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

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Revision 2150 - (hide annotations)
Wed Dec 10 05:57:12 2008 UTC (10 years, 4 months ago) by caltinay
File size: 84711 byte(s)
Removed unnecessary "magic name length".

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

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