/[escript]/trunk/dataexporter/src/NodeData.cpp
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Annotation of /trunk/dataexporter/src/NodeData.cpp

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Revision 2853 - (hide annotations)
Mon Jan 18 01:46:05 2010 UTC (9 years, 8 months ago) by caltinay
File size: 9308 byte(s)
Do not attempt to read node file data if #nodes=0.

1 caltinay 2183
2     /*******************************************************
3     *
4 jfenwick 2548 * Copyright (c) 2003-2009 by University of Queensland
5 caltinay 2183 * Earth Systems Science Computational Center (ESSCC)
6     * http://www.uq.edu.au/esscc
7     *
8     * Primary Business: Queensland, Australia
9     * Licensed under the Open Software License version 3.0
10     * http://www.opensource.org/licenses/osl-3.0.php
11     *
12     *******************************************************/
13    
14 caltinay 2810 #include <escriptexport/NodeData.h>
15    
16     extern "C" {
17     #include <finley/Mesh.h>
18     #include <finley/NodeFile.h>
19     }
20    
21     #if USE_NETCDF
22 caltinay 2183 #include <netcdf.hh>
23 caltinay 2810 #endif
24    
25     #if USE_SILO
26 caltinay 2183 #include <silo.h>
27     #endif
28    
29     using namespace std;
30    
31 caltinay 2810 namespace escriptexport {
32 caltinay 2187
33 caltinay 2183 //
34 caltinay 2810 // Constructor with name
35 caltinay 2183 //
36 caltinay 2810 NodeData::NodeData(const string& meshName) :
37     numDims(0), numNodes(0), name(meshName)
38 caltinay 2183 {
39     }
40    
41     //
42     //
43     //
44 caltinay 2810 NodeData::NodeData(NodeData_ptr fullNodes, IntVec& requiredNodes,
45     const string& meshName) :
46     name(meshName)
47 caltinay 2183 {
48 caltinay 2810 numDims = fullNodes->numDims;
49     nodeDist = fullNodes->nodeDist;
50    
51     // first: find the unique set of required nodes and their IDs while
52     // updating the contents of requiredNodes at the same time
53     // requiredNodes contains node indices (not IDs!)
54     IntVec::iterator it;
55     IndexMap indexMap; // maps old index to new index
56     size_t newIndex = 0;
57    
58     for (it = requiredNodes.begin(); it != requiredNodes.end(); it++) {
59     IndexMap::iterator res = indexMap.find(*it);
60     if (res == indexMap.end()) {
61     nodeID.push_back(fullNodes->nodeID[*it]);
62     nodeTag.push_back(fullNodes->nodeTag[*it]);
63     nodeGDOF.push_back(fullNodes->nodeGDOF[*it]);
64     nodeGNI.push_back(fullNodes->nodeGNI[*it]);
65     nodeGRDFI.push_back(fullNodes->nodeGRDFI[*it]);
66     nodeGRNI.push_back(fullNodes->nodeGRNI[*it]);
67     indexMap[*it] = newIndex;
68     *it = newIndex++;
69     } else {
70     *it = res->second;
71     }
72     }
73    
74     // second: now that we know how many nodes we need use the map to fill
75     // the coordinates
76     numNodes = newIndex;
77     for (int dim=0; dim<numDims; dim++) {
78     const float* origC = fullNodes->coords[dim];
79     float* c = new float[numNodes];
80     coords.push_back(c);
81     IndexMap::const_iterator mIt;
82 caltinay 2834 for (mIt = indexMap.begin(); mIt != indexMap.end(); mIt++) {
83 caltinay 2810 c[mIt->second] = origC[mIt->first];
84 caltinay 2834 }
85 caltinay 2810 }
86     }
87    
88     //
89     // Copy constructor
90     //
91     NodeData::NodeData(const NodeData& m)
92     {
93 caltinay 2183 numDims = m.numDims;
94     numNodes = m.numNodes;
95     nodeID = m.nodeID;
96 caltinay 2810 nodeTag = m.nodeTag;
97     nodeGDOF = m.nodeGDOF;
98     nodeGNI = m.nodeGNI;
99     nodeGRDFI = m.nodeGRDFI;
100     nodeGRNI = m.nodeGRNI;
101     nodeDist = m.nodeDist;
102 caltinay 2183 name = m.name;
