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

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Revision 1716 - (hide annotations)
Thu Aug 21 05:03:49 2008 UTC (10 years, 8 months ago) by gross
File size: 84445 byte(s)
getListOfTags method added to FunctionSpace class
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 phornby 1455 #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH 256
28    
29 jgs 82 using namespace std;
30     using namespace escript;
31    
32     namespace finley {
33 jgs 149
34 jgs 82 //
35 jgs 149 // define the static constants
36 jgs 82 MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
37     const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
38     const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
39     const int MeshAdapter::Nodes=FINLEY_NODES;
40 gross 1062 const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
41 jgs 82 const int MeshAdapter::Elements=FINLEY_ELEMENTS;
42 gross 1059 const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
43 jgs 82 const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
44 gross 1059 const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
45 jgs 82 const int MeshAdapter::Points=FINLEY_POINTS;
46     const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
47 gross 1059 const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
48 jgs 82 const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49 gross 1059 const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
50 jgs 82
51     MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52     {
53 phornby 1628 setFunctionSpaceTypeNames();
54     //
55     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
56     // for us.
57     m_finleyMesh.reset(finleyMesh,null_deleter());
58 jgs 82 }
59 jgs 149
60 jgs 82 //
61     // The copy constructor should just increment the use count
62     MeshAdapter::MeshAdapter(const MeshAdapter& in):
63     m_finleyMesh(in.m_finleyMesh)
64     {
65 phornby 1628 setFunctionSpaceTypeNames();
66 jgs 82 }
67    
68     MeshAdapter::~MeshAdapter()
69     {
70 phornby 1628 //
71     // I hope the case for the pointer being zero has been taken care of.
72     // cout << "In MeshAdapter destructor." << endl;
73     if (m_finleyMesh.unique()) {
74     Finley_Mesh_free(m_finleyMesh.get());
75     }
76 jgs 82 }
77    
78 ksteube 1312 int MeshAdapter::getMPISize() const
79     {
80     return m_finleyMesh.get()->MPIInfo->size;
81     }
82     int MeshAdapter::getMPIRank() const
83     {
84     return m_finleyMesh.get()->MPIInfo->rank;
85     }
86    
87    
88 jgs 82 Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
89     return m_finleyMesh.get();
90     }
91    
92     void MeshAdapter::write(const std::string& fileName) const
93     {
94 phornby 1628 char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
95     strcpy(fName,fileName.c_str());
96     Finley_Mesh_write(m_finleyMesh.get(),fName);
97     checkFinleyError();
98     TMPMEMFREE(fName);
99 jgs 82 }
100    
101 ksteube 1339 void MeshAdapter::Print_Mesh_Info(const bool full=false) const
102 ksteube 1326 {
103 phornby 1628 Finley_PrintMesh_Info(m_finleyMesh.get(), full);
104 ksteube 1326 }
105    
106 ksteube 1312 void MeshAdapter::dump(const std::string& fileName) const
107     {
108 ksteube 1343 #ifdef USE_NETCDF
109 ksteube 1347 const NcDim* ncdims[12];
110 trankine 1632 NcVar *ids;
111 ksteube 1343 int *int_ptr;
112     Finley_Mesh *mesh = m_finleyMesh.get();
113 ksteube 1347 Finley_TagMap* tag_map;
114     int num_Tags = 0;
115 ksteube 1343 int mpi_size = mesh->MPIInfo->size;
116     int mpi_rank = mesh->MPIInfo->rank;
117     int numDim = mesh->Nodes->numDim;
118     int numNodes = mesh->Nodes->numNodes;
119     int num_Elements = mesh->Elements->numElements;
120     int num_FaceElements = mesh->FaceElements->numElements;
121     int num_ContactElements = mesh->ContactElements->numElements;
122     int num_Points = mesh->Points->numElements;
123     int num_Elements_numNodes = mesh->Elements->numNodes;
124     int num_FaceElements_numNodes = mesh->FaceElements->numNodes;
125     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
126    
127 phornby 1628 // I don't think the strdup is needed since Paso_MPI_appendRankToFileName
128     // does it's own allocation.
129     // char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);
130    
131     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
132     mpi_size, mpi_rank);
133    
134 ksteube 1347 /* Figure out how much storage is required for tags */
135     tag_map = mesh->TagMap;
136     if (tag_map) {
137 phornby 1628 while (tag_map) {
138     num_Tags++;
139     tag_map=tag_map->next;
140     }
141 ksteube 1347 }
142    
143 ksteube 1343 // NetCDF error handler
144     NcError err(NcError::verbose_nonfatal);
145     // Create the file.
146     NcFile dataFile(newFileName, NcFile::Replace);
147     // check if writing was successful
148     if (!dataFile.is_valid())
149 phornby 1628 throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
150 ksteube 1343
151     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
152     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
153 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
154 ksteube 1343 if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
155 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
156 ksteube 1343 if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
157 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
158 ksteube 1343 if (num_Elements>0)
159     if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
160 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
161 ksteube 1343 if (num_FaceElements>0)
162     if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
163 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
164 ksteube 1343 if (num_ContactElements>0)
165     if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
166 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
167 ksteube 1343 if (num_Points>0)
168     if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
169 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
170 ksteube 1343 if (num_Elements>0)
171     if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
172 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
173 ksteube 1343 if (num_FaceElements>0)
174     if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
175 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
176 ksteube 1343 if (num_ContactElements>0)
177     if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
178 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
179 ksteube 1347 if (num_Tags>0)
180     if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
181 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
182 ksteube 1343
183 ksteube 1345 // Attributes: MPI size, MPI rank, Name, order, reduced_order
184 ksteube 1343 if (!dataFile.add_att("mpi_size", mpi_size) )
185 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
186 ksteube 1343 if (!dataFile.add_att("mpi_rank", mpi_rank) )
187 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
188 ksteube 1343 if (!dataFile.add_att("Name",mesh->Name) )
189 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
190 ksteube 1345 if (!dataFile.add_att("numDim",numDim) )
191 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
192 ksteube 1343 if (!dataFile.add_att("order",mesh->order) )
193 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
194 ksteube 1343 if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
195 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
196 ksteube 1345 if (!dataFile.add_att("numNodes",numNodes) )
197 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
198 ksteube 1343 if (!dataFile.add_att("num_Elements",num_Elements) )
199 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
200 ksteube 1343 if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
201 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
202 ksteube 1343 if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
203 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
204 ksteube 1343 if (!dataFile.add_att("num_Points",num_Points) )
205 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
206 ksteube 1346 if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
207 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
208 ksteube 1346 if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
209 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
210 ksteube 1346 if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
211 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
212 ksteube 1347 if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
213     throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
214     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
215     throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
216     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
217     throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
218     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
219     throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
220     if (!dataFile.add_att("num_Tags", num_Tags) )
221     throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
222 ksteube 1343
223     // // // // // Nodes // // // // //
224    
225 ksteube 1345 // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
226     if (numNodes>0) {
227    
228 phornby 1628 // Nodes Id
229     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
230     throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
231     int_ptr = &mesh->Nodes->Id[0];
232     if (! (ids->put(int_ptr, numNodes)) )
233     throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
234 ksteube 1343
235 phornby 1628 // Nodes Tag
236     if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
237     throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
238     int_ptr = &mesh->Nodes->Tag[0];
239     if (! (ids->put(int_ptr, numNodes)) )
240     throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
241 ksteube 1343
242 phornby 1628 // Nodes gDOF
243     if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
244     throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
245     int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
246     if (! (ids->put(int_ptr, numNodes)) )
