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

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Revision 1872 - (hide annotations)
Mon Oct 13 00:18:55 2008 UTC (10 years, 10 months ago) by jfenwick
File size: 85032 byte(s)
Closing the moreshared branch

1 jgs 472
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4     * Copyright (c) 2003-2008 by University of Queensland
5     * Earth Systems Science Computational Center (ESSCC)
6     * http://www.uq.edu.au/esscc
7     *
8     * Primary Business: Queensland, Australia
9     * Licensed under the Open Software License version 3.0
10     * http://www.opensource.org/licenses/osl-3.0.php
11     *
12     *******************************************************/
13 ksteube 1312
14 ksteube 1811
15 jgs 203 #include "MeshAdapter.h"
16 robwdcock 682 #include "escript/Data.h"
17     #include "escript/DataFactory.h"
18 ksteube 1343 #ifdef USE_NETCDF
19     #include <netcdfcpp.h>
20     #endif
21 ksteube 1800 #ifdef PASO_MPI
22     #include <mpi.h>
23     #include "paso/Paso_MPI.h"
24     #endif
25 ksteube 1312 extern "C" {
26     #include "escript/blocktimer.h"
27     }
28     #include <vector>
29 jgs 480
30 phornby 1455 #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH 256
31    
32 jgs 82 using namespace std;
33     using namespace escript;
34    
35     namespace finley {
36 jgs 149
37 jgs 82 //
38 jgs 149 // define the static constants
39 jgs 82 MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
40     const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
41     const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
42     const int MeshAdapter::Nodes=FINLEY_NODES;
43 gross 1062 const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
44 jgs 82 const int MeshAdapter::Elements=FINLEY_ELEMENTS;
45 gross 1059 const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
46 jgs 82 const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
47 gross 1059 const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
48 jgs 82 const int MeshAdapter::Points=FINLEY_POINTS;
49     const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
50 gross 1059 const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
51 jgs 82 const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
52 gross 1059 const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
53 jgs 82
54     MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
55     {
56 phornby 1628 setFunctionSpaceTypeNames();
57     //
58     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
59     // for us.
60     m_finleyMesh.reset(finleyMesh,null_deleter());
61 jgs 82 }
62 jgs 149
63 jgs 82 //
64     // The copy constructor should just increment the use count
65     MeshAdapter::MeshAdapter(const MeshAdapter& in):
66     m_finleyMesh(in.m_finleyMesh)
67     {
68 phornby 1628 setFunctionSpaceTypeNames();
69 jgs 82 }
70    
71     MeshAdapter::~MeshAdapter()
72     {
73 phornby 1628 //
74     // I hope the case for the pointer being zero has been taken care of.
75     // cout << "In MeshAdapter destructor." << endl;
76     if (m_finleyMesh.unique()) {
77     Finley_Mesh_free(m_finleyMesh.get());
78     }
79 jgs 82 }
80    
81 ksteube 1312 int MeshAdapter::getMPISize() const
82     {
83     return m_finleyMesh.get()->MPIInfo->size;
84     }
85     int MeshAdapter::getMPIRank() const
86     {
87     return m_finleyMesh.get()->MPIInfo->rank;
88     }
89    
90    
91 jgs 82 Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
92     return m_finleyMesh.get();
93     }
94    
95     void MeshAdapter::write(const std::string& fileName) const
96     {
97 phornby 1628 char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
98     strcpy(fName,fileName.c_str());
99     Finley_Mesh_write(m_finleyMesh.get(),fName);
100     checkFinleyError();
101     TMPMEMFREE(fName);
102 jgs 82 }
103    
104 ksteube 1339 void MeshAdapter::Print_Mesh_Info(const bool full=false) const
105 ksteube 1326 {
106 phornby 1628 Finley_PrintMesh_Info(m_finleyMesh.get(), full);
107 ksteube 1326 }
108    
109 ksteube 1312 void MeshAdapter::dump(const std::string& fileName) const
110     {
111 ksteube 1343 #ifdef USE_NETCDF
112 ksteube 1347 const NcDim* ncdims[12];
113 trankine 1632 NcVar *ids;
114 ksteube 1343 int *int_ptr;
115     Finley_Mesh *mesh = m_finleyMesh.get();
116 ksteube 1347 Finley_TagMap* tag_map;
117     int num_Tags = 0;
118 ksteube 1343 int mpi_size = mesh->MPIInfo->size;
119     int mpi_rank = mesh->MPIInfo->rank;
120     int numDim = mesh->Nodes->numDim;
121     int numNodes = mesh->Nodes->numNodes;
122     int num_Elements = mesh->Elements->numElements;
123     int num_FaceElements = mesh->FaceElements->numElements;
124     int num_ContactElements = mesh->ContactElements->numElements;
125     int num_Points = mesh->Points->numElements;
126     int num_Elements_numNodes = mesh->Elements->numNodes;
127     int num_FaceElements_numNodes = mesh->FaceElements->numNodes;
128     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
129 ksteube 1800 #ifdef PASO_MPI
130     MPI_Status status;
131     #endif
132 ksteube 1343
133 ksteube 1800 /* Incoming token indicates it's my turn to write */
134     #ifdef PASO_MPI
135     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
136     #endif
137    
138 phornby 1628 char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
139     mpi_size, mpi_rank);
140    
141 ksteube 1347 /* Figure out how much storage is required for tags */
142     tag_map = mesh->TagMap;
143 ksteube 1800 num_Tags = 0;
144 ksteube 1347 if (tag_map) {
145 phornby 1628 while (tag_map) {
146     num_Tags++;
147     tag_map=tag_map->next;
148     }
149 ksteube 1347 }
150    
151 ksteube 1343 // NetCDF error handler
152     NcError err(NcError::verbose_nonfatal);
153     // Create the file.
154     NcFile dataFile(newFileName, NcFile::Replace);
155     // check if writing was successful
156     if (!dataFile.is_valid())
157 phornby 1628 throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
158 ksteube 1343
159     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
160     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
161 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
162 ksteube 1343 if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
163 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
164 ksteube 1343 if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
165 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
166 ksteube 1343 if (num_Elements>0)
167     if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
168 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
169 ksteube 1343 if (num_FaceElements>0)
170     if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
171 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
172 ksteube 1343 if (num_ContactElements>0)
173     if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
174 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
175 ksteube 1343 if (num_Points>0)
176     if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
177 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
178 ksteube 1343 if (num_Elements>0)
179     if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
180 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
181 ksteube 1343 if (num_FaceElements>0)
182     if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
183 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
184 ksteube 1343 if (num_ContactElements>0)
185     if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
186 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
187 ksteube 1347 if (num_Tags>0)
188     if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
189 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
190 ksteube 1343
191 ksteube 1345 // Attributes: MPI size, MPI rank, Name, order, reduced_order
192 ksteube 1343 if (!dataFile.add_att("mpi_size", mpi_size) )
193 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
194 ksteube 1343 if (!dataFile.add_att("mpi_rank", mpi_rank) )
195 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
196 ksteube 1343 if (!dataFile.add_att("Name",mesh->Name) )
197 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
198 ksteube 1345 if (!dataFile.add_att("numDim",numDim) )
199 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
200 ksteube 1343 if (!dataFile.add_att("order",mesh->order) )
201 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
202 ksteube 1343 if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
203 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
204 ksteube 1345 if (!dataFile.add_att("numNodes",numNodes) )
205 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
206 ksteube 1343 if (!dataFile.add_att("num_Elements",num_Elements) )
207 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
208 ksteube 1343 if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
209 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
210 ksteube 1343 if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
211 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
212 ksteube 1343 if (!dataFile.add_att("num_Points",num_Points) )
213 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
214 ksteube 1346 if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
215 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
216 ksteube 1346 if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
217 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
218 ksteube 1346 if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
219 phornby 1628 throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
220 ksteube 1347 if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
221     throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
222     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
223     throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
224     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
225     throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
226     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
227     throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
228     if (!dataFile.add_att("num_Tags", num_Tags) )
229     throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
230 ksteube 1343
231     // // // // // Nodes // // // // //
232    
233 ksteube 1345 // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
234     if (numNodes>0) {
235    
236 phornby 1628 // Nodes Id
237     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