103     for (int i=0; i<numDims; i++) {
104     float* c = new float[numNodes];
105     copy(m.coords[i], m.coords[i]+numNodes, c);
106     coords.push_back(c);
107     }
108     }
109    
110     //
111     //
112     //
113 caltinay 2810 NodeData::~NodeData()
114 caltinay 2183 {
115     CoordArray::iterator it;
116     for (it = coords.begin(); it != coords.end(); it++)
117     delete[] *it;
118     }
119    
120     //
121     //
122     //
123 caltinay 2810 bool NodeData::initFromFinley(const Finley_NodeFile* finleyFile)
124 caltinay 2183 {
125 caltinay 2810 numDims = finleyFile->numDim;
126     numNodes = finleyFile->numNodes;
127    
128 caltinay 2853 int mpisize = finleyFile->MPIInfo->size;
129     iPtr = finleyFile->nodesDistribution->first_component;
130     nodeDist.clear();
131     nodeDist.insert(nodeDist.end(), mpisize+1, 0);
132     copy(iPtr, iPtr+mpisize+1, nodeDist.begin());
133    
134 caltinay 2810 CoordArray::iterator it;
135     for (it = coords.begin(); it != coords.end(); it++)
136     delete[] *it;
137     coords.clear();
138 caltinay 2853 nodeID.clear();
139     nodeTag.clear();
140     nodeGDOF.clear();
141     nodeGNI.clear();
142     nodeGRDFI.clear();
143     nodeGRNI.clear();
144 caltinay 2810
145     if (numNodes > 0) {
146     for (int i=0; i<numDims; i++) {
147     double* srcPtr = finleyFile->Coordinates + i;
148     float* c = new float[numNodes];
149     coords.push_back(c);
150     for (int j=0; j<numNodes; j++, srcPtr+=numDims) {
151     *c++ = (float) *srcPtr;
152     }
153     }
154    
155     int* iPtr;
156    
157     iPtr = finleyFile->Id;
158     nodeID.insert(nodeID.end(), numNodes, 0);
159     copy(iPtr, iPtr+numNodes, nodeID.begin());
160    
161     iPtr = finleyFile->Tag;
162     nodeTag.insert(nodeTag.end(), numNodes, 0);
163     copy(iPtr, iPtr+numNodes, nodeTag.begin());
164    
165     iPtr = finleyFile->globalDegreesOfFreedom;
166     nodeGDOF.insert(nodeGDOF.end(), numNodes, 0);
167     copy(iPtr, iPtr+numNodes, nodeGDOF.begin());
168    
169     iPtr = finleyFile->globalNodesIndex;
170     nodeGNI.insert(nodeGNI.end(), numNodes, 0);
171     copy(iPtr, iPtr+numNodes, nodeGNI.begin());
172    
173     iPtr = finleyFile->globalReducedDOFIndex;
174     nodeGRDFI.insert(nodeGRDFI.end(), numNodes, 0);
175     copy(iPtr, iPtr+numNodes, nodeGRDFI.begin());
176    
177     iPtr = finleyFile->globalReducedNodesIndex;
178     nodeGRNI.insert(nodeGRNI.end(), numNodes, 0);
179     copy(iPtr, iPtr+numNodes, nodeGRNI.begin());
180    
181     }
182     return true;
183     }
184    
185     //
186     //
187     //
188     bool NodeData::readFromNc(NcFile* ncFile)
189     {
190     #if USE_NETCDF
191 caltinay 2183 NcAtt* att;
192     NcVar* var;
193    
194 caltinay 2810 att = ncFile->get_att("numDim");
195 caltinay 2183 numDims = att->as_int(0);
196    
197 caltinay 2810 att = ncFile->get_att("numNodes");
198 caltinay 2183 numNodes = att->as_int(0);
199    
200 caltinay 2810 att = ncFile->get_att("mpi_size");
201     int mpisize = att->as_int(0);
202    
203 caltinay 2853 nodeDist.clear();
204     nodeDist.insert(nodeDist.end(), mpisize+1, 0);
205     var = ncFile->get_var("Nodes_NodeDistribution");
206     var->get(&nodeDist[0], mpisize+1);
207    
208 caltinay 2810 CoordArray::iterator it;
209     for (it = coords.begin(); it != coords.end(); it++)
210     delete[] *it;
211 caltinay 2183 coords.clear();
212     nodeID.clear();
213 caltinay 2810 nodeTag.clear();
214     nodeGDOF.clear();
215     nodeGNI.clear();
216     nodeGRDFI.clear();
217     nodeGRNI.clear();
218    
219 caltinay 2853 // Only attempt to read further if there are any nodes.
220     // Having no nodes is not an error.
