Nodes):
1804 jgs 82 case(DegreesOfFreedom):
1805     return false;
1806     default:
1807 jgs 150 stringstream temp;
1808     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1809     throw FinleyAdapterException(temp.str());
1810 jgs 82 }
1811     break;
1812     default:
1813 jgs 150 stringstream temp;
1814     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1815     throw FinleyAdapterException(temp.str());
1816 jgs 82 break;
1817     }
1818     checkFinleyError();
1819     return false;
1820     }
1821 jgs 149
1822 jgs 82 bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
1823     {
1824     return false;
1825     }
1826 jgs 104
1827 jgs 121 bool MeshAdapter::operator==(const AbstractDomain& other) const
1828 jgs 82 {
1829 jgs 121 const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1830     if (temp!=0) {
1831     return (m_finleyMesh==temp->m_finleyMesh);
1832     } else {
1833     return false;
1834     }
1835 jgs 82 }
1836    
1837 jgs 121 bool MeshAdapter::operator!=(const AbstractDomain& other) const
1838 jgs 104 {
1839 jgs 121 return !(operator==(other));
1840 jgs 104 }
1841    
1842 jgs 150 int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const
1843 jgs 102 {
1844 jgs 150 int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1845     checkPasoError();
1846 jgs 102 return out;
1847     }
1848 jgs 149
1849 jgs 480 escript::Data MeshAdapter::getX() const
1850 jgs 102 {
1851     return continuousFunction(asAbstractContinuousDomain()).getX();
1852     }
1853 jgs 149
1854 jgs 480 escript::Data MeshAdapter::getNormal() const
1855 jgs 102 {
1856     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1857     }
1858 jgs 149
1859 jgs 480 escript::Data MeshAdapter::getSize() const
1860 jgs 102 {
1861     return function(asAbstractContinuousDomain()).getSize();
1862     }
1863    
1864 gross 1062 int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1865     {
1866     int *out=0,i;
1867     Finley_Mesh* mesh=m_finleyMesh.get();
1868     switch (functionSpaceType) {
1869     case(Nodes):
1870 ksteube 1312 out=mesh->Nodes->Id;
1871     break;
1872 gross 1062 case(ReducedNodes):
1873 ksteube 1312 out=mesh->Nodes->reducedNodesId;
1874 gross 1062 break;
1875     case(Elements):
1876 gross 1080 out=mesh->Elements->Id;
1877 gross 1062 break;
1878     case(ReducedElements):
1879     out=mesh->Elements->Id;
1880     break;
1881     case(FaceElements):
1882     out=mesh->FaceElements->Id;
1883     break;
1884     case(ReducedFaceElements):
1885     out=mesh->FaceElements->Id;
1886     break;
1887     case(Points):
1888     out=mesh->Points->Id;
1889     break;
1890     case(ContactElementsZero):
1891     out=mesh->ContactElements->Id;
1892     break;
1893     case(ReducedContactElementsZero):
1894     out=mesh->ContactElements->Id;
1895     break;
1896     case(ContactElementsOne):
1897     out=mesh->ContactElements->Id;
1898     break;
1899     case(ReducedContactElementsOne):
1900     out=mesh->ContactElements->Id;
1901     break;
1902     case(DegreesOfFreedom):
1903 ksteube 1312 out=mesh->Nodes->degreesOfFreedomId;
1904 gross 1062 break;
1905     case(ReducedDegreesOfFreedom):
1906 ksteube 1312 out=mesh->Nodes->reducedDegreesOfFreedomId;
1907 gross 1062 break;
1908     default:
1909     stringstream temp;
1910     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1911     throw FinleyAdapterException(temp.str());
1912     break;
1913     }
1914     return out;
1915     }
1916 jgs 110 int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1917     {
1918 gross 547 int out=0;
1919     Finley_Mesh* mesh=m_finleyMesh.get();
1920     switch (functionSpaceType) {
1921     case(Nodes):
1922     out=mesh->Nodes->Tag[sampleNo];
1923     break;
1924 gross 1062 case(ReducedNodes):
1925     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1926     break;
1927 gross 547 case(Elements):
1928     out=mesh->Elements->Tag[sampleNo];
1929     break;
1930 gross 1062 case(ReducedElements):
1931     out=mesh->Elements->Tag[sampleNo];
1932     break;
1933 gross 547 case(FaceElements):
1934     out=mesh->FaceElements->Tag[sampleNo];
1935     break;
1936 gross 1062 case(ReducedFaceElements):
1937     out=mesh->FaceElements->Tag[sampleNo];
1938     break;
1939 gross 547 case(Points):
1940     out=mesh->Points->Tag[sampleNo];
1941     break;