247     throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
248 ksteube 1343
249 phornby 1628 // Nodes global node index
250     if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
251     throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
252     int_ptr = &mesh->Nodes->globalNodesIndex[0];
253     if (! (ids->put(int_ptr, numNodes)) )
254     throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
255 ksteube 1343
256 phornby 1628 // Nodes grDof
257     if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
258     throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
259     int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
260     if (! (ids->put(int_ptr, numNodes)) )
261     throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
262 ksteube 1343
263 phornby 1628 // Nodes grNI
264     if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
265     throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
266     int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
267     if (! (ids->put(int_ptr, numNodes)) )
268     throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
269 ksteube 1343
270 phornby 1628 // Nodes Coordinates
271     if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
272     throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
273     if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
274     throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
275 ksteube 1343
276 phornby 1628 // Nodes degreesOfFreedomDistribution
277     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
278     throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
279     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
280     if (! (ids->put(int_ptr, mpi_size+1)) )
281     throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
282 ksteube 1343
283 ksteube 1345 }
284    
285 ksteube 1343 // // // // // Elements // // // // //
286    
287     if (num_Elements>0) {
288    
289 phornby 1628 // Temp storage to gather node IDs
290     int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);
291 ksteube 1343
292 phornby 1628 // Elements_Id
293     if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
294     throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
295     int_ptr = &mesh->Elements->Id[0];
296     if (! (ids->put(int_ptr, num_Elements)) )
297     throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
298 ksteube 1343
299 phornby 1628 // Elements_Tag
300     if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
301     throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
302     int_ptr = &mesh->Elements->Tag[0];
303     if (! (ids->put(int_ptr, num_Elements)) )
304     throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
305 ksteube 1343
306 phornby 1628 // Elements_Owner
307     if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
308     throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
309     int_ptr = &mesh->Elements->Owner[0];
310     if (! (ids->put(int_ptr, num_Elements)) )
311     throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
312 ksteube 1343
313 phornby 1628 // Elements_Color
314     if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
315     throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
316     int_ptr = &mesh->Elements->Color[0];
317     if (! (ids->put(int_ptr, num_Elements)) )
318     throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
319 ksteube 1343
320 phornby 1628 // Elements_Nodes
321     for (int i=0; i<num_Elements; i++)
322     for (int j=0; j<num_Elements_numNodes; j++)
323     Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];
324     if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
325     throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
326     if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )
327     throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
328 ksteube 1343
329 phornby 1628 TMPMEMFREE(Elements_Nodes);
330 ksteube 1344
331 ksteube 1343 }
332    
333     // // // // // Face_Elements // // // // //
334    
335     if (num_FaceElements>0) {
336    
337 phornby 1628 // Temp storage to gather node IDs
338     int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);
339 ksteube 1343
340 phornby 1628 // FaceElements_Id
341     if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
342     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
343     int_ptr = &mesh->FaceElements->Id[0];
344     if (! (ids->put(int_ptr, num_FaceElements)) )
345     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
346 ksteube 1343
347 phornby 1628 // FaceElements_Tag
348     if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
349     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
350     int_ptr = &mesh->FaceElements->Tag[0];
351     if (! (ids->put(int_ptr, num_FaceElements)) )
352     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
353 ksteube 1343
354 phornby 1628 // FaceElements_Owner
355     if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
356     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
357     int_ptr = &mesh->FaceElements->Owner[0];
358     if (! (ids->put(int_ptr, num_FaceElements)) )
359     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
360 ksteube 1343
361 phornby 1628 // FaceElements_Color
362     if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
363     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
364     int_ptr = &mesh->FaceElements->Color[0];
365     if (! (ids->put(int_ptr, num_FaceElements)) )
366     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
367 ksteube 1343
368 phornby 1628 // FaceElements_Nodes
369     for (int i=0; i<num_FaceElements; i++)
370     for (int j=0; j<num_FaceElements_numNodes; j++)
371     FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];
372     if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
373     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
374     if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
375     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
376 ksteube 1343
377 phornby 1628 TMPMEMFREE(FaceElements_Nodes);
378 ksteube 1344
379 ksteube 1343 }
380    
381     // // // // // Contact_Elements // // // // //
382    
383     if (num_ContactElements>0) {
384    
385 phornby 1628 // Temp storage to gather node IDs
386     int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);
387 ksteube 1343
388 phornby 1628 // ContactElements_Id
389     if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
390     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
391     int_ptr = &mesh->ContactElements->Id[0];
392     if (! (ids->put(int_ptr, num_ContactElements)) )
393     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
394 ksteube 1343
395 phornby 1628 // ContactElements_Tag
396     if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
397     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
398     int_ptr = &mesh->ContactElements->Tag[0];
399     if (! (ids->put(int_ptr, num_ContactElements)) )
400     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
401 ksteube 1343
402 phornby 1628 // ContactElements_Owner
403     if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
404     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
405     int_ptr = &mesh->ContactElements->Owner[0];
406     if (! (ids->put(int_ptr, num_ContactElements)) )
407     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
408 ksteube 1343
409 phornby 1628 // ContactElements_Color
410     if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
411     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
412     int_ptr = &mesh->ContactElements->Color[0];
413     if (! (ids->put(int_ptr, num_ContactElements)) )
414     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
415 ksteube 1343
416 phornby 1628 // ContactElements_Nodes
417     for (int i=0; i<num_ContactElements; i++)
418     for (int j=0; j<num_ContactElements_numNodes; j++)
419     ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];
420     if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
421     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
422     if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
423     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
424 ksteube 1343
425 phornby 1628 TMPMEMFREE(ContactElements_Nodes);
426 ksteube 1344
427 ksteube 1343 }
428    
429     // // // // // Points // // // // //
430    
431     if (num_Points>0) {
432    
433 phornby 1628 fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
434 ksteube 1343
435 phornby 1628 // Temp storage to gather node IDs
436     int *Points_Nodes = TMPMEMALLOC(num_Points,int);
437 ksteube 1343
438 phornby 1628 // Points_Id
439     if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
440     throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
441     int_ptr = &mesh->Points->Id[0];
442     if (! (ids->put(int_ptr, num_Points)) )
443     throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
444 ksteube 1343
445 phornby 1628 // Points_Tag
446     if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
447     throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
448     int_ptr = &mesh->Points->Tag[0];
449     if (! (ids->put(int_ptr, num_Points)) )
450     throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
451 ksteube 1343
452 phornby 1628 // Points_Owner
453     if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
454     throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
455     int_ptr = &mesh->Points->Owner[0];
456     if (! (ids->put(int_ptr, num_Points)) )
457     throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
458 ksteube 1343
459 phornby 1628 // Points_Color
460     if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
461     throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
462     int_ptr = &mesh->Points->Color[0];
463     if (! (ids->put(int_ptr, num_Points)) )
464     throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
465 ksteube 1343
466 phornby 1628 // Points_Nodes
467     // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
468     for (int i=0; i<num_Points; i++)
469     Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];
470     if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
471     throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