238     throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
239     int_ptr = &mesh->Nodes->Id[0];
240     if (! (ids->put(int_ptr, numNodes)) )
241     throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
242 ksteube 1343
243 phornby 1628 // Nodes Tag
244     if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
245     throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
246     int_ptr = &mesh->Nodes->Tag[0];
247     if (! (ids->put(int_ptr, numNodes)) )
248     throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
249 ksteube 1343
250 phornby 1628 // Nodes gDOF
251     if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
252     throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
253     int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
254     if (! (ids->put(int_ptr, numNodes)) )
255     throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
256 ksteube 1343
257 phornby 1628 // Nodes global node index
258     if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
259     throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
260     int_ptr = &mesh->Nodes->globalNodesIndex[0];
261     if (! (ids->put(int_ptr, numNodes)) )
262     throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
263 ksteube 1343
264 phornby 1628 // Nodes grDof
265     if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
266     throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
267     int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
268     if (! (ids->put(int_ptr, numNodes)) )
269     throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
270 ksteube 1343
271 phornby 1628 // Nodes grNI
272     if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
273     throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
274     int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
275     if (! (ids->put(int_ptr, numNodes)) )
276     throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
277 ksteube 1343
278 phornby 1628 // Nodes Coordinates
279     if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
280     throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
281     if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
282     throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
283 ksteube 1343
284 phornby 1628 // Nodes degreesOfFreedomDistribution
285     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
286     throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
287     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
288     if (! (ids->put(int_ptr, mpi_size+1)) )
289     throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
290 ksteube 1343
291 ksteube 1755 // Nodes nodeDistribution
292     if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
293     throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
294     int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
295     if (! (ids->put(int_ptr, mpi_size+1)) )
296     throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
297    
298 ksteube 1345 }
299    
300 ksteube 1343 // // // // // Elements // // // // //
301    
302     if (num_Elements>0) {
303    
304 phornby 1628 // Elements_Id
305     if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
306     throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
307     int_ptr = &mesh->Elements->Id[0];
308     if (! (ids->put(int_ptr, num_Elements)) )
309     throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
310 ksteube 1343
311 phornby 1628 // Elements_Tag
312     if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
313     throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
314     int_ptr = &mesh->Elements->Tag[0];
315     if (! (ids->put(int_ptr, num_Elements)) )
316     throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
317 ksteube 1343
318 phornby 1628 // Elements_Owner
319     if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
320     throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
321     int_ptr = &mesh->Elements->Owner[0];
322     if (! (ids->put(int_ptr, num_Elements)) )
323     throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
324 ksteube 1343
325 phornby 1628 // Elements_Color
326     if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
327     throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
328     int_ptr = &mesh->Elements->Color[0];
329     if (! (ids->put(int_ptr, num_Elements)) )
330     throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
331 ksteube 1343
332 phornby 1628 // Elements_Nodes
333     if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
334     throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
335 ksteube 1777 if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
336 phornby 1628 throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
337 ksteube 1343
338     }
339    
340     // // // // // Face_Elements // // // // //
341    
342     if (num_FaceElements>0) {
343    
344 phornby 1628 // FaceElements_Id
345     if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
346     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
347     int_ptr = &mesh->FaceElements->Id[0];
348     if (! (ids->put(int_ptr, num_FaceElements)) )
349     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
350 ksteube 1343
351 phornby 1628 // FaceElements_Tag
352     if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
353     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
354     int_ptr = &mesh->FaceElements->Tag[0];
355     if (! (ids->put(int_ptr, num_FaceElements)) )
356     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
357 ksteube 1343
358 phornby 1628 // FaceElements_Owner
359     if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
360     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
361     int_ptr = &mesh->FaceElements->Owner[0];
362     if (! (ids->put(int_ptr, num_FaceElements)) )
363     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
364 ksteube 1343
365 phornby 1628 // FaceElements_Color
366     if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
367     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
368     int_ptr = &mesh->FaceElements->Color[0];
369     if (! (ids->put(int_ptr, num_FaceElements)) )
370     throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
371 ksteube 1343
372 phornby 1628 // FaceElements_Nodes
373     if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
374     throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
375 ksteube 1777 if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
376 phornby 1628 throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
377 ksteube 1343
378     }
379    
380     // // // // // Contact_Elements // // // // //
381    
382     if (num_ContactElements>0) {
383    
384 phornby 1628 // ContactElements_Id
385     if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
386     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
387     int_ptr = &mesh->ContactElements->Id[0];
388     if (! (ids->put(int_ptr, num_ContactElements)) )
389     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
390 ksteube 1343
391 phornby 1628 // ContactElements_Tag
392     if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
393     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
394     int_ptr = &mesh->ContactElements->Tag[0];
395     if (! (ids->put(int_ptr, num_ContactElements)) )
396     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
397 ksteube 1343
398 phornby 1628 // ContactElements_Owner
399     if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
400     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
401     int_ptr = &mesh->ContactElements->Owner[0];
402     if (! (ids->put(int_ptr, num_ContactElements)) )
403     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
404 ksteube 1343
405 phornby 1628 // ContactElements_Color
406     if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
407     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
408     int_ptr = &mesh->ContactElements->Color[0];
409     if (! (ids->put(int_ptr, num_ContactElements)) )
410     throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
411 ksteube 1343
412 phornby 1628 // ContactElements_Nodes
413     if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
414     throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
415 ksteube 1777 if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
416 phornby 1628 throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
417 ksteube 1343
418     }
419    
420     // // // // // Points // // // // //
421    
422     if (num_Points>0) {
423    
424 phornby 1628 fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
425 ksteube 1343
426 phornby 1628 // Points_Id
427     if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
428     throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
429     int_ptr = &mesh->Points->Id[0];
430     if (! (ids->put(int_ptr, num_Points)) )
431     throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
432 ksteube 1343
433 phornby 1628 // Points_Tag
434     if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
435     throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
436     int_ptr = &mesh->Points->Tag[0];
437     if (! (ids->put(int_ptr, num_Points)) )
438     throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
439 ksteube 1343
440 phornby 1628 // Points_Owner
441     if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
442     throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
443     int_ptr = &mesh->Points->Owner[0];
444     if (! (ids->put(int_ptr, num_Points)) )
445     throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
446 ksteube 1343
447 phornby 1628 // Points_Color
448     if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
449     throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
450     int_ptr = &mesh->Points->Color[0];
451     if (! (ids->put(int_ptr, num_Points)) )
452     throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
453 ksteube 1343
454 phornby 1628 // Points_Nodes
455     // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
456     if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
457     throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
458 ksteube 1777 if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
459 phornby 1628 throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
460 ksteube 1343
461     }
462    
463     // // // // // TagMap // // // // //
464    
