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

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Revision 1455 - (hide annotations)
Thu Feb 28 17:19:44 2008 UTC (11 years, 1 month ago) by phornby
File size: 85670 byte(s)
Merge of branches/windows_from_1431_trunk.

Revamp of the exception system.
Fix unused vars and signed/unsigned comparisons.
defined a macro THROW(ARG) in the system_dep.h's to
deal with the expectations of declarations on different architectures.

Details in the logs of branches/windows_from_1431_trunk.

pre-merge snapshot of the trunk in tags/trunk_at_1452


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

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