472     if (! (ids->put(&(Points_Nodes[0]), num_Points)) )
473     throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
474 ksteube 1343
475 phornby 1628 TMPMEMFREE(Points_Nodes);
476 ksteube 1344
477 ksteube 1343 }
478    
479     // // // // // TagMap // // // // //
480    
481 ksteube 1347 if (num_Tags>0) {
482 ksteube 1343
483 phornby 1628 // Temp storage to gather node IDs
484     int *Tags_keys = TMPMEMALLOC(num_Tags, int);
485     char name_temp[4096];
486 ksteube 1347
487 phornby 1628 /* Copy tag data into temp arrays */
488     tag_map = mesh->TagMap;
489     if (tag_map) {
490     int i = 0;
491     while (tag_map) {
492     Tags_keys[i++] = tag_map->tag_key;
493     tag_map=tag_map->next;
494     }
495     }
496 ksteube 1347
497 phornby 1628 // Tags_keys
498     if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
499     throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
500     int_ptr = &Tags_keys[0];
501     if (! (ids->put(int_ptr, num_Tags)) )
502     throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
503 ksteube 1347
504 phornby 1628 // Tags_names_*
505     // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
506     // because the NetCDF manual doesn't tell how to do an array of strings
507     tag_map = mesh->TagMap;
508     if (tag_map) {
509     int i = 0;
510     while (tag_map) {
511     sprintf(name_temp, "Tags_name_%d", i);
512     if (!dataFile.add_att(name_temp, tag_map->name) )
513     throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
514     tag_map=tag_map->next;
515     i++;
516     }
517     }
518 ksteube 1347
519 phornby 1628 TMPMEMFREE(Tags_keys);
520 ksteube 1347
521     }
522    
523    
524 ksteube 1343 // NetCDF file is closed by destructor of NcFile object
525     #else
526     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
527     #endif /* USE_NETCDF */
528     checkFinleyError();
529 ksteube 1312 }
530    
531 jgs 82 string MeshAdapter::getDescription() const
532     {
533 phornby 1628 return "FinleyMesh";
534 jgs 82 }
535    
536     string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
537     {
538 phornby 1628 FunctionSpaceNamesMapType::iterator loc;
539     loc=m_functionSpaceTypeNames.find(functionSpaceType);
540     if (loc==m_functionSpaceTypeNames.end()) {
541     return "Invalid function space type code.";
542     } else {
543     return loc->second;
544     }
545 jgs 82 }
546    
547     bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
548     {
549 phornby 1628 FunctionSpaceNamesMapType::iterator loc;
550     loc=m_functionSpaceTypeNames.find(functionSpaceType);
551     return (loc!=m_functionSpaceTypeNames.end());
552 jgs 82 }
553    
554     void MeshAdapter::setFunctionSpaceTypeNames()
555     {
556 phornby 1628 m_functionSpaceTypeNames.insert
557     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
558     m_functionSpaceTypeNames.insert
559     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
560     m_functionSpaceTypeNames.insert
561     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
562     m_functionSpaceTypeNames.insert
563     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
564     m_functionSpaceTypeNames.insert
565     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
566     m_functionSpaceTypeNames.insert
567     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
568     m_functionSpaceTypeNames.insert
569     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
570     m_functionSpaceTypeNames.insert
571     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
572     m_functionSpaceTypeNames.insert
573     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
574     m_functionSpaceTypeNames.insert
575     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
576     m_functionSpaceTypeNames.insert
577     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
578     m_functionSpaceTypeNames.insert
579     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
580     m_functionSpaceTypeNames.insert
581     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
582 jgs 82 }
583    
584     int MeshAdapter::getContinuousFunctionCode() const
585     {
586 phornby 1628 return Nodes;
587 jgs 82 }
588 gross 1062 int MeshAdapter::getReducedContinuousFunctionCode() const
589     {
590 phornby 1628 return ReducedNodes;
591 gross 1062 }
592 jgs 149
593 jgs 82 int MeshAdapter::getFunctionCode() const
594     {
595 phornby 1628 return Elements;
596 jgs 82 }
597 gross 1059 int MeshAdapter::getReducedFunctionCode() const
598     {
599 phornby 1628 return ReducedElements;
600 gross 1059 }
601 jgs 149
602 jgs 82 int MeshAdapter::getFunctionOnBoundaryCode() const
603     {
604 phornby 1628 return FaceElements;
605 jgs 82 }
606 gross 1059 int MeshAdapter::getReducedFunctionOnBoundaryCode() const
607     {
608 phornby 1628 return ReducedFaceElements;
609 gross 1059 }
610 jgs 149
611 jgs 82 int MeshAdapter::getFunctionOnContactZeroCode() const
612     {
613 phornby 1628 return ContactElementsZero;
614 jgs 82 }
615 gross 1059 int MeshAdapter::getReducedFunctionOnContactZeroCode() const
616     {
617 phornby 1628 return ReducedContactElementsZero;
618 gross 1059 }
619 jgs 149
620 jgs 82 int MeshAdapter::getFunctionOnContactOneCode() const
621     {
622 phornby 1628 return ContactElementsOne;
623 jgs 82 }
624 gross 1059 int MeshAdapter::getReducedFunctionOnContactOneCode() const
625     {
626 phornby 1628 return ReducedContactElementsOne;
627 gross 1059 }
628 jgs 82
629     int MeshAdapter::getSolutionCode() const
630     {
631 phornby 1628 return DegreesOfFreedom;
632 jgs 82 }
633 jgs 149
634 jgs 82 int MeshAdapter::getReducedSolutionCode() const
635     {
636 phornby 1628 return ReducedDegreesOfFreedom;
637 jgs 82 }
638 jgs 149
639 jgs 82 int MeshAdapter::getDiracDeltaFunctionCode() const
640     {
641 phornby 1628 return Points;
642 jgs 82 }
643 jgs 149
644 jgs 82 //
645     // return the spatial dimension of the Mesh:
646     //
647     int MeshAdapter::getDim() const
648     {
649 phornby 1628 int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
650     checkFinleyError();
651     return numDim;
652 jgs 82 }
653 jgs 149
654 jgs 82 //
655     // return the number of data points per sample and the number of samples
656     // needed to represent data on a parts of the mesh.
657     //
658     pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
659     {
660     int numDataPointsPerSample=0;
661     int numSamples=0;
662     Finley_Mesh* mesh=m_finleyMesh.get();
663     switch (functionSpaceCode) {
664 phornby 1628 case(Nodes):
665     numDataPointsPerSample=1;
666     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
667     break;
668     case(ReducedNodes):
669     numDataPointsPerSample=1;
670     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
671     break;
672     case(Elements):
673     if (mesh->Elements!=NULL) {
674     numSamples=mesh->Elements->numElements;
675     numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
676     }
677     break;
678     case(ReducedElements):
679     if (mesh->Elements!=NULL) {
680     numSamples=mesh->Elements->numElements;
681     numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
682     }
683     break;
684     case(FaceElements):
685     if (mesh->FaceElements!=NULL) {
686     numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
687     numSamples=mesh->FaceElements->numElements;
688     }
689     break;
690     case(ReducedFaceElements):
691     if (mesh->FaceElements!=NULL) {
692     numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
693     numSamples=mesh->FaceElements->numElements;
694     }
695     break;
696     case(Points):
697     if (mesh->Points!=NULL) {
698     numDataPointsPerSample=1;
699     numSamples=mesh->Points->numElements;
700     }
701     break;
702     case(ContactElementsZero):
703     if (mesh->ContactElements!=NULL) {
704     numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
705     numSamples=mesh->ContactElements->numElements;
706     }
707     break;
708     case(ReducedContactElementsZero):
709     if (mesh->ContactElements!=NULL) {
710     numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
711     numSamples=mesh->ContactElements->numElements;
712     }
713     break;
714     case(ContactElementsOne):
715     if (mesh->ContactElements!=NULL) {
716     numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
717     numSamples=mesh->ContactElements->numElements;
718     }
719     break;
720     case(ReducedContactElementsOne):
721     if (mesh->ContactElements!=NULL) {
722     numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
723     numSamples=mesh->ContactElements->numElements;
724     }
725     break;
726     case(DegreesOfFreedom):
727     if (mesh->Nodes!=NULL) {
728     numDataPointsPerSample=1;
729     numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
730     }
731     break;
732     case(ReducedDegreesOfFreedom):
733     if (mesh->Nodes!=NULL) {
734     numDataPointsPerSample=1;
735     numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
736     }
737     break;
738     default:
739     stringstream temp;
740     temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
741     throw FinleyAdapterException(temp.str());
742     break;
743     }
744     return pair<int,int>(numDataPointsPerSample,numSamples);
745 jgs 82 }
746 jgs 149
747 jgs 82 //
748     // adds linear PDE of second order into a given stiffness matrix and right hand side:
749     //
750     void MeshAdapter::addPDEToSystem(
751 phornby 1628 SystemMatrixAdapter& mat, escript::Data& rhs,
752     const escript::Data& A, const escript::Data& B, const escript::Data& C,const escript::Data& D,const escript::Data& X,const escript::Data& Y,
753     const escript::Data& d, const escript::Data& y,
754     const escript::Data& d_contact,const escript::Data& y_contact) const
755 jgs 82 {
756 gross 798 escriptDataC _rhs=rhs.getDataC();
757     escriptDataC _A =A.getDataC();
758     escriptDataC _B=B.getDataC();
759     escriptDataC _C=C.getDataC();
760     escriptDataC _D=D.getDataC();
761     escriptDataC _X=X.getDataC();
762     escriptDataC _Y=Y.getDataC();
763     escriptDataC _d=d.getDataC();
764     escriptDataC _y=y.getDataC();
765     escriptDataC _d_contact=d_contact.getDataC();
766     escriptDataC _y_contact=y_contact.getDataC();
767 bcumming 751
768 jgs 82 Finley_Mesh* mesh=m_finleyMesh.get();