465 ksteube 1347 if (num_Tags>0) {
466 ksteube 1343
467 phornby 1628 // Temp storage to gather node IDs
468     int *Tags_keys = TMPMEMALLOC(num_Tags, int);
469     char name_temp[4096];
470 ksteube 1347
471 phornby 1628 /* Copy tag data into temp arrays */
472     tag_map = mesh->TagMap;
473     if (tag_map) {
474     int i = 0;
475     while (tag_map) {
476     Tags_keys[i++] = tag_map->tag_key;
477     tag_map=tag_map->next;
478     }
479     }
480 ksteube 1347
481 phornby 1628 // Tags_keys
482     if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
483     throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
484     int_ptr = &Tags_keys[0];
485     if (! (ids->put(int_ptr, num_Tags)) )
486     throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
487 ksteube 1347
488 phornby 1628 // Tags_names_*
489     // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
490     // because the NetCDF manual doesn't tell how to do an array of strings
491     tag_map = mesh->TagMap;
492     if (tag_map) {
493     int i = 0;
494     while (tag_map) {
495     sprintf(name_temp, "Tags_name_%d", i);
496     if (!dataFile.add_att(name_temp, tag_map->name) )
497     throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
498     tag_map=tag_map->next;
499     i++;
500     }
501     }
502 ksteube 1347
503 phornby 1628 TMPMEMFREE(Tags_keys);
504 ksteube 1347
505     }
506    
507 ksteube 1800 /* Send token to next MPI process so he can take his turn */
508     #ifdef PASO_MPI
509     if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
510     #endif
511 ksteube 1347
512 ksteube 1343 // NetCDF file is closed by destructor of NcFile object
513 ksteube 1800
514 ksteube 1343 #else
515     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
516     #endif /* USE_NETCDF */
517     checkFinleyError();
518 ksteube 1312 }
519    
520 jgs 82 string MeshAdapter::getDescription() const
521     {
522 phornby 1628 return "FinleyMesh";
523 jgs 82 }
524    
525     string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
526     {
527 phornby 1628 FunctionSpaceNamesMapType::iterator loc;
528     loc=m_functionSpaceTypeNames.find(functionSpaceType);
529     if (loc==m_functionSpaceTypeNames.end()) {
530     return "Invalid function space type code.";
531     } else {
532     return loc->second;
533     }
534 jgs 82 }
535    
536     bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
537     {
538 phornby 1628 FunctionSpaceNamesMapType::iterator loc;
539     loc=m_functionSpaceTypeNames.find(functionSpaceType);
540     return (loc!=m_functionSpaceTypeNames.end());
541 jgs 82 }
542    
543     void MeshAdapter::setFunctionSpaceTypeNames()
544     {
545 phornby 1628 m_functionSpaceTypeNames.insert
546     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
547     m_functionSpaceTypeNames.insert
548     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
549     m_functionSpaceTypeNames.insert
550     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
551     m_functionSpaceTypeNames.insert
552     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
553     m_functionSpaceTypeNames.insert
554     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
555     m_functionSpaceTypeNames.insert
556     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
557     m_functionSpaceTypeNames.insert
558     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
559     m_functionSpaceTypeNames.insert
560     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
561     m_functionSpaceTypeNames.insert
562     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
563     m_functionSpaceTypeNames.insert
564     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
565     m_functionSpaceTypeNames.insert
566     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
567     m_functionSpaceTypeNames.insert
568     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
569     m_functionSpaceTypeNames.insert
570     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
571 jgs 82 }
572    
573     int MeshAdapter::getContinuousFunctionCode() const
574     {
575 phornby 1628 return Nodes;
576 jgs 82 }
577 gross 1062 int MeshAdapter::getReducedContinuousFunctionCode() const
578     {
579 phornby 1628 return ReducedNodes;
580 gross 1062 }
581 jgs 149
582 jgs 82 int MeshAdapter::getFunctionCode() const
583     {
584 phornby 1628 return Elements;
585 jgs 82 }
586 gross 1059 int MeshAdapter::getReducedFunctionCode() const
587     {
588 phornby 1628 return ReducedElements;
589 gross 1059 }
590 jgs 149
591 jgs 82 int MeshAdapter::getFunctionOnBoundaryCode() const
592     {
593 phornby 1628 return FaceElements;
594 jgs 82 }
595 gross 1059 int MeshAdapter::getReducedFunctionOnBoundaryCode() const
596     {
597 phornby 1628 return ReducedFaceElements;
598 gross 1059 }
599 jgs 149
600 jgs 82 int MeshAdapter::getFunctionOnContactZeroCode() const
601     {
602 phornby 1628 return ContactElementsZero;
603 jgs 82 }
604 gross 1059 int MeshAdapter::getReducedFunctionOnContactZeroCode() const
605     {
606 phornby 1628 return ReducedContactElementsZero;
607 gross 1059 }
608 jgs 149
609 jgs 82 int MeshAdapter::getFunctionOnContactOneCode() const
610     {
611 phornby 1628 return ContactElementsOne;
612 jgs 82 }
613 gross 1059 int MeshAdapter::getReducedFunctionOnContactOneCode() const
614     {
615 phornby 1628 return ReducedContactElementsOne;
616 gross 1059 }
617 jgs 82
618     int MeshAdapter::getSolutionCode() const
619     {
620 phornby 1628 return DegreesOfFreedom;
621 jgs 82 }
622 jgs 149
623 jgs 82 int MeshAdapter::getReducedSolutionCode() const
624     {
625 phornby 1628 return ReducedDegreesOfFreedom;
626 jgs 82 }
627 jgs 149
628 jgs 82 int MeshAdapter::getDiracDeltaFunctionCode() const
629     {
630 phornby 1628 return Points;
631 jgs 82 }
632 jgs 149
633 jgs 82 //
634     // return the spatial dimension of the Mesh:
635     //
636     int MeshAdapter::getDim() const
637     {
638 phornby 1628 int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
639     checkFinleyError();
640     return numDim;
641 jgs 82 }
642 jgs 149
643 jgs 82 //
644 ksteube 1754 // Return the number of data points summed across all MPI processes
645     //
646     int MeshAdapter::getNumDataPointsGlobal() const
647     {
648     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
649     }
650    
651     //
652 jgs 82 // return the number of data points per sample and the number of samples
653     // needed to represent data on a parts of the mesh.
654     //
655     pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
656     {
657     int numDataPointsPerSample=0;
658     int numSamples=0;
659     Finley_Mesh* mesh=m_finleyMesh.get();
660     switch (functionSpaceCode) {
661 phornby 1628 case(Nodes):
662     numDataPointsPerSample=1;
663     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
664     break;
665     case(ReducedNodes):
666     numDataPointsPerSample=1;
667     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
668     break;
669     case(Elements):
670     if (mesh->Elements!=NULL) {
671     numSamples=mesh->Elements->numElements;
672     numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
673     }
674     break;
675     case(ReducedElements):
676     if (mesh->Elements!=NULL) {
677     numSamples=mesh->Elements->numElements;
678     numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
679     }
680     break;
681     case(FaceElements):
682     if (mesh->FaceElements!=NULL) {
683     numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
684     numSamples=mesh->FaceElements->numElements;
685     }
686     break;
687     case(ReducedFaceElements):
688     if (mesh->FaceElements!=NULL) {
689     numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
690     numSamples=mesh->FaceElements->numElements;
691     }
692     break;
693     case(Points):
694     if (mesh->Points!=NULL) {
695     numDataPointsPerSample=1;
696     numSamples=mesh->Points->numElements;
697     }
698     break;
699     case(ContactElementsZero):
700     if (mesh->ContactElements!=NULL) {
701     numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
702     numSamples=mesh->ContactElements->numElements;
703     }
704     break;
705     case(ReducedContactElementsZero):
706     if (mesh->ContactElements!=NULL) {
707     numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
708     numSamples=mesh->ContactElements->numElements;
709     }
710     break;
711     case(ContactElementsOne):
712     if (mesh->ContactElements!=NULL) {
713     numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
714     numSamples=mesh->ContactElements->numElements;
715     }
716     break;
717     case(ReducedContactElementsOne):
718     if (mesh->ContactElements!=NULL) {
719     numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
720     numSamples=mesh->ContactElements->numElements;
721     }
722     break;
723     case(DegreesOfFreedom):
724     if (mesh->Nodes!=NULL) {
725     numDataPointsPerSample=1;
726     numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
727     }
728     break;
729     case(ReducedDegreesOfFreedom):
730     if (mesh->Nodes!=NULL) {
731     numDataPointsPerSample=1;
732     numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
733     }
734     break;
735     default:
736     stringstream temp;
737     temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
738     throw FinleyAdapterException(temp.str());
739     break;
740     }
741     return pair<int,int>(numDataPointsPerSample,numSamples);
742 jgs 82 }
743 jgs 149
744 jgs 82 //
745     // adds linear PDE of second order into a given stiffness matrix and right hand side:
746     //
747     void MeshAdapter::addPDEToSystem(
748 phornby 1628 SystemMatrixAdapter& mat, escript::Data& rhs,
749     const escript::Data& A, const escript::Data& B, const escript::Data& C,const escript::Data& D,const escript::Data& X,const escript::Data& Y,
750     const escript::Data& d, const escript::Data& y,
751     const escript::Data& d_contact,const escript::Data& y_contact) const
752 jgs 82 {
753 gross 798 escriptDataC _rhs=rhs.getDataC();
754     escriptDataC _A =A.getDataC();
755     escriptDataC _B=B.getDataC();
756     escriptDataC _C=C.getDataC();
757     escriptDataC _D=D.getDataC();
758     escriptDataC _X=X.getDataC();
759     escriptDataC _Y=Y.getDataC();
760     escriptDataC _d=d.getDataC();
761     escriptDataC _y=y.getDataC();
762     escriptDataC _d_contact=d_contact.getDataC();
763     escriptDataC _y_contact=y_contact.getDataC();
764 bcumming 751
