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

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Revision 1800 - (hide annotations)
Thu Sep 18 05:28:20 2008 UTC (10 years, 9 months ago) by ksteube
File size: 83999 byte(s)
Serialized parallel I/O when writing mesh or data to NetCDF file on multiple MPI processors.
Added domain method getMPIComm() to complement getMPISize() and getMPIRank().

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

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