769 gross 798
770 bcumming 751 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
771 jgs 82 checkFinleyError();
772 bcumming 751
773 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
774 jgs 82 checkFinleyError();
775 bcumming 751
776 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
777 jgs 82 checkFinleyError();
778     }
779 jgs 149
780 gross 1204 void MeshAdapter::addPDEToLumpedSystem(
781 phornby 1628 escript::Data& mat,
782     const escript::Data& D,
783     const escript::Data& d) const
784 gross 1204 {
785     escriptDataC _mat=mat.getDataC();
786     escriptDataC _D=D.getDataC();
787     escriptDataC _d=d.getDataC();
788    
789     Finley_Mesh* mesh=m_finleyMesh.get();
790 ksteube 1312
791 gross 1204 Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
792     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
793    
794     checkFinleyError();
795     }
796    
797    
798 jgs 82 //
799 jgs 102 // adds linear PDE of second order into the right hand side only
800     //
801 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
802 jgs 102 {
803     Finley_Mesh* mesh=m_finleyMesh.get();
804 jgs 147
805 gross 798 escriptDataC _rhs=rhs.getDataC();
806     escriptDataC _X=X.getDataC();
807     escriptDataC _Y=Y.getDataC();
808     escriptDataC _y=y.getDataC();
809     escriptDataC _y_contact=y_contact.getDataC();
810    
811     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
812 jgs 102 checkFinleyError();
813 jgs 147
814 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
815     checkFinleyError();
816 jgs 147
817 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
818 jgs 102 checkFinleyError();
819     }
820 gross 1367 //
821     // adds PDE of second order into a transport problem
822     //
823     void MeshAdapter::addPDEToTransportProblem(
824 phornby 1628 TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
825     const escript::Data& A, const escript::Data& B, const escript::Data& C,
826     const escript::Data& D,const escript::Data& X,const escript::Data& Y,
827     const escript::Data& d, const escript::Data& y,
828     const escript::Data& d_contact,const escript::Data& y_contact) const
829 gross 1367 {
830     DataArrayView::ShapeType shape;
831 gross 1370 source.expand();
832 gross 1367 escriptDataC _source=source.getDataC();
833     escriptDataC _M=M.getDataC();
834     escriptDataC _A=A.getDataC();
835     escriptDataC _B=B.getDataC();
836     escriptDataC _C=C.getDataC();
837     escriptDataC _D=D.getDataC();
838     escriptDataC _X=X.getDataC();
839     escriptDataC _Y=Y.getDataC();
840     escriptDataC _d=d.getDataC();
841     escriptDataC _y=y.getDataC();
842     escriptDataC _d_contact=d_contact.getDataC();
843     escriptDataC _y_contact=y_contact.getDataC();
844 jgs 149
845 gross 1367 Finley_Mesh* mesh=m_finleyMesh.get();
846     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
847 phornby 1628
848 gross 1407 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
849 gross 1367 checkFinleyError();
850    
851 gross 1407 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
852 gross 1367 checkFinleyError();
853    
854     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
855     checkFinleyError();
856    
857     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
858     checkFinleyError();
859     }
860    
861 jgs 102 //
862 jgs 82 // interpolates data between different function spaces:
863     //
864 jgs 480 void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
865 jgs 82 {
866 phornby 1628 const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
867     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
868     if (inDomain!=*this)
869     throw FinleyAdapterException("Error - Illegal domain of interpolant.");
870     if (targetDomain!=*this)
871     throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
872 jgs 82
873 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
874     escriptDataC _target=target.getDataC();
875     escriptDataC _in=in.getDataC();
876     switch(in.getFunctionSpace().getTypeCode()) {
877     case(Nodes):
878     switch(target.getFunctionSpace().getTypeCode()) {
879     case(Nodes):
880     case(ReducedNodes):
881     case(DegreesOfFreedom):
882     case(ReducedDegreesOfFreedom):
883     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
884     break;
885     case(Elements):
886     case(ReducedElements):
887     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
888     break;
889     case(FaceElements):
890     case(ReducedFaceElements):
891     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
892     break;
893     case(Points):
894     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
895     break;
896     case(ContactElementsZero):
897     case(ReducedContactElementsZero):
898     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
899     break;
900     case(ContactElementsOne):
901     case(ReducedContactElementsOne):
902     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
903     break;
904     default:
905     stringstream temp;
906     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
907     throw FinleyAdapterException(temp.str());
908     break;
909     }
910     break;
911     case(ReducedNodes):
912     switch(target.getFunctionSpace().getTypeCode()) {
913     case(Nodes):
914     case(ReducedNodes):
915     case(DegreesOfFreedom):
916     case(ReducedDegreesOfFreedom):
917     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
918     break;
919     case(Elements):
920     case(ReducedElements):
921     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
922     break;
923     case(FaceElements):
924     case(ReducedFaceElements):
925     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
926     break;
927     case(Points):
928     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
929     break;
930     case(ContactElementsZero):
931     case(ReducedContactElementsZero):
932     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
933     break;
934     case(ContactElementsOne):
935     case(ReducedContactElementsOne):
936     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
937     break;
938     default:
939     stringstream temp;
940     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
941     throw FinleyAdapterException(temp.str());
942     break;
943     }
944     break;
945     case(Elements):
946     if (target.getFunctionSpace().getTypeCode()==Elements) {
947     Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
948     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
949     Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
950     } else {
951     throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
952     }
953     break;
954     case(ReducedElements):
955     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
956     Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
957     } else {
958     throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
959     }
960     break;
961     case(FaceElements):
962     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
963     Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
964     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
965     Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
966     } else {
967     throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
968     }
969     break;
970     case(ReducedFaceElements):
971     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
972     Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
973     } else {
974     throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
975     }
976     break;
977     case(Points):
978     if (target.getFunctionSpace().getTypeCode()==Points) {
979     Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
980     } else {
981     throw FinleyAdapterException("Error - No interpolation with data on points possible.");
982     }
983     break;
984     case(ContactElementsZero):
985     case(ContactElementsOne):
986     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
987     Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
988     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
989     Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
990     } else {
991     throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
992     }
993     break;
994     case(ReducedContactElementsZero):
995     case(ReducedContactElementsOne):
996     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
997     Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
998     } else {
999     throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1000     }
1001     break;
1002     case(DegreesOfFreedom):
1003     switch(target.getFunctionSpace().getTypeCode()) {
1004     case(ReducedDegreesOfFreedom):
1005     case(DegreesOfFreedom):
1006     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1007     break;
1008 ksteube 1312
1009 phornby 1628 case(Nodes):
1010     case(ReducedNodes):
1011     if (getMPISize()>1) {
1012     escript::Data temp=escript::Data(in);
1013     temp.expand();
1014     escriptDataC _in2 = temp.getDataC();
1015     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1016     } else {
1017     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1018     }
1019     break;
1020     case(Elements):
1021     case(ReducedElements):
1022     if (getMPISize()>1) {
1023     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1024     escriptDataC _in2 = temp.getDataC();
1025     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1026     } else {
1027     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1028     }
1029     break;
1030     case(FaceElements):
1031     case(ReducedFaceElements):
1032     if (getMPISize()>1) {
1033     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1034     escriptDataC _in2 = temp.getDataC();
1035     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1036 ksteube 1312
1037 phornby 1628 } else {
1038     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1039     }
1040     break;
1041     case(Points):
1042     if (getMPISize()>1) {
1043     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1044     escriptDataC _in2 = temp.getDataC();
1045     } else {
1046     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1047     }
1048     break;