765 jgs 82 Finley_Mesh* mesh=m_finleyMesh.get();
766 gross 798
767 bcumming 751 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
768 jgs 82 checkFinleyError();
769 bcumming 751
770 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
771 jgs 82 checkFinleyError();
772 bcumming 751
773 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
774 jgs 82 checkFinleyError();
775     }
776 jgs 149
777 gross 1204 void MeshAdapter::addPDEToLumpedSystem(
778 phornby 1628 escript::Data& mat,
779     const escript::Data& D,
780     const escript::Data& d) const
781 gross 1204 {
782     escriptDataC _mat=mat.getDataC();
783     escriptDataC _D=D.getDataC();
784     escriptDataC _d=d.getDataC();
785    
786     Finley_Mesh* mesh=m_finleyMesh.get();
787 ksteube 1312
788 gross 1204 Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
789     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
790    
791     checkFinleyError();
792     }
793    
794    
795 jgs 82 //
796 jgs 102 // adds linear PDE of second order into the right hand side only
797     //
798 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
799 jgs 102 {
800     Finley_Mesh* mesh=m_finleyMesh.get();
801 jgs 147
802 gross 798 escriptDataC _rhs=rhs.getDataC();
803     escriptDataC _X=X.getDataC();
804     escriptDataC _Y=Y.getDataC();
805     escriptDataC _y=y.getDataC();
806     escriptDataC _y_contact=y_contact.getDataC();
807    
808     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
809 jgs 102 checkFinleyError();
810 jgs 147
811 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
812     checkFinleyError();
813 jgs 147
814 gross 798 Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
815 jgs 102 checkFinleyError();
816     }
817 gross 1367 //
818     // adds PDE of second order into a transport problem
819     //
820     void MeshAdapter::addPDEToTransportProblem(
821 phornby 1628 TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
822     const escript::Data& A, const escript::Data& B, const escript::Data& C,
823     const escript::Data& D,const escript::Data& X,const escript::Data& Y,
824     const escript::Data& d, const escript::Data& y,
825     const escript::Data& d_contact,const escript::Data& y_contact) const
826 gross 1367 {
827 jfenwick 1796 DataTypes::ShapeType shape;
828 gross 1370 source.expand();
829 gross 1367 escriptDataC _source=source.getDataC();
830     escriptDataC _M=M.getDataC();
831     escriptDataC _A=A.getDataC();
832     escriptDataC _B=B.getDataC();
833     escriptDataC _C=C.getDataC();
834     escriptDataC _D=D.getDataC();
835     escriptDataC _X=X.getDataC();
836     escriptDataC _Y=Y.getDataC();
837     escriptDataC _d=d.getDataC();
838     escriptDataC _y=y.getDataC();
839     escriptDataC _d_contact=d_contact.getDataC();
840     escriptDataC _y_contact=y_contact.getDataC();
841 jgs 149
842 gross 1367 Finley_Mesh* mesh=m_finleyMesh.get();
843     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
844 phornby 1628
845 gross 1407 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
846 gross 1367 checkFinleyError();
847    
848 gross 1407 Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
849 gross 1367 checkFinleyError();
850    
851     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
852     checkFinleyError();
853    
854     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
855     checkFinleyError();
856     }
857    
858 jgs 102 //
859 jgs 82 // interpolates data between different function spaces:
860     //
861 jgs 480 void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
862 jgs 82 {
863 jfenwick 1872 const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
864     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
865 phornby 1628 if (inDomain!=*this)
866     throw FinleyAdapterException("Error - Illegal domain of interpolant.");
867     if (targetDomain!=*this)
868     throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
869 jgs 82
870 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
871     escriptDataC _target=target.getDataC();
872     escriptDataC _in=in.getDataC();
873     switch(in.getFunctionSpace().getTypeCode()) {
874     case(Nodes):
875     switch(target.getFunctionSpace().getTypeCode()) {
876     case(Nodes):
877     case(ReducedNodes):
878     case(DegreesOfFreedom):
879     case(ReducedDegreesOfFreedom):
880     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
881     break;
882     case(Elements):
883     case(ReducedElements):
884     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
885     break;
886     case(FaceElements):
887     case(ReducedFaceElements):
888     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
889     break;
890     case(Points):
891     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
892     break;
893     case(ContactElementsZero):
894     case(ReducedContactElementsZero):
895     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
896     break;
897     case(ContactElementsOne):
898     case(ReducedContactElementsOne):
899     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
900     break;
901     default:
902     stringstream temp;
903     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
904     throw FinleyAdapterException(temp.str());
905     break;
906     }
907     break;
908     case(ReducedNodes):
909     switch(target.getFunctionSpace().getTypeCode()) {
910     case(Nodes):
911     case(ReducedNodes):
912     case(DegreesOfFreedom):
913     case(ReducedDegreesOfFreedom):
914     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
915     break;
916     case(Elements):
917     case(ReducedElements):
918     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
919     break;
920     case(FaceElements):
921     case(ReducedFaceElements):
922     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
923     break;
924     case(Points):
925     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
926     break;
927     case(ContactElementsZero):
928     case(ReducedContactElementsZero):
929     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
930     break;
931     case(ContactElementsOne):
932     case(ReducedContactElementsOne):
933     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
934     break;
935     default:
936     stringstream temp;
937     temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
938     throw FinleyAdapterException(temp.str());
939     break;
940     }
941     break;
942     case(Elements):
943     if (target.getFunctionSpace().getTypeCode()==Elements) {
944     Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
945     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
946     Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
947     } else {
948     throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
949     }
950     break;
951     case(ReducedElements):
952     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
953     Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
954     } else {
955     throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
956     }
957     break;
958     case(FaceElements):
959     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
960     Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
961     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
962     Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
963     } else {
964     throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
965     }
966     break;
967     case(ReducedFaceElements):
968     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
969     Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
970     } else {
971     throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
972     }
973     break;
974     case(Points):
975     if (target.getFunctionSpace().getTypeCode()==Points) {
976     Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
977     } else {
978     throw FinleyAdapterException("Error - No interpolation with data on points possible.");
979     }
980     break;
981     case(ContactElementsZero):
982     case(ContactElementsOne):
983     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
984     Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
985     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
986     Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
987     } else {
988     throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
989     }
990     break;
991     case(ReducedContactElementsZero):
992     case(ReducedContactElementsOne):
993     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
994     Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
995     } else {
996     throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
997     }
998     break;
999     case(DegreesOfFreedom):
1000     switch(target.getFunctionSpace().getTypeCode()) {
1001     case(ReducedDegreesOfFreedom):
1002     case(DegreesOfFreedom):
1003     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1004     break;
1005 ksteube 1312
1006 phornby 1628 case(Nodes):
1007     case(ReducedNodes):
1008     if (getMPISize()>1) {
1009     escript::Data temp=escript::Data(in);
1010     temp.expand();
1011     escriptDataC _in2 = temp.getDataC();
1012     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1013     } else {
1014     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1015     }
1016     break;
1017     case(Elements):
1018     case(ReducedElements):
1019     if (getMPISize()>1) {
1020     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1021     escriptDataC _in2 = temp.getDataC();
1022     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1023     } else {
1024     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1025     }
1026     break;
1027     case(FaceElements):
1028     case(ReducedFaceElements):
1029     if (getMPISize()>1) {
1030     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1031     escriptDataC _in2 = temp.getDataC();
1032     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1033 ksteube 1312
1034 phornby 1628 } else {
1035     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1036     }
1037     break;
1038     case(Points):
1039     if (getMPISize()>1) {
1040     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1041     escriptDataC _in2 = temp.getDataC();
1042     } else {
1043     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1044     }
1045     break;
1046     case(ContactElementsZero):
1047     case(ContactElementsOne):
1048     case(ReducedContactElementsZero):