221     if (numNodes > 0) {
222     var = ncFile->get_var("Nodes_Coordinates");
223     for (int i=0; i<numDims; i++) {
224     float* c = new float[numNodes];
225     var->set_cur(0, i);
226     var->get(c, numNodes, 1);
227     coords.push_back(c);
228     }
229 caltinay 2810
230 caltinay 2853 nodeID.insert(nodeID.end(), numNodes, 0);
231     var = ncFile->get_var("Nodes_Id");
232     var->get(&nodeID[0], numNodes);
233    
234     nodeTag.insert(nodeTag.end(), numNodes, 0);
235     var = ncFile->get_var("Nodes_Tag");
236     var->get(&nodeTag[0], numNodes);
237    
238     nodeGDOF.insert(nodeGDOF.end(), numNodes, 0);
239     var = ncFile->get_var("Nodes_gDOF");
240     var->get(&nodeGDOF[0], numNodes);
241    
242     nodeGNI.insert(nodeGNI.end(), numNodes, 0);
243     var = ncFile->get_var("Nodes_gNI");
244     var->get(&nodeGNI[0], numNodes);
245    
246     nodeGRDFI.insert(nodeGRDFI.end(), numNodes, 0);
247     var = ncFile->get_var("Nodes_grDfI");
248     var->get(&nodeGRDFI[0], numNodes);
249    
250     nodeGRNI.insert(nodeGRNI.end(), numNodes, 0);
251     var = ncFile->get_var("Nodes_grNI");
252     var->get(&nodeGRNI[0], numNodes);
253     }
254    
255 caltinay 2183 return true;
256 caltinay 2810 #else // !USE_NETCDF
257     return false;
258     #endif
259 caltinay 2183 }
260    
261     //
262     //
263     //
264 caltinay 2834 const IntVec& NodeData::getVarDataByName(const string& name) const
265 caltinay 2183 {
266 caltinay 2810 if (name == "Nodes_Id")
267     return nodeID;
268     else if (name == "Nodes_Tag")
269     return nodeTag;
270     else if (name == "Nodes_gDOF")
271     return nodeGDOF;
272     else if (name == "Nodes_gNI")
273     return nodeGNI;
274     else if (name == "Nodes_grDfI")
275     return nodeGRDFI;
276     else if (name == "Nodes_grNI")
277     return nodeGRNI;
278     else
279     throw "Invalid variable name";
280     }
281    
282     //
283     //
284     //
285     StringVec NodeData::getVarNames() const
286     {
287     StringVec res;
288     if (numNodes > 0) {
289     res.push_back("Nodes_Id");
290     res.push_back("Nodes_Tag");
291     res.push_back("Nodes_gDOF");
292     res.push_back("Nodes_gNI");
293     res.push_back("Nodes_grDfI");
294     res.push_back("Nodes_grNI");
295     }
296     return res;
297     }
298    
299     //
300     //
301     //
302     bool NodeData::writeToSilo(DBfile* dbfile)
303     {
304     #if USE_SILO
305     if (numNodes == 0)
306     return true;
307    
308 caltinay 2183 int ret;
309    
310 caltinay 2810 if (siloPath != "") {
311 caltinay 2183 ret = DBSetDir(dbfile, siloPath.c_str());
312     if (ret != 0)
313     return false;
314     }
315 caltinay 2810 string siloMeshName = getFullSiloName();
316    
317     // Write node-centered variables
318     ret = DBPutUcdvar1(dbfile, "Nodes_Id", siloMeshName.c_str(),
319 caltinay 2183 (float*)&nodeID[0], numNodes, NULL, 0, DB_INT, DB_NODECENT, NULL);
320    
321 caltinay 2810 if (ret == 0)
322     ret = DBPutUcdvar1(dbfile, "Nodes_Tag", siloMeshName.c_str(),
323     (float*)&nodeTag[0], numNodes, NULL, 0, DB_INT,
324     DB_NODECENT, NULL);
325     if (ret == 0)
326     ret = DBPutUcdvar1(dbfile, "Nodes_gDOF", siloMeshName.c_str(),
327     (float*)&nodeGDOF[0], numNodes, NULL, 0, DB_INT,
328     DB_NODECENT, NULL);
329     if (ret == 0)
330     ret = DBPutUcdvar1(dbfile, "Nodes_gNI", siloMeshName.c_str(),
331     (float*)&nodeGNI[0], numNodes, NULL, 0, DB_INT,
332     DB_NODECENT, NULL);
333     if (ret == 0)
334     ret = DBPutUcdvar1(dbfile, "Nodes_grDfI", siloMeshName.c_str(),
335     (float*)&nodeGRDFI[0], numNodes, NULL, 0, DB_INT,
336     DB_NODECENT, NULL);
337     if (ret == 0)
338     ret = DBPutUcdvar1(dbfile, "Nodes_grNI", siloMeshName.c_str(),
339     (float*)&nodeGRNI[0], numNodes, NULL, 0, DB_INT,
340     DB_NODECENT, NULL);
341    
342 caltinay 2183 DBSetDir(dbfile, "/");
343     return (ret == 0);
344    
345 caltinay 2810 #else // !USE_SILO
346 caltinay 2183 return false;
347     #endif
348     }
349    
350 caltinay 2810 } // namespace escriptexport
351 caltinay 2187

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