1049     case(ContactElementsZero):
1050     case(ContactElementsOne):
1051     case(ReducedContactElementsZero):
1052     case(ReducedContactElementsOne):
1053     if (getMPISize()>1) {
1054     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1055     escriptDataC _in2 = temp.getDataC();
1056     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1057     } else {
1058     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1059     }
1060     break;
1061     default:
1062     stringstream temp;
1063     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1064     throw FinleyAdapterException(temp.str());
1065     break;
1066     }
1067     break;
1068     case(ReducedDegreesOfFreedom):
1069     switch(target.getFunctionSpace().getTypeCode()) {
1070     case(Nodes):
1071     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1072     break;
1073     case(ReducedNodes):
1074     if (getMPISize()>1) {
1075     escript::Data temp=escript::Data(in);
1076     temp.expand();
1077     escriptDataC _in2 = temp.getDataC();
1078     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1079     } else {
1080     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1081     }
1082     break;
1083     case(DegreesOfFreedom):
1084     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1085     break;
1086     case(ReducedDegreesOfFreedom):
1087     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1088     break;
1089     case(Elements):
1090     case(ReducedElements):
1091     if (getMPISize()>1) {
1092     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1093     escriptDataC _in2 = temp.getDataC();
1094     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1095     } else {
1096     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1097     }
1098     break;
1099     case(FaceElements):
1100     case(ReducedFaceElements):
1101     if (getMPISize()>1) {
1102     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1103     escriptDataC _in2 = temp.getDataC();
1104     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1105     } else {
1106     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1107     }
1108     break;
1109     case(Points):
1110     if (getMPISize()>1) {
1111     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1112     escriptDataC _in2 = temp.getDataC();
1113     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1114     } else {
1115     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1116     }
1117     break;
1118     case(ContactElementsZero):
1119     case(ContactElementsOne):
1120     case(ReducedContactElementsZero):
1121     case(ReducedContactElementsOne):
1122     if (getMPISize()>1) {
1123     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1124     escriptDataC _in2 = temp.getDataC();
1125     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1126     } else {
1127     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1128     }
1129     break;
1130     default:
1131     stringstream temp;
1132     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1133     throw FinleyAdapterException(temp.str());
1134     break;
1135     }
1136     break;
1137     default:
1138     stringstream temp;
1139     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1140     throw FinleyAdapterException(temp.str());
1141     break;
1142     }
1143     checkFinleyError();
1144 jgs 82 }
1145    
1146     //
1147     // copies the locations of sample points into x:
1148     //
1149 jgs 480 void MeshAdapter::setToX(escript::Data& arg) const
1150 jgs 82 {
1151 phornby 1628 const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1152     if (argDomain!=*this)
1153     throw FinleyAdapterException("Error - Illegal domain of data point locations");
1154     Finley_Mesh* mesh=m_finleyMesh.get();
1155     // in case of values node coordinates we can do the job directly:
1156     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1157     escriptDataC _arg=arg.getDataC();
1158     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1159     } else {
1160     escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1161     escriptDataC _tmp_data=tmp_data.getDataC();
1162     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1163     // this is then interpolated onto arg:
1164     interpolateOnDomain(arg,tmp_data);
1165     }
1166     checkFinleyError();
1167 jgs 82 }
1168 jgs 149
1169 jgs 82 //
1170     // return the normal vectors at the location of data points as a Data object:
1171     //
1172 jgs 480 void MeshAdapter::setToNormal(escript::Data& normal) const
1173 jgs 82 {
1174 phornby 1628 const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());
1175     if (normalDomain!=*this)
1176     throw FinleyAdapterException("Error - Illegal domain of normal locations");
1177     Finley_Mesh* mesh=m_finleyMesh.get();
1178     escriptDataC _normal=normal.getDataC();
1179     switch(normal.getFunctionSpace().getTypeCode()) {
1180     case(Nodes):
1181     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1182     break;
1183     case(ReducedNodes):
1184     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1185     break;
1186     case(Elements):
1187     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1188     break;
1189     case(ReducedElements):
1190     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1191     break;
1192     case (FaceElements):
1193     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1194     break;
1195     case (ReducedFaceElements):
1196     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1197     break;
1198     case(Points):
1199     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1200     break;
1201     case (ContactElementsOne):
1202     case (ContactElementsZero):
1203     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1204     break;
1205     case (ReducedContactElementsOne):
1206     case (ReducedContactElementsZero):
1207     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1208     break;
1209     case(DegreesOfFreedom):
1210     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1211     break;
1212     case(ReducedDegreesOfFreedom):
1213     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1214     break;
1215     default:
1216 jgs 150 stringstream temp;
1217     temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1218     throw FinleyAdapterException(temp.str());
1219 jgs 82 break;
1220 phornby 1628 }
1221     checkFinleyError();
1222 jgs 82 }
1223 jgs 149
1224 jgs 82 //
1225     // interpolates data to other domain:
1226     //
1227 jgs 480 void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1228 jgs 82 {
1229 phornby 1628 const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
1230     if (targetDomain!=*this)
1231     throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1232 jgs 82
1233 phornby 1628 throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1234 jgs 82 }
1235 jgs 149
1236 jgs 82 //
1237     // calculates the integral of a function defined of arg:
1238     //
1239 jgs 480 void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1240 jgs 82 {
1241 phornby 1628 const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1242     if (argDomain!=*this)
1243     throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1244 jgs 82
1245 phornby 1628 double blocktimer_start = blocktimer_time();
1246     Finley_Mesh* mesh=m_finleyMesh.get();
1247     escriptDataC _temp;
1248     escript::Data temp;
1249     escriptDataC _arg=arg.getDataC();
1250     switch(arg.getFunctionSpace().getTypeCode()) {
1251     case(Nodes):
1252     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1253     _temp=temp.getDataC();
1254     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1255     break;
1256     case(ReducedNodes):
1257     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1258     _temp=temp.getDataC();
1259     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1260     break;
1261     case(Elements):
1262     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1263     break;
1264     case(ReducedElements):
1265     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1266     break;
1267     case(FaceElements):
1268     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1269     break;
1270     case(ReducedFaceElements):
1271     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1272     break;
1273     case(Points):
1274     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1275     break;
1276     case(ContactElementsZero):
1277     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1278     break;
1279     case(ReducedContactElementsZero):
1280     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1281     break;
1282     case(ContactElementsOne):
1283     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1284     break;
1285     case(ReducedContactElementsOne):
1286     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287     break;
1288     case(DegreesOfFreedom):
1289     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1290     _temp=temp.getDataC();
1291     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1292     break;
1293     case(ReducedDegreesOfFreedom):
1294     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1295     _temp=temp.getDataC();
1296     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1297     break;
1298     default:
1299     stringstream temp;
1300     temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1301     throw FinleyAdapterException(temp.str());
1302     break;
1303     }
1304     checkFinleyError();
1305     blocktimer_increment("integrate()", blocktimer_start);
1306 jgs 82 }
1307 jgs 149
1308 jgs 82 //
1309     // calculates the gradient of arg:
1310     //
1311 jgs 480 void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1312 jgs 82 {
1313 phornby 1628 const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1314     if (argDomain!=*this)
1315     throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1316     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());
1317     if (gradDomain!=*this)
1318     throw FinleyAdapterException("Error - Illegal domain of gradient");
1319 jgs 82
1320 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1321     escriptDataC _grad=grad.getDataC();
1322     escriptDataC nodeDataC;
1323     escript::Data temp;
1324     if (getMPISize()>1) {