1049     case(ReducedContactElementsOne):
1050     if (getMPISize()>1) {
1051     escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) );
1052     escriptDataC _in2 = temp.getDataC();
1053     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1054     } else {
1055     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1056     }
1057     break;
1058     default:
1059     stringstream temp;
1060     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1061     throw FinleyAdapterException(temp.str());
1062     break;
1063     }
1064     break;
1065     case(ReducedDegreesOfFreedom):
1066     switch(target.getFunctionSpace().getTypeCode()) {
1067     case(Nodes):
1068     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1069     break;
1070     case(ReducedNodes):
1071     if (getMPISize()>1) {
1072     escript::Data temp=escript::Data(in);
1073     temp.expand();
1074     escriptDataC _in2 = temp.getDataC();
1075     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1076     } else {
1077     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1078     }
1079     break;
1080     case(DegreesOfFreedom):
1081     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1082     break;
1083     case(ReducedDegreesOfFreedom):
1084     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1085     break;
1086     case(Elements):
1087     case(ReducedElements):
1088     if (getMPISize()>1) {
1089     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1090     escriptDataC _in2 = temp.getDataC();
1091     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1092     } else {
1093     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1094     }
1095     break;
1096     case(FaceElements):
1097     case(ReducedFaceElements):
1098     if (getMPISize()>1) {
1099     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1100     escriptDataC _in2 = temp.getDataC();
1101     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1102     } else {
1103     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1104     }
1105     break;
1106     case(Points):
1107     if (getMPISize()>1) {
1108     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1109     escriptDataC _in2 = temp.getDataC();
1110     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1111     } else {
1112     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1113     }
1114     break;
1115     case(ContactElementsZero):
1116     case(ContactElementsOne):
1117     case(ReducedContactElementsZero):
1118     case(ReducedContactElementsOne):
1119     if (getMPISize()>1) {
1120     escript::Data temp=escript::Data( in, reducedContinuousFunction(asAbstractContinuousDomain()) );
1121     escriptDataC _in2 = temp.getDataC();
1122     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1123     } else {
1124     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1125     }
1126     break;
1127     default:
1128     stringstream temp;
1129     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1130     throw FinleyAdapterException(temp.str());
1131     break;
1132     }
1133     break;
1134     default:
1135     stringstream temp;
1136     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1137     throw FinleyAdapterException(temp.str());
1138     break;
1139     }
1140     checkFinleyError();
1141 jgs 82 }
1142    
1143     //
1144     // copies the locations of sample points into x:
1145     //
1146 jgs 480 void MeshAdapter::setToX(escript::Data& arg) const
1147 jgs 82 {
1148 jfenwick 1872 const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1149 phornby 1628 if (argDomain!=*this)
1150     throw FinleyAdapterException("Error - Illegal domain of data point locations");
1151     Finley_Mesh* mesh=m_finleyMesh.get();
1152     // in case of values node coordinates we can do the job directly:
1153     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1154     escriptDataC _arg=arg.getDataC();
1155     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1156     } else {
1157     escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1158     escriptDataC _tmp_data=tmp_data.getDataC();
1159     Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1160     // this is then interpolated onto arg:
1161     interpolateOnDomain(arg,tmp_data);
1162     }
1163     checkFinleyError();
1164 jgs 82 }
1165 jgs 149
1166 jgs 82 //
1167     // return the normal vectors at the location of data points as a Data object:
1168     //
1169 jgs 480 void MeshAdapter::setToNormal(escript::Data& normal) const
1170 jgs 82 {
1171 jfenwick 1872 /* const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1172     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1173 phornby 1628 if (normalDomain!=*this)
1174     throw FinleyAdapterException("Error - Illegal domain of normal locations");
1175     Finley_Mesh* mesh=m_finleyMesh.get();
1176     escriptDataC _normal=normal.getDataC();
1177     switch(normal.getFunctionSpace().getTypeCode()) {
1178     case(Nodes):
1179     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1180     break;
1181     case(ReducedNodes):
1182     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1183     break;
1184     case(Elements):
1185     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1186     break;
1187     case(ReducedElements):
1188     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1189     break;
1190     case (FaceElements):
1191     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1192     break;
1193     case (ReducedFaceElements):
1194     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1195     break;
1196     case(Points):
1197     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1198     break;
1199     case (ContactElementsOne):
1200     case (ContactElementsZero):
1201     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1202     break;
1203     case (ReducedContactElementsOne):
1204     case (ReducedContactElementsZero):
1205     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1206     break;
1207     case(DegreesOfFreedom):
1208     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1209     break;
1210     case(ReducedDegreesOfFreedom):
1211     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1212     break;
1213     default:
1214 jgs 150 stringstream temp;
1215     temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1216     throw FinleyAdapterException(temp.str());
1217 jgs 82 break;
1218 phornby 1628 }
1219     checkFinleyError();
1220 jgs 82 }
1221 jgs 149
1222 jgs 82 //
1223     // interpolates data to other domain:
1224     //
1225 jgs 480 void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1226 jgs 82 {
1227 jfenwick 1872 const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
1228 phornby 1628 if (targetDomain!=*this)
1229     throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1230 jgs 82
1231 phornby 1628 throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1232 jgs 82 }
1233 jgs 149
1234 jgs 82 //
1235     // calculates the integral of a function defined of arg:
1236     //
1237 jgs 480 void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1238 jgs 82 {
1239 jfenwick 1872 const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1240 phornby 1628 if (argDomain!=*this)
1241     throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1242 jgs 82
1243 phornby 1628 double blocktimer_start = blocktimer_time();
1244     Finley_Mesh* mesh=m_finleyMesh.get();
1245     escriptDataC _temp;
1246     escript::Data temp;
1247     escriptDataC _arg=arg.getDataC();
1248     switch(arg.getFunctionSpace().getTypeCode()) {
1249     case(Nodes):
1250 jfenwick 1872 temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1251 phornby 1628 _temp=temp.getDataC();
1252     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1253     break;
1254     case(ReducedNodes):
1255 jfenwick 1872 temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1256 phornby 1628 _temp=temp.getDataC();
1257     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1258     break;
1259     case(Elements):
1260     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1261     break;
1262     case(ReducedElements):
1263     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1264     break;
1265     case(FaceElements):
1266     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1267     break;
1268     case(ReducedFaceElements):
1269     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1270     break;
1271     case(Points):
1272     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1273     break;
1274     case(ContactElementsZero):
1275     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1276     break;
1277     case(ReducedContactElementsZero):
1278     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1279     break;
1280     case(ContactElementsOne):
1281     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1282     break;
1283     case(ReducedContactElementsOne):
1284     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1285     break;
1286     case(DegreesOfFreedom):
1287 jfenwick 1872 temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1288 phornby 1628 _temp=temp.getDataC();
1289     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1290     break;
1291     case(ReducedDegreesOfFreedom):
1292 jfenwick 1872 temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1293 phornby 1628 _temp=temp.getDataC();
1294     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1295     break;
1296     default:
1297     stringstream temp;
1298     temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1299     throw FinleyAdapterException(temp.str());
1300     break;
1301     }
1302     checkFinleyError();
1303     blocktimer_increment("integrate()", blocktimer_start);
1304 jgs 82 }
1305 jgs 149
1306 jgs 82 //
1307     // calculates the gradient of arg:
1308     //
1309 jgs 480 void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1310 jgs 82 {
1311 jfenwick 1872 const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1312 phornby 1628 if (argDomain!=*this)
1313     throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1314 jfenwick 1872 const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1315 phornby 1628 if (gradDomain!=*this)
1316     throw FinleyAdapterException("Error - Illegal domain of gradient");
1317 jgs 82
1318 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1319     escriptDataC _grad=grad.getDataC();
1320     escriptDataC nodeDataC;
1321     escript::Data temp;
