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

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Revision 1754 - (hide annotations)
Sun Sep 7 22:07:26 2008 UTC (10 years, 10 months ago) by ksteube
File size: 84431 byte(s)
Added new test suite run_inputOutput.py to systematically test I/O.
Can determine if two domains are same with Fourier analysis.
Added new method getNumDataPointsGlobal to return number of DPs of a distributed mesh.
Reading of tags in ReadMeshMPI failed occasionally, should be more robust now.

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

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