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

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Revision 1755 - (hide annotations)
Mon Sep 8 01:34:40 2008 UTC (10 years, 10 months ago) by ksteube
File size: 85272 byte(s)
Added new field to NetCDF dump of mesh

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

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