/[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 1801 - (hide annotations)
Fri Sep 19 01:37:09 2008 UTC (10 years, 7 months ago) by ksteube
Original Path: trunk/finley/src/CPPAdapter/MeshAdapter.cpp
File size: 83909 byte(s)
Fixed serialization of I/O for MPI...code didn't compile without MPI

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

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