1942     case(ContactElementsZero):
1943     out=mesh->ContactElements->Tag[sampleNo];
1944     break;
1945 gross 1062 case(ReducedContactElementsZero):
1946     out=mesh->ContactElements->Tag[sampleNo];
1947     break;
1948 gross 547 case(ContactElementsOne):
1949     out=mesh->ContactElements->Tag[sampleNo];
1950     break;
1951 gross 1062 case(ReducedContactElementsOne):
1952     out=mesh->ContactElements->Tag[sampleNo];
1953 gross 547 break;
1954     case(DegreesOfFreedom):
1955 gross 1062 throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1956 gross 547 break;
1957     case(ReducedDegreesOfFreedom):
1958 gross 1062 throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1959 gross 547 break;
1960     default:
1961     stringstream temp;
1962     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1963     throw FinleyAdapterException(temp.str());
1964     break;
1965     }
1966     return out;
1967 jgs 110 }
1968    
1969 gross 1062
1970 gross 767 void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1971     {
1972     Finley_Mesh* mesh=m_finleyMesh.get();
1973     escriptDataC tmp=mask.getDataC();
1974     switch(functionSpaceType) {
1975     case(Nodes):
1976     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1977     break;
1978 gross 1062 case(ReducedNodes):
1979     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1980     break;
1981 gross 767 case(DegreesOfFreedom):
1982     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1983     break;
1984     case(ReducedDegreesOfFreedom):
1985     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1986     break;
1987     case(Elements):
1988     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1989     break;
1990 gross 1062 case(ReducedElements):
1991     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1992     break;
1993 gross 767 case(FaceElements):
1994     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1995     break;
1996 gross 1062 case(ReducedFaceElements):
1997     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1998     break;
1999 gross 767 case(Points):
2000     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2001     break;
2002     case(ContactElementsZero):
2003     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2004     break;
2005 gross 1062 case(ReducedContactElementsZero):
2006     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2007     break;
2008 gross 767 case(ContactElementsOne):
2009     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2010     break;
2011 gross 1062 case(ReducedContactElementsOne):
2012     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2013     break;
2014 gross 767 default:
2015     stringstream temp;
2016     temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2017     throw FinleyAdapterException(temp.str());
2018     }
2019     checkFinleyError();
2020     return;
2021     }
2022    
2023 gross 1044 void MeshAdapter::setTagMap(const std::string& name, int tag)
2024     {
2025     Finley_Mesh* mesh=m_finleyMesh.get();
2026     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2027     checkPasoError();
2028     // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2029     }
2030 gross 767
2031 gross 1044 int MeshAdapter::getTag(const std::string& name) const
2032     {
2033     Finley_Mesh* mesh=m_finleyMesh.get();
2034     int tag=0;
2035     tag=Finley_Mesh_getTag(mesh, name.c_str());
2036     checkPasoError();
2037     // throwStandardException("MeshAdapter::getTag is not implemented.");
2038     return tag;
2039     }
2040    
2041     bool MeshAdapter::isValidTagName(const std::string& name) const
2042     {
2043     Finley_Mesh* mesh=m_finleyMesh.get();
2044     return Finley_Mesh_isValidTagName(mesh,name.c_str());
2045     }
2046    
2047     std::string MeshAdapter::showTagNames() const
2048     {
2049     stringstream temp;
2050     Finley_Mesh* mesh=m_finleyMesh.get();
2051     Finley_TagMap* tag_map=mesh->TagMap;
2052     while (tag_map) {
2053     temp << tag_map->name;
2054     tag_map=tag_map->next;
2055     if (tag_map) temp << ", ";
2056     }
2057 ksteube 1312 return temp.str();
2058 gross 1044 }
2059    
2060 jgs 82 } // end of namespace

Properties

Name Value
svn:eol-style native
svn:keywords Author Date Id Revision

  ViewVC Help
Powered by ViewVC 1.1.26