/[escript]/branches/ripleygmg_from_3668/ripley/src/Rectangle.cpp
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Revision 3701 - (hide annotations)
Fri Dec 2 02:04:58 2011 UTC (8 years ago) by caltinay
File size: 28971 byte(s)
Prepared interpolation methods.

1 caltinay 3691
2     /*******************************************************
3     *
4     * Copyright (c) 2003-2011 by University of Queensland
5     * 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     #include <ripley/Rectangle.h>
15     extern "C" {
16     #include "paso/SystemMatrixPattern.h"
17     }
18    
19     #if USE_SILO
20     #include <silo.h>
21     #ifdef ESYS_MPI
22     #include <pmpio.h>
23     #endif
24     #endif
25    
26     #include <iomanip>
27    
28     using namespace std;
29    
30     namespace ripley {
31    
32     Rectangle::Rectangle(int n0, int n1, double l0, double l1, int d0, int d1) :
33     RipleyDomain(2),
34     m_gNE0(n0),
35     m_gNE1(n1),
36     m_l0(l0),
37     m_l1(l1),
38     m_NX(d0),
39     m_NY(d1)
40     {
41     // ensure number of subdivisions is valid and nodes can be distributed
42     // among number of ranks
43     if (m_NX*m_NY != m_mpiInfo->size)
44     throw RipleyException("Invalid number of spatial subdivisions");
45    
46     if (n0%m_NX > 0 || n1%m_NY > 0)
47     throw RipleyException("Number of elements must be separable into number of ranks in each dimension");
48    
49     // local number of elements
50     m_NE0 = n0/m_NX;
51     m_NE1 = n1/m_NY;
52     // local number of nodes (not necessarily owned)
53     m_N0 = m_NE0+1;
54     m_N1 = m_NE1+1;
55     // bottom-left node is at (offset0,offset1) in global mesh
56     m_offset0 = m_NE0*(m_mpiInfo->rank%m_NX);
57     m_offset1 = m_NE1*(m_mpiInfo->rank/m_NX);
58     populateSampleIds();
59     }
60    
61     Rectangle::~Rectangle()
62     {
63     }
64    
65     string Rectangle::getDescription() const
66     {
67     return "ripley::Rectangle";
68     }
69    
70     bool Rectangle::operator==(const AbstractDomain& other) const
71     {
72     if (dynamic_cast<const Rectangle*>(&other))
73     return this==&other;
74    
75     return false;
76     }
77    
78     void Rectangle::dump(const string& fileName) const
79     {
80     #if USE_SILO
81     string fn(fileName);
82     if (fileName.length() < 6 || fileName.compare(fileName.length()-5, 5, ".silo") != 0) {
83     fn+=".silo";
84     }
85    
86     const int NUM_SILO_FILES = 1;
87     const char* blockDirFmt = "/block%04d";
88     int driver=DB_HDF5;
89     string siloPath;
90     DBfile* dbfile = NULL;
91    
92     #ifdef ESYS_MPI
93     PMPIO_baton_t* baton = NULL;
94     #endif
95    
96     if (m_mpiInfo->size > 1) {
97     #ifdef ESYS_MPI
98     baton = PMPIO_Init(NUM_SILO_FILES, PMPIO_WRITE, m_mpiInfo->comm,
99     0x1337, PMPIO_DefaultCreate, PMPIO_DefaultOpen,
100     PMPIO_DefaultClose, (void*)&driver);
101     // try the fallback driver in case of error
102     if (!baton && driver != DB_PDB) {
103     driver = DB_PDB;
104     baton = PMPIO_Init(NUM_SILO_FILES, PMPIO_WRITE, m_mpiInfo->comm,
105     0x1338, PMPIO_DefaultCreate, PMPIO_DefaultOpen,
106     PMPIO_DefaultClose, (void*)&driver);
107     }
108     if (baton) {
109     char str[64];
110     snprintf(str, 64, blockDirFmt, PMPIO_RankInGroup(baton, m_mpiInfo->rank));
111     siloPath = str;
112     dbfile = (DBfile*) PMPIO_WaitForBaton(baton, fn.c_str(), siloPath.c_str());
113     }
114     #endif
115     } else {