1322     if (getMPISize()>1) {
1323 ksteube 1312 if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1324 phornby 1628 temp=escript::Data( arg, continuousFunction(asAbstractContinuousDomain()) );
1325     nodeDataC = temp.getDataC();
1326 ksteube 1312 } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1327 phornby 1628 temp=escript::Data( arg, reducedContinuousFunction(asAbstractContinuousDomain()) );
1328     nodeDataC = temp.getDataC();
1329 ksteube 1312 } else {
1330 phornby 1628 nodeDataC = arg.getDataC();
1331 ksteube 1312 }
1332 phornby 1628 } else {
1333     nodeDataC = arg.getDataC();
1334     }
1335     switch(grad.getFunctionSpace().getTypeCode()) {
1336     case(Nodes):
1337     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1338     break;
1339     case(ReducedNodes):
1340     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1341     break;
1342     case(Elements):
1343     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1344     break;
1345     case(ReducedElements):
1346     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1347     break;
1348     case(FaceElements):
1349     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1350     break;
1351     case(ReducedFaceElements):
1352     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1353     break;
1354     case(Points):
1355     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1356     break;
1357     case(ContactElementsZero):
1358     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1359     break;
1360     case(ReducedContactElementsZero):
1361     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1362     break;
1363     case(ContactElementsOne):
1364     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1365     break;
1366     case(ReducedContactElementsOne):
1367     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1368     break;
1369     case(DegreesOfFreedom):
1370     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1371     break;
1372     case(ReducedDegreesOfFreedom):
1373     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1374     break;
1375     default:
1376     stringstream temp;
1377     temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1378     throw FinleyAdapterException(temp.str());
1379     break;
1380     }
1381     checkFinleyError();
1382 jgs 82 }
1383 jgs 149
1384 jgs 82 //
1385     // returns the size of elements:
1386     //
1387 jgs 480 void MeshAdapter::setToSize(escript::Data& size) const
1388 jgs 82 {
1389 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1390     escriptDataC tmp=size.getDataC();
1391     switch(size.getFunctionSpace().getTypeCode()) {
1392     case(Nodes):
1393     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1394     break;
1395     case(ReducedNodes):
1396     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1397     break;
1398     case(Elements):
1399     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1400     break;
1401     case(ReducedElements):
1402     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1403     break;
1404     case(FaceElements):
1405     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1406     break;
1407     case(ReducedFaceElements):
1408     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1409     break;
1410     case(Points):
1411     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1412     break;
1413     case(ContactElementsZero):
1414     case(ContactElementsOne):
1415     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1416     break;
1417     case(ReducedContactElementsZero):
1418     case(ReducedContactElementsOne):
1419     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1420     break;
1421     case(DegreesOfFreedom):
1422     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1423     break;
1424     case(ReducedDegreesOfFreedom):
1425     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1426     break;
1427     default:
1428     stringstream temp;
1429     temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1430     throw FinleyAdapterException(temp.str());
1431     break;
1432     }
1433     checkFinleyError();
1434 jgs 82 }
1435 jgs 149
1436 jgs 82 // sets the location of nodes:
1437 jgs 480 void MeshAdapter::setNewX(const escript::Data& new_x)
1438 jgs 82 {
1439 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1440     escriptDataC tmp;
1441 jfenwick 1872 const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1442 phornby 1628 if (newDomain!=*this)
1443     throw FinleyAdapterException("Error - Illegal domain of new point locations");
1444     tmp = new_x.getDataC();
1445     Finley_Mesh_setCoordinates(mesh,&tmp);
1446     checkFinleyError();
1447 jgs 82 }
1448 jgs 149
1449 jgs 82 // saves a data array in openDX format:
1450 jgs 153 void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1451     {
1452 phornby 1628 unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1453     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1454     /* win32 refactor */
1455     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1456     for(int i=0;i<num_data;i++)
1457     {
1458     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1459     }
1460 jgs 153
1461 phornby 1628 escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1462     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1463 woo409 757
1464 phornby 1628 boost::python::list keys=arg.keys();
1465     for (int i=0;i<num_data;++i) {
1466     std::string n=boost::python::extract<std::string>(keys[i]);
1467     escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1468 jfenwick 1872 if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1469 phornby 1628 throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1470     data[i]=d.getDataC();
1471     ptr_data[i]= &(data[i]);
1472     if (n.length()>MAX_namelength-1) {
1473     strncpy(names[i],n.c_str(),MAX_namelength-1);
1474     names[i][MAX_namelength-1]='\0';
1475     } else {
1476     strcpy(names[i],n.c_str());
1477     }
1478     }
1479     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1480     checkFinleyError();
1481    
1482     /* win32 refactor */
1483     TMPMEMFREE(data);
1484     TMPMEMFREE(ptr_data);
1485     for(int i=0;i<num_data;i++)
1486     {
1487     TMPMEMFREE(names[i]);
1488     }
1489     TMPMEMFREE(names);
1490 woo409 757
1491 phornby 1628 return;
1492 jgs 82 }
1493 jgs 149
1494 jgs 110 // saves a data array in openVTK format:
1495 jgs 153 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1496     {
1497 phornby 1628 unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1498     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1499     /* win32 refactor */
1500     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1501     for(int i=0;i<num_data;i++)
1502     {
1503     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1504     }
1505 jgs 153
1506 phornby 1628 escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1507     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1508 woo409 757
1509 phornby 1628 boost::python::list keys=arg.keys();
1510     for (int i=0;i<num_data;++i) {
1511     std::string n=boost::python::extract<std::string>(keys[i]);
1512     escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1513 jfenwick 1872 if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1514 phornby 1628 throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain");
1515     data[i]=d.getDataC();
1516     ptr_data[i]=&(data[i]);
1517     if (n.length()>MAX_namelength-1) {
1518     strncpy(names[i],n.c_str(),MAX_namelength-1);
1519     names[i][MAX_namelength-1]='\0';
1520     } else {
1521     strcpy(names[i],n.c_str());
1522     }
1523     }
1524     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1525 dhawcroft 793
1526 phornby 1628 checkFinleyError();
1527     /* win32 refactor */
1528     TMPMEMFREE(data);
1529     TMPMEMFREE(ptr_data);
1530     for(int i=0;i<num_data;i++)
1531     {
1532     TMPMEMFREE(names[i]);
1533     }
1534     TMPMEMFREE(names);
1535 woo409 757
1536 phornby 1628 return;
1537 jgs 110 }
1538 phornby 1628
1539    
1540 jgs 82 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1541     SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1542 phornby 1628 const int row_blocksize,
1543     const escript::FunctionSpace& row_functionspace,
1544     const int column_blocksize,
1545     const escript::FunctionSpace& column_functionspace,
1546     const int type) const
1547 jgs 82 {
1548 phornby 1628 int reduceRowOrder=0;
1549     int reduceColOrder=0;
1550     // is the domain right?
1551 jfenwick 1872 const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1552 phornby 1628 if (row_domain!=*this)
1553     throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1554 jfenwick 1872 const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1555 phornby 1628 if (col_domain!=*this)
1556     throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1557     // is the function space type right
1558     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1559     reduceRowOrder=0;
1560     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1561     reduceRowOrder=1;
1562     } else {
1563     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1564     }
1565     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1566     reduceColOrder=0;
1567     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1568     reduceColOrder=1;
1569     } else {
1570     throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1571     }
1572     // generate matrix:
1573    
1574     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1575     checkFinleyError();
1576     Paso_SystemMatrix* fsystemMatrix;
1577     int trilinos = 0;
1578     if (trilinos) {
1579 ksteube 1312 #ifdef TRILINOS
1580     /* Allocation Epetra_VrbMatrix here */
1581     #endif
1582 phornby 1628 }
1583     else {
1584 ksteube 1312 fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1585 phornby 1628 }
1586     checkPasoError();
1587     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1588     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1589 jgs 82 }
1590 gross 1366 // creates a TransportProblemAdapter
1591     TransportProblemAdapter MeshAdapter::newTransportProblem(
1592 phornby 1628 const double theta,
1593     const int blocksize,
1594     const escript::FunctionSpace& functionspace,
1595     const int type) const
1596 gross 1366 {
1597 phornby 1628 int reduceOrder=0;
1598     // is the domain right?
