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

Annotation of /trunk/finley/src/CPPAdapter/MeshAdapter.cpp

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1796 - (hide annotations)
Wed Sep 17 01:45:46 2008 UTC (10 years, 10 months ago) by jfenwick
File size: 83416 byte(s)
Merged noarrayview branch onto trunk.


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

Properties

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

  ViewVC Help
Powered by ViewVC 1.1.26