1325 ksteube 1312 if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1326 phornby 1628 temp=escript::Data( arg, continuousFunction(asAbstractContinuousDomain()) );
1327     nodeDataC = temp.getDataC();
1328 ksteube 1312 } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1329 phornby 1628 temp=escript::Data( arg, reducedContinuousFunction(asAbstractContinuousDomain()) );
1330     nodeDataC = temp.getDataC();
1331 ksteube 1312 } else {
1332 phornby 1628 nodeDataC = arg.getDataC();
1333 ksteube 1312 }
1334 phornby 1628 } else {
1335     nodeDataC = arg.getDataC();
1336     }
1337     switch(grad.getFunctionSpace().getTypeCode()) {
1338     case(Nodes):
1339     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1340     break;
1341     case(ReducedNodes):
1342     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1343     break;
1344     case(Elements):
1345     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1346     break;
1347     case(ReducedElements):
1348     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1349     break;
1350     case(FaceElements):
1351     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1352     break;
1353     case(ReducedFaceElements):
1354     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1355     break;
1356     case(Points):
1357     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1358     break;
1359     case(ContactElementsZero):
1360     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1361     break;
1362     case(ReducedContactElementsZero):
1363     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1364     break;
1365     case(ContactElementsOne):
1366     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1367     break;
1368     case(ReducedContactElementsOne):
1369     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370     break;
1371     case(DegreesOfFreedom):
1372     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1373     break;
1374     case(ReducedDegreesOfFreedom):
1375     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1376     break;
1377     default:
1378     stringstream temp;
1379     temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1380     throw FinleyAdapterException(temp.str());
1381     break;
1382     }
1383     checkFinleyError();
1384 jgs 82 }
1385 jgs 149
1386 jgs 82 //
1387     // returns the size of elements:
1388     //
1389 jgs 480 void MeshAdapter::setToSize(escript::Data& size) const
1390 jgs 82 {
1391 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1392     escriptDataC tmp=size.getDataC();
1393     switch(size.getFunctionSpace().getTypeCode()) {
1394     case(Nodes):
1395     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1396     break;
1397     case(ReducedNodes):
1398     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1399     break;
1400     case(Elements):
1401     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1402     break;
1403     case(ReducedElements):
1404     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1405     break;
1406     case(FaceElements):
1407     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1408     break;
1409     case(ReducedFaceElements):
1410     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1411     break;
1412     case(Points):
1413     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1414     break;
1415     case(ContactElementsZero):
1416     case(ContactElementsOne):
1417     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1418     break;
1419     case(ReducedContactElementsZero):
1420     case(ReducedContactElementsOne):
1421     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1422     break;
1423     case(DegreesOfFreedom):
1424     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1425     break;
1426     case(ReducedDegreesOfFreedom):
1427     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1428     break;
1429     default:
1430     stringstream temp;
1431     temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1432     throw FinleyAdapterException(temp.str());
1433     break;
1434     }
1435     checkFinleyError();
1436 jgs 82 }
1437 jgs 149
1438 jgs 82 // sets the location of nodes:
1439 jgs 480 void MeshAdapter::setNewX(const escript::Data& new_x)
1440 jgs 82 {
1441 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1442     escriptDataC tmp;
1443     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1444     if (newDomain!=*this)
1445     throw FinleyAdapterException("Error - Illegal domain of new point locations");
1446     tmp = new_x.getDataC();
1447     Finley_Mesh_setCoordinates(mesh,&tmp);
1448     checkFinleyError();
1449 jgs 82 }
1450 jgs 149
1451 jgs 82 // saves a data array in openDX format:
1452 jgs 153 void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1453     {
1454 phornby 1628 unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1455     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1456     /* win32 refactor */
1457     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1458     for(int i=0;i<num_data;i++)
1459     {
1460     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1461     }
1462 jgs 153
1463 phornby 1628 escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1464     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1465 woo409 757
1466 phornby 1628 boost::python::list keys=arg.keys();
1467     for (int i=0;i<num_data;++i) {
1468     std::string n=boost::python::extract<std::string>(keys[i]);
1469     escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1470     if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1471     throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1472     data[i]=d.getDataC();
1473     ptr_data[i]= &(data[i]);
1474     if (n.length()>MAX_namelength-1) {
1475     strncpy(names[i],n.c_str(),MAX_namelength-1);
1476     names[i][MAX_namelength-1]='\0';
1477     } else {
1478     strcpy(names[i],n.c_str());
1479     }
1480     }
1481     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1482     checkFinleyError();
1483    
1484     /* win32 refactor */
1485     TMPMEMFREE(data);
1486     TMPMEMFREE(ptr_data);
1487     for(int i=0;i<num_data;i++)
1488     {
1489     TMPMEMFREE(names[i]);
1490     }
1491     TMPMEMFREE(names);
1492 woo409 757
1493 phornby 1628 return;
1494 jgs 82 }
1495 jgs 149
1496 jgs 110 // saves a data array in openVTK format:
1497 jgs 153 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1498     {
1499 phornby 1628 unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1500     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1501     /* win32 refactor */
1502     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1503     for(int i=0;i<num_data;i++)
1504     {
1505     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1506     }
1507 jgs 153
1508 phornby 1628 escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1509     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1510 woo409 757
1511 phornby 1628 boost::python::list keys=arg.keys();
1512     for (int i=0;i<num_data;++i) {
1513     std::string n=boost::python::extract<std::string>(keys[i]);
1514     escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1515     if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1516     throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1517     data[i]=d.getDataC();
1518     ptr_data[i]=&(data[i]);
1519     if (n.length()>MAX_namelength-1) {
1520     strncpy(names[i],n.c_str(),MAX_namelength-1);
1521     names[i][MAX_namelength-1]='\0';
1522     } else {
1523     strcpy(names[i],n.c_str());
1524     }
1525     }
1526     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1527 dhawcroft 793
1528 phornby 1628 checkFinleyError();
1529     /* win32 refactor */
1530     TMPMEMFREE(data);
1531     TMPMEMFREE(ptr_data);
1532     for(int i=0;i<num_data;i++)
1533     {
1534     TMPMEMFREE(names[i]);
1535     }
1536     TMPMEMFREE(names);
1537 woo409 757
1538 phornby 1628 return;
1539 jgs 110 }
1540 phornby 1628
1541    
1542 jgs 82 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1543     SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1544 phornby 1628 const int row_blocksize,
1545     const escript::FunctionSpace& row_functionspace,
1546     const int column_blocksize,
1547     const escript::FunctionSpace& column_functionspace,
1548     const int type) const
1549 jgs 82 {
1550 phornby 1628 int reduceRowOrder=0;
1551     int reduceColOrder=0;
1552     // is the domain right?
1553     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());
1554     if (row_domain!=*this)
1555     throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1556     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());
1557     if (col_domain!=*this)
1558     throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1559     // is the function space type right
1560     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1561     reduceRowOrder=0;
1562     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1563     reduceRowOrder=1;
1564     } else {
1565     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1566     }
1567     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1568     reduceColOrder=0;
1569     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1570     reduceColOrder=1;
1571     } else {
1572     throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1573     }
1574     // generate matrix:
1575    
1576     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1577     checkFinleyError();
1578     Paso_SystemMatrix* fsystemMatrix;
1579     int trilinos = 0;
1580     if (trilinos) {
1581 ksteube 1312 #ifdef TRILINOS
1582     /* Allocation Epetra_VrbMatrix here */
1583     #endif
1584 phornby 1628 }
1585     else {
1586 ksteube 1312 fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1587 phornby 1628 }
1588     checkPasoError();
1589     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1590     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1591 jgs 82 }
1592 gross 1366 // creates a TransportProblemAdapter
1593     TransportProblemAdapter MeshAdapter::newTransportProblem(
1594 phornby 1628 const double theta,
1595     const int blocksize,
1596     const escript::FunctionSpace& functionspace,
1597     const int type) const
1598 gross 1366 {
1599 phornby 1628 int reduceOrder=0;
1600     // is the domain right?