1599 jfenwick 1872 const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1600 phornby 1628 if (domain!=*this)
1601     throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1602     // is the function space type right
1603     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1604     reduceOrder=0;
1605     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1606     reduceOrder=1;
1607     } else {
1608     throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1609     }
1610     // generate matrix:
1611    
1612     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1613     checkFinleyError();
1614     Paso_FCTransportProblem* transportProblem;
1615     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1616     checkPasoError();
1617     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1618     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1619 gross 1366 }
1620 jgs 149
1621 jgs 82 //
1622     // vtkObject MeshAdapter::createVtkObject() const
1623     // TODO:
1624     //
1625 jgs 149
1626 jgs 82 //
1627     // returns true if data at the atom_type is considered as being cell centered:
1628     bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1629     {
1630 phornby 1628 switch(functionSpaceCode) {
1631     case(Nodes):
1632     case(DegreesOfFreedom):
1633     case(ReducedDegreesOfFreedom):
1634     return false;
1635     break;
1636     case(Elements):
1637     case(FaceElements):
1638     case(Points):
1639     case(ContactElementsZero):
1640     case(ContactElementsOne):
1641     case(ReducedElements):
1642     case(ReducedFaceElements):
1643     case(ReducedContactElementsZero):
1644     case(ReducedContactElementsOne):
1645     return true;
1646     break;
1647     default:
1648     stringstream temp;
1649     temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1650     throw FinleyAdapterException(temp.str());
1651     break;
1652     }
1653     checkFinleyError();
1654     return false;
1655 jgs 82 }
1656 jgs 149
1657 jgs 82 bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1658     {
1659 phornby 1628 switch(functionSpaceType_source) {
1660     case(Nodes):
1661     switch(functionSpaceType_target) {
1662     case(Nodes):
1663     case(ReducedNodes):
1664     case(ReducedDegreesOfFreedom):
1665     case(DegreesOfFreedom):
1666     case(Elements):
1667     case(ReducedElements):
1668     case(FaceElements):
1669     case(ReducedFaceElements):
1670     case(Points):
1671     case(ContactElementsZero):
1672     case(ReducedContactElementsZero):
1673     case(ContactElementsOne):
1674     case(ReducedContactElementsOne):
1675     return true;
1676     default:
1677     stringstream temp;
1678     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1679     throw FinleyAdapterException(temp.str());
1680     }
1681     break;
1682     case(ReducedNodes):
1683     switch(functionSpaceType_target) {
1684     case(ReducedNodes):
1685     case(ReducedDegreesOfFreedom):
1686     case(Elements):
1687     case(ReducedElements):
1688     case(FaceElements):
1689     case(ReducedFaceElements):
1690     case(Points):
1691     case(ContactElementsZero):
1692     case(ReducedContactElementsZero):
1693     case(ContactElementsOne):
1694     case(ReducedContactElementsOne):
1695     return true;
1696     case(Nodes):
1697     case(DegreesOfFreedom):
1698     return false;
1699     default:
1700     stringstream temp;
1701     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1702     throw FinleyAdapterException(temp.str());
1703     }
1704     break;
1705     case(Elements):
1706     if (functionSpaceType_target==Elements) {
1707     return true;
1708     } else if (functionSpaceType_target==ReducedElements) {
1709     return true;
1710     } else {
1711     return false;
1712     }
1713     case(ReducedElements):
1714     if (functionSpaceType_target==ReducedElements) {
1715     return true;
1716     } else {
1717     return false;
1718     }
1719     case(FaceElements):
1720     if (functionSpaceType_target==FaceElements) {
1721     return true;
1722     } else if (functionSpaceType_target==ReducedFaceElements) {
1723     return true;
1724     } else {
1725     return false;
1726     }
1727     case(ReducedFaceElements):
1728     if (functionSpaceType_target==ReducedFaceElements) {
1729     return true;
1730     } else {
1731     return false;
1732     }
1733     case(Points):
1734     if (functionSpaceType_target==Points) {
1735     return true;
1736     } else {
1737     return false;
1738     }
1739     case(ContactElementsZero):
1740     case(ContactElementsOne):
1741     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1742     return true;
1743     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1744     return true;
1745     } else {
1746     return false;
1747     }
1748     case(ReducedContactElementsZero):
1749     case(ReducedContactElementsOne):
1750     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1751     return true;
1752     } else {
1753     return false;
1754     }
1755     case(DegreesOfFreedom):
1756     switch(functionSpaceType_target) {
1757     case(ReducedDegreesOfFreedom):
1758     case(DegreesOfFreedom):
1759     case(Nodes):
1760     case(ReducedNodes):
1761     case(Elements):
1762     case(ReducedElements):
1763     case(Points):
1764     case(FaceElements):
1765     case(ReducedFaceElements):
1766     case(ContactElementsZero):
1767     case(ReducedContactElementsZero):
1768     case(ContactElementsOne):
1769     case(ReducedContactElementsOne):
1770     return true;
1771     default:
1772     stringstream temp;
1773     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1774     throw FinleyAdapterException(temp.str());
1775     }
1776     break;
1777     case(ReducedDegreesOfFreedom):
1778     switch(functionSpaceType_target) {
1779     case(ReducedDegreesOfFreedom):
1780     case(ReducedNodes):
1781     case(Elements):
1782     case(ReducedElements):
1783     case(FaceElements):
1784     case(ReducedFaceElements):
1785     case(Points):
1786     case(ContactElementsZero):
1787     case(ReducedContactElementsZero):
1788     case(ContactElementsOne):
1789     case(ReducedContactElementsOne):
1790     return true;
1791     case(Nodes):
1792     case(DegreesOfFreedom):
1793     return false;
1794     default:
1795     stringstream temp;
1796     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1797     throw FinleyAdapterException(temp.str());
1798     }
1799     break;
1800     default:
1801     stringstream temp;
1802     temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1803     throw FinleyAdapterException(temp.str());
1804     break;
1805     }
1806     checkFinleyError();
1807     return false;
1808 jgs 82 }
1809 jgs 149
1810 jgs 82 bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
1811     {
1812 phornby 1628 return false;
1813 jgs 82 }
1814 jgs 104
1815 jgs 121 bool MeshAdapter::operator==(const AbstractDomain& other) const
1816 jgs 82 {
1817 phornby 1628 const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1818     if (temp!=0) {
1819     return (m_finleyMesh==temp->m_finleyMesh);
1820     } else {
1821     return false;
1822     }
1823 jgs 82 }
1824    
1825 jgs 121 bool MeshAdapter::operator!=(const AbstractDomain& other) const
1826 jgs 104 {
1827 phornby 1628 return !(operator==(other));
1828 jgs 104 }
1829    
1830 gross 1859 int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1831 jgs 102 {
1832 gross 1859 int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1833 jgs 150 checkPasoError();
1834 jgs 102 return out;
1835     }
1836 gross 1859 int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1837     {
1838     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1839     checkPasoError();
1840     return out;
1841     }
1842 jgs 149
1843 jgs 480 escript::Data MeshAdapter::getX() const
1844 jgs 102 {
1845 phornby 1628 return continuousFunction(asAbstractContinuousDomain()).getX();
1846 jgs 102 }
1847 jgs 149
1848 jgs 480 escript::Data MeshAdapter::getNormal() const
1849 jgs 102 {
1850 phornby 1628 return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1851 jgs 102 }
1852 jgs 149
1853 jgs 480 escript::Data MeshAdapter::getSize() const
1854 jgs 102 {
1855 jfenwick 1872 return escript::function(asAbstractContinuousDomain()).getSize();
1856 jgs 102 }
1857    
1858 gross 1062 int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1859     {
1860 phornby 1628 int *out = NULL;
1861     Finley_Mesh* mesh=m_finleyMesh.get();
1862     switch (functionSpaceType) {
1863     case(Nodes):
1864     out=mesh->Nodes->Id;
1865     break;
1866     case(ReducedNodes):
1867     out=mesh->Nodes->reducedNodesId;
1868     break;
1869     case(Elements):
1870     out=mesh->Elements->Id;
1871     break;
1872     case(ReducedElements):
1873     out=mesh->Elements->Id;
1874     break;
1875     case(FaceElements):
1876     out=mesh->FaceElements->Id;
1877     break;
1878     case(ReducedFaceElements):
1879     out=mesh->FaceElements->Id;
1880     break;
1881     case(Points):
1882     out=mesh->Points->Id;
1883     break;
1884     case(ContactElementsZero):
1885     out=mesh->ContactElements->Id;
1886     break;
