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

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Revision 1990 - (hide annotations)
Fri Nov 7 04:19:07 2008 UTC (10 years, 5 months ago) by ksteube
Original Path: trunk/finley/src/CPPAdapter/MeshAdapter.cpp
File size: 85320 byte(s)
Changes to avoid compiler warnings
Finley files now pass -Wall on gcc 4.3.2
	saveVTK.c: replaced printf(string) with printf("%s", string)
	MeshAdapterFactory.cpp: moved a few lines to avoid possible use of uninitialized vars
	MeshAdapter.cpp: initialized ncdims in mesh dump
There is still a warning from a boost include file

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