1601     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1602     if (domain!=*this)
1603     throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1604     // is the function space type right
1605     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1606     reduceOrder=0;
1607     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1608     reduceOrder=1;
1609     } else {
1610     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1611     }
1612     // generate matrix:
1613    
1614     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1615     checkFinleyError();
1616     Paso_FCTransportProblem* transportProblem;
1617     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1618     checkPasoError();
1619     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1620     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1621 gross 1366 }
1622 jgs 149
1623 jgs 82 //
1624     // vtkObject MeshAdapter::createVtkObject() const
1625     // TODO:
1626     //
1627 jgs 149
1628 jgs 82 //
1629     // returns true if data at the atom_type is considered as being cell centered:
1630     bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1631     {
1632 phornby 1628 switch(functionSpaceCode) {
1633     case(Nodes):
1634     case(DegreesOfFreedom):
1635     case(ReducedDegreesOfFreedom):
1636     return false;
1637     break;
1638     case(Elements):
1639     case(FaceElements):
1640     case(Points):
1641     case(ContactElementsZero):
1642     case(ContactElementsOne):
1643     case(ReducedElements):
1644     case(ReducedFaceElements):
1645     case(ReducedContactElementsZero):
1646     case(ReducedContactElementsOne):
1647     return true;
1648     break;
1649     default:
1650     stringstream temp;
1651     temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1652     throw FinleyAdapterException(temp.str());
1653     break;
1654     }
1655     checkFinleyError();
1656     return false;
1657 jgs 82 }
1658 jgs 149
1659 jgs 82 bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1660     {
1661 phornby 1628 switch(functionSpaceType_source) {
1662     case(Nodes):
1663     switch(functionSpaceType_target) {
1664     case(Nodes):
1665     case(ReducedNodes):
1666     case(ReducedDegreesOfFreedom):
1667     case(DegreesOfFreedom):
1668     case(Elements):
1669     case(ReducedElements):
1670     case(FaceElements):
1671     case(ReducedFaceElements):
1672     case(Points):
1673     case(ContactElementsZero):
1674     case(ReducedContactElementsZero):
1675     case(ContactElementsOne):
1676     case(ReducedContactElementsOne):
1677     return true;
1678     default:
1679     stringstream temp;
1680     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1681     throw FinleyAdapterException(temp.str());
1682     }
1683     break;
1684     case(ReducedNodes):
1685     switch(functionSpaceType_target) {
1686     case(ReducedNodes):
1687     case(ReducedDegreesOfFreedom):
1688     case(Elements):
1689     case(ReducedElements):
1690     case(FaceElements):
1691     case(ReducedFaceElements):
1692     case(Points):
1693     case(ContactElementsZero):
1694     case(ReducedContactElementsZero):
1695     case(ContactElementsOne):
1696     case(ReducedContactElementsOne):
1697     return true;
1698     case(Nodes):
1699     case(DegreesOfFreedom):
1700     return false;
1701     default:
1702     stringstream temp;
1703     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1704     throw FinleyAdapterException(temp.str());
1705     }
1706     break;
1707     case(Elements):
1708     if (functionSpaceType_target==Elements) {
1709     return true;
1710     } else if (functionSpaceType_target==ReducedElements) {
1711     return true;
1712     } else {
1713     return false;
1714     }
1715     case(ReducedElements):
1716     if (functionSpaceType_target==ReducedElements) {
1717     return true;
1718     } else {
1719     return false;
1720     }
1721     case(FaceElements):
1722     if (functionSpaceType_target==FaceElements) {
1723     return true;
1724     } else if (functionSpaceType_target==ReducedFaceElements) {
1725     return true;
1726     } else {
1727     return false;
1728     }
1729     case(ReducedFaceElements):
1730     if (functionSpaceType_target==ReducedFaceElements) {
1731     return true;
1732     } else {
1733     return false;
1734     }
1735     case(Points):
1736     if (functionSpaceType_target==Points) {
1737     return true;
1738     } else {
1739     return false;
1740     }
1741     case(ContactElementsZero):
1742     case(ContactElementsOne):
1743     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1744     return true;
1745     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1746     return true;
1747     } else {
1748     return false;
1749     }
1750     case(ReducedContactElementsZero):
1751     case(ReducedContactElementsOne):
1752     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1753     return true;
1754     } else {
1755     return false;
1756     }
1757     case(DegreesOfFreedom):
1758     switch(functionSpaceType_target) {
1759     case(ReducedDegreesOfFreedom):
1760     case(DegreesOfFreedom):
1761     case(Nodes):
1762     case(ReducedNodes):
1763     case(Elements):
1764     case(ReducedElements):
1765     case(Points):
1766     case(FaceElements):
1767     case(ReducedFaceElements):
1768     case(ContactElementsZero):
1769     case(ReducedContactElementsZero):
1770     case(ContactElementsOne):
1771     case(ReducedContactElementsOne):
1772     return true;
1773     default:
1774     stringstream temp;
1775     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1776     throw FinleyAdapterException(temp.str());
1777     }
1778     break;
1779     case(ReducedDegreesOfFreedom):
1780     switch(functionSpaceType_target) {
1781     case(ReducedDegreesOfFreedom):
1782     case(ReducedNodes):
1783     case(Elements):
1784     case(ReducedElements):
1785     case(FaceElements):
1786     case(ReducedFaceElements):
1787     case(Points):
1788     case(ContactElementsZero):
1789     case(ReducedContactElementsZero):
1790     case(ContactElementsOne):
1791     case(ReducedContactElementsOne):
1792     return true;
1793     case(Nodes):
1794     case(DegreesOfFreedom):
1795     return false;
1796     default:
1797     stringstream temp;
1798     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1799     throw FinleyAdapterException(temp.str());
1800     }
1801     break;
1802     default:
1803     stringstream temp;
1804     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1805     throw FinleyAdapterException(temp.str());
1806     break;
1807     }
1808     checkFinleyError();
1809     return false;
1810 jgs 82 }
1811 jgs 149
1812 jgs 82 bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
1813     {
1814 phornby 1628 return false;
1815 jgs 82 }
1816 jgs 104
1817 jgs 121 bool MeshAdapter::operator==(const AbstractDomain& other) const
1818 jgs 82 {
1819 phornby 1628 const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1820     if (temp!=0) {
1821     return (m_finleyMesh==temp->m_finleyMesh);
1822     } else {
1823     return false;
1824     }
1825 jgs 82 }
1826    
1827 jgs 121 bool MeshAdapter::operator!=(const AbstractDomain& other) const
1828 jgs 104 {
1829 phornby 1628 return !(operator==(other));
1830 jgs 104 }
1831    
1832 jgs 150 int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const
1833 jgs 102 {
1834 jgs 150 int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1835     checkPasoError();
1836 jgs 102 return out;
1837     }
1838 jgs 149
1839 jgs 480 escript::Data MeshAdapter::getX() const
1840 jgs 102 {
1841 phornby 1628 return continuousFunction(asAbstractContinuousDomain()).getX();
1842 jgs 102 }
1843 jgs 149
1844 jgs 480 escript::Data MeshAdapter::getNormal() const
1845 jgs 102 {
1846 phornby 1628 return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1847 jgs 102 }
1848 jgs 149
1849 jgs 480 escript::Data MeshAdapter::getSize() const
1850 jgs 102 {
1851 phornby 1628 return function(asAbstractContinuousDomain()).getSize();
1852 jgs 102 }
1853    
1854 gross 1062 int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1855     {
1856 phornby 1628 int *out = NULL;
1857     Finley_Mesh* mesh=m_finleyMesh.get();
1858     switch (functionSpaceType) {
1859     case(Nodes):
1860     out=mesh->Nodes->Id;
1861     break;
1862     case(ReducedNodes):
1863     out=mesh->Nodes->reducedNodesId;
1864     break;
1865     case(Elements):
1866     out=mesh->Elements->Id;
1867     break;
1868     case(ReducedElements):
1869     out=mesh->Elements->Id;
1870     break;
1871     case(FaceElements):
1872     out=mesh->FaceElements->Id;
1873     break;
1874     case(ReducedFaceElements):