1887     case(ReducedContactElementsZero):
1888     out=mesh->ContactElements->Id;
1889     break;
1890     case(ContactElementsOne):
1891     out=mesh->ContactElements->Id;
1892     break;
1893     case(ReducedContactElementsOne):
1894     out=mesh->ContactElements->Id;
1895     break;
1896     case(DegreesOfFreedom):
1897     out=mesh->Nodes->degreesOfFreedomId;
1898     break;
1899     case(ReducedDegreesOfFreedom):
1900     out=mesh->Nodes->reducedDegreesOfFreedomId;
1901     break;
1902     default:
1903 gross 1062 stringstream temp;
1904     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1905     throw FinleyAdapterException(temp.str());
1906     break;
1907 phornby 1628 }
1908     return out;
1909 gross 1062 }
1910 jgs 110 int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1911     {
1912 phornby 1628 int out=0;
1913     Finley_Mesh* mesh=m_finleyMesh.get();
1914     switch (functionSpaceType) {
1915     case(Nodes):
1916     out=mesh->Nodes->Tag[sampleNo];
1917     break;
1918     case(ReducedNodes):
1919     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1920     break;
1921     case(Elements):
1922     out=mesh->Elements->Tag[sampleNo];
1923     break;
1924     case(ReducedElements):
1925     out=mesh->Elements->Tag[sampleNo];
1926     break;
1927     case(FaceElements):
1928     out=mesh->FaceElements->Tag[sampleNo];
1929     break;
1930     case(ReducedFaceElements):
1931     out=mesh->FaceElements->Tag[sampleNo];
1932     break;
1933     case(Points):
1934     out=mesh->Points->Tag[sampleNo];
1935     break;
1936     case(ContactElementsZero):
1937     out=mesh->ContactElements->Tag[sampleNo];
1938     break;
1939     case(ReducedContactElementsZero):
1940     out=mesh->ContactElements->Tag[sampleNo];
1941     break;
1942     case(ContactElementsOne):
1943     out=mesh->ContactElements->Tag[sampleNo];
1944     break;
1945     case(ReducedContactElementsOne):
1946     out=mesh->ContactElements->Tag[sampleNo];
1947     break;
1948     case(DegreesOfFreedom):
1949     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1950     break;
1951     case(ReducedDegreesOfFreedom):
1952     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1953     break;
1954     default:
1955     stringstream temp;
1956     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1957     throw FinleyAdapterException(temp.str());
1958     break;
1959     }
1960     return out;
1961 jgs 110 }
1962    
1963 gross 1062
1964 gross 767 void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1965     {
1966 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
1967     escriptDataC tmp=mask.getDataC();
1968     switch(functionSpaceType) {
1969     case(Nodes):
1970     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1971     break;
1972     case(ReducedNodes):
1973     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1974     break;
1975     case(DegreesOfFreedom):
1976     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1977     break;
1978     case(ReducedDegreesOfFreedom):
1979     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1980     break;
1981     case(Elements):
1982     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1983     break;
1984     case(ReducedElements):
1985     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1986     break;
1987     case(FaceElements):
1988     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1989     break;
1990     case(ReducedFaceElements):
1991     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1992     break;
1993     case(Points):
1994     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1995     break;
1996     case(ContactElementsZero):
1997     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1998     break;
1999     case(ReducedContactElementsZero):
2000     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2001     break;
2002     case(ContactElementsOne):
2003     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2004     break;
2005     case(ReducedContactElementsOne):
2006     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2007     break;
2008     default:
2009     stringstream temp;
2010     temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2011     throw FinleyAdapterException(temp.str());
2012     }
2013     checkFinleyError();
2014     return;
2015 gross 767 }
2016    
2017 gross 1044 void MeshAdapter::setTagMap(const std::string& name, int tag)
2018     {
2019 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
2020     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2021     checkPasoError();
2022     // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2023 gross 1044 }
2024 gross 767
2025 gross 1044 int MeshAdapter::getTag(const std::string& name) const
2026     {
2027 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
2028     int tag=0;
2029     tag=Finley_Mesh_getTag(mesh, name.c_str());
2030     checkPasoError();
2031     // throwStandardException("MeshAdapter::getTag is not implemented.");
2032     return tag;
2033 gross 1044 }
2034    
2035     bool MeshAdapter::isValidTagName(const std::string& name) const
2036     {
2037 phornby 1628 Finley_Mesh* mesh=m_finleyMesh.get();
2038     return Finley_Mesh_isValidTagName(mesh,name.c_str());
2039 gross 1044 }
2040    
2041     std::string MeshAdapter::showTagNames() const
2042     {
2043 phornby 1628 stringstream temp;
2044     Finley_Mesh* mesh=m_finleyMesh.get();
2045     Finley_TagMap* tag_map=mesh->TagMap;
2046     while (tag_map) {
2047     temp << tag_map->name;
2048     tag_map=tag_map->next;
2049     if (tag_map) temp << ", ";
2050     }
2051     return temp.str();
2052 gross 1044 }
2053    
2054 gross 1716 int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2055     {
2056     Finley_Mesh* mesh=m_finleyMesh.get();
2057     dim_t numTags=0;
2058     switch(functionSpaceCode) {
2059     case(Nodes):
2060     numTags=mesh->Nodes->numTagsInUse;
2061     break;
2062     case(ReducedNodes):
2063     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2064     break;
2065     case(DegreesOfFreedom):
2066     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2067     break;
2068     case(ReducedDegreesOfFreedom):
2069     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2070     break;
2071     case(Elements):
2072     case(ReducedElements):
2073     numTags=mesh->Elements->numTagsInUse;
2074     break;
2075     case(FaceElements):
2076     case(ReducedFaceElements):
2077     numTags=mesh->FaceElements->numTagsInUse;
2078     break;
2079     case(Points):
2080     numTags=mesh->Points->numTagsInUse;
2081     break;
2082     case(ContactElementsZero):
2083     case(ReducedContactElementsZero):
2084     case(ContactElementsOne):
2085     case(ReducedContactElementsOne):
2086     numTags=mesh->ContactElements->numTagsInUse;
2087     break;
2088     default:
2089     stringstream temp;
2090     temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2091     throw FinleyAdapterException(temp.str());
2092     }
2093     return numTags;
2094     }
2095     int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2096     {
2097     Finley_Mesh* mesh=m_finleyMesh.get();
2098     index_t* tags=NULL;
2099     switch(functionSpaceCode) {
2100     case(Nodes):
2101     tags=mesh->Nodes->tagsInUse;
2102     break;
2103     case(ReducedNodes):
2104     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2105     break;
2106     case(DegreesOfFreedom):
2107     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2108     break;
2109     case(ReducedDegreesOfFreedom):
2110     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2111     break;
2112     case(Elements):
2113     case(ReducedElements):
2114     tags=mesh->Elements->tagsInUse;
2115     break;
2116     case(FaceElements):
2117     case(ReducedFaceElements):
2118     tags=mesh->FaceElements->tagsInUse;
2119     break;
2120     case(Points):
2121     tags=mesh->Points->tagsInUse;
2122     break;
2123     case(ContactElementsZero):
2124     case(ReducedContactElementsZero):
2125     case(ContactElementsOne):
2126     case(ReducedContactElementsOne):
2127     tags=mesh->ContactElements->tagsInUse;
2128     break;
2129     default:
2130     stringstream temp;
2131     temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2132     throw FinleyAdapterException(temp.str());
2133     }
2134     return tags;
2135     }
2136    
2137    
2138 jfenwick 1802 bool MeshAdapter::canTag(int functionSpaceCode) const
2139     {
2140     switch(functionSpaceCode) {
2141     case(Nodes):
2142     case(Elements):
2143     case(ReducedElements):
2144     case(FaceElements):
2145     case(ReducedFaceElements):
2146     case(Points):
2147     case(ContactElementsZero):
2148     case(ReducedContactElementsZero):
2149     case(ContactElementsOne):
2150     case(ReducedContactElementsOne):
2151     return true;
2152     case(ReducedNodes):
2153     case(DegreesOfFreedom):
2154     case(ReducedDegreesOfFreedom):
2155     return false;
2156     default:
2157     return false;
2158     }
2159     }
2160    
2161    
2162 jgs 82 } // end of namespace

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