1875     out=mesh->FaceElements->Id;
1876     break;
1877     case(Points):
1878     out=mesh->Points->Id;
1879     break;
1880     case(ContactElementsZero):
1881     out=mesh->ContactElements->Id;
1882     break;
1883     case(ReducedContactElementsZero):
1884     out=mesh->ContactElements->Id;
1885     break;
1886     case(ContactElementsOne):
1887     out=mesh->ContactElements->Id;
1888     break;
1889     case(ReducedContactElementsOne):
1890     out=mesh->ContactElements->Id;
1891     break;
1892     case(DegreesOfFreedom):
1893     out=mesh->Nodes->degreesOfFreedomId;
1894     break;
1895     case(ReducedDegreesOfFreedom):
1896     out=mesh->Nodes->reducedDegreesOfFreedomId;
1897     break;
1898     default:
1899 gross 1062 stringstream temp;
1900     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1901     throw FinleyAdapterException(temp.str());
1902     break;
1903 phornby 1628 }
1904     return out;
1905 gross 1062 }
1906 jgs 110 int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1907     {
1908 phornby 1628 int out=0;
1909     Finley_Mesh* mesh=m_finleyMesh.get();
1910     switch (functionSpaceType) {
1911     case(Nodes):
1912     out=mesh->Nodes->Tag[sampleNo];
1913     break;
1914     case(ReducedNodes):
1915     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1916     break;
1917     case(Elements):
1918     out=mesh->Elements->Tag[sampleNo];
1919     break;
1920     case(ReducedElements):
1921     out=mesh->Elements->Tag[sampleNo];
1922     break;
1923     case(FaceElements):
1924     out=mesh->FaceElements->Tag[sampleNo];
1925     break;
1926     case(ReducedFaceElements):
1927     out=mesh->FaceElements->Tag[sampleNo];
1928     break;
1929     case(Points):
1930     out=mesh->Points->Tag[sampleNo];
1931     break;
1932     case(ContactElementsZero):
1933     out=mesh->ContactElements->Tag[sampleNo];
1934     break;
1935     case(ReducedContactElementsZero):
1936     out=mesh->ContactElements->Tag[sampleNo];
1937     break;
1938     case(ContactElementsOne):
1939     out=mesh->ContactElements->Tag[sampleNo];
1940     break;
1941     case(ReducedContactElementsOne):
1942     out=mesh->ContactElements->Tag[sampleNo];
1943     break;
1944     case(DegreesOfFreedom):
1945     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1946     break;
1947     case(ReducedDegreesOfFreedom):
1948     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1949     break;
1950     default:
1951     stringstream temp;
1952     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1953     throw FinleyAdapterException(temp.str());
1954     break;
1955     }
1956     return out;
1957 jgs 110 }
1958    
1959 gross 1062
1960 gross 767 void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1961     {
1962 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1963     escriptDataC tmp=mask.getDataC();
1964     switch(functionSpaceType) {
1965     case(Nodes):
1966     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1967     break;
1968     case(ReducedNodes):
1969     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1970     break;
1971     case(DegreesOfFreedom):
1972     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1973     break;
1974     case(ReducedDegreesOfFreedom):
1975     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1976     break;
1977     case(Elements):
1978     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1979     break;
1980     case(ReducedElements):
1981     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1982     break;
1983     case(FaceElements):
1984     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1985     break;
1986     case(ReducedFaceElements):
1987     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1988     break;
1989     case(Points):
1990     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1991     break;
1992     case(ContactElementsZero):
1993     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1994     break;
1995     case(ReducedContactElementsZero):
1996     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1997     break;
1998     case(ContactElementsOne):
1999     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2000     break;
2001     case(ReducedContactElementsOne):
2002     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2003     break;
2004     default:
2005     stringstream temp;
2006     temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2007     throw FinleyAdapterException(temp.str());
2008     }
2009     checkFinleyError();
2010     return;
2011 gross 767 }
2012    
2013 gross 1044 void MeshAdapter::setTagMap(const std::string& name, int tag)
2014     {
2015 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
2016     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2017     checkPasoError();
2018     // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2019 gross 1044 }
2020 gross 767
2021 gross 1044 int MeshAdapter::getTag(const std::string& name) const
2022     {
2023 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
2024     int tag=0;
2025     tag=Finley_Mesh_getTag(mesh, name.c_str());
2026     checkPasoError();
2027     // throwStandardException("MeshAdapter::getTag is not implemented.");
2028     return tag;
2029 gross 1044 }
2030    
2031     bool MeshAdapter::isValidTagName(const std::string& name) const
2032     {
2033 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
2034     return Finley_Mesh_isValidTagName(mesh,name.c_str());
2035 gross 1044 }
2036    
2037     std::string MeshAdapter::showTagNames() const
2038     {
2039 phornby 1628 stringstream temp;
2040     Finley_Mesh* mesh=m_finleyMesh.get();
2041     Finley_TagMap* tag_map=mesh->TagMap;
2042     while (tag_map) {
2043     temp << tag_map->name;
2044     tag_map=tag_map->next;
2045     if (tag_map) temp << ", ";
2046     }
2047     return temp.str();
2048 gross 1044 }
2049    
2050 gross 1716 int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2051     {
2052     Finley_Mesh* mesh=m_finleyMesh.get();
2053     dim_t numTags=0;
2054     switch(functionSpaceCode) {
2055     case(Nodes):
2056     numTags=mesh->Nodes->numTagsInUse;
2057     break;
2058     case(ReducedNodes):
2059     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2060     break;
2061     case(DegreesOfFreedom):
2062     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2063     break;
2064     case(ReducedDegreesOfFreedom):
2065     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2066     break;
2067     case(Elements):
2068     case(ReducedElements):
2069     numTags=mesh->Elements->numTagsInUse;
2070     break;
2071     case(FaceElements):
2072     case(ReducedFaceElements):
2073     numTags=mesh->FaceElements->numTagsInUse;
2074     break;
2075     case(Points):
2076     numTags=mesh->Points->numTagsInUse;
2077     break;
2078     case(ContactElementsZero):
2079     case(ReducedContactElementsZero):
2080     case(ContactElementsOne):
2081     case(ReducedContactElementsOne):
2082     numTags=mesh->ContactElements->numTagsInUse;
2083     break;
2084     default:
2085     stringstream temp;
2086     temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2087     throw FinleyAdapterException(temp.str());
2088     }
2089     return numTags;
2090     }
2091     int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2092     {
2093     Finley_Mesh* mesh=m_finleyMesh.get();
2094     index_t* tags=NULL;
2095     switch(functionSpaceCode) {
2096     case(Nodes):
2097     tags=mesh->Nodes->tagsInUse;
2098     break;
2099     case(ReducedNodes):
2100     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2101     break;
2102     case(DegreesOfFreedom):
2103     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2104     break;
2105     case(ReducedDegreesOfFreedom):
2106     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2107     break;
2108     case(Elements):
2109     case(ReducedElements):
2110     tags=mesh->Elements->tagsInUse;
2111     break;
2112     case(FaceElements):
2113     case(ReducedFaceElements):
2114     tags=mesh->FaceElements->tagsInUse;
2115     break;
2116     case(Points):
2117     tags=mesh->Points->tagsInUse;
2118     break;
2119     case(ContactElementsZero):
2120     case(ReducedContactElementsZero):
2121     case(ContactElementsOne):
2122     case(ReducedContactElementsOne):
2123     tags=mesh->ContactElements->tagsInUse;
2124     break;
2125     default:
2126     stringstream temp;
2127     temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2128     throw FinleyAdapterException(temp.str());
2129     }
2130     return tags;
2131     }
2132    
2133    
2134 jgs 82 } // end of namespace

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