116     dbfile = DBCreate(fn.c_str(), DB_CLOBBER, DB_LOCAL,
117     getDescription().c_str(), driver);
118     // try the fallback driver in case of error
119     if (!dbfile && driver != DB_PDB) {
120     driver = DB_PDB;
121     dbfile = DBCreate(fn.c_str(), DB_CLOBBER, DB_LOCAL,
122     getDescription().c_str(), driver);
123     }
124     }
125    
126     if (!dbfile)
127     throw RipleyException("dump: Could not create Silo file");
128    
129     /*
130     if (driver==DB_HDF5) {
131     // gzip level 1 already provides good compression with minimal
132     // performance penalty. Some tests showed that gzip levels >3 performed
133     // rather badly on escript data both in terms of time and space
134     DBSetCompression("ERRMODE=FALLBACK METHOD=GZIP LEVEL=1");
135     }
136     */
137    
138     boost::scoped_ptr<double> x(new double[m_N0]);
139     boost::scoped_ptr<double> y(new double[m_N1]);
140     double* coords[2] = { x.get(), y.get() };
141 caltinay 3697 pair<double,double> xdx = getFirstCoordAndSpacing(0);
142     pair<double,double> ydy = getFirstCoordAndSpacing(1);
143 caltinay 3691 #pragma omp parallel
144     {
145     #pragma omp for
146     for (dim_t i0 = 0; i0 < m_N0; i0++) {
147 caltinay 3697 coords[0][i0]=xdx.first+i0*xdx.second;
148 caltinay 3691 }
149     #pragma omp for
150     for (dim_t i1 = 0; i1 < m_N1; i1++) {
151 caltinay 3697 coords[1][i1]=ydy.first+i1*ydy.second;
152 caltinay 3691 }
153     }
154 caltinay 3697 IndexVector dims = getNumNodesPerDim();
155    
156     // write mesh
157     DBPutQuadmesh(dbfile, "mesh", NULL, coords, &dims[0], 2, DB_DOUBLE,
158 caltinay 3691 DB_COLLINEAR, NULL);
159    
160 caltinay 3697 // write node ids
161     DBPutQuadvar1(dbfile, "nodeId", "mesh", (void*)&m_nodeId[0], &dims[0], 2,
162     NULL, 0, DB_INT, DB_NODECENT, NULL);
163    
164     // write element ids
165     dims = getNumElementsPerDim();
166     DBPutQuadvar1(dbfile, "elementId", "mesh", (void*)&m_elementId[0],
167     &dims[0], 2, NULL, 0, DB_INT, DB_ZONECENT, NULL);
168    
169     // rank 0 writes multimesh and multivar
170 caltinay 3691 if (m_mpiInfo->rank == 0) {
171     vector<string> tempstrings;
172 caltinay 3697 vector<char*> names;
173 caltinay 3691 for (dim_t i=0; i<m_mpiInfo->size; i++) {
174     stringstream path;
175     path << "/block" << setw(4) << setfill('0') << right << i << "/mesh";
176     tempstrings.push_back(path.str());
177 caltinay 3697 names.push_back((char*)tempstrings.back().c_str());
178 caltinay 3691 }
179 caltinay 3697 vector<int> types(m_mpiInfo->size, DB_QUAD_RECT);
180 caltinay 3691 DBSetDir(dbfile, "/");
181 caltinay 3697 DBPutMultimesh(dbfile, "multimesh", m_mpiInfo->size, &names[0],
182     &types[0], NULL);
183     tempstrings.clear();
184     names.clear();
185     for (dim_t i=0; i<m_mpiInfo->size; i++) {
186     stringstream path;
187     path << "/block" << setw(4) << setfill('0') << right << i << "/nodeId";
188     tempstrings.push_back(path.str());
189     names.push_back((char*)tempstrings.back().c_str());
190     }
191     types.assign(m_mpiInfo->size, DB_QUADVAR);
192     DBPutMultivar(dbfile, "nodeId", m_mpiInfo->size, &names[0],
193     &types[0], NULL);
194     tempstrings.clear();
195     names.clear();
196     for (dim_t i=0; i<m_mpiInfo->size; i++) {
197     stringstream path;
198     path << "/block" << setw(4) << setfill('0') << right << i << "/elementId";
199     tempstrings.push_back(path.str());
200     names.push_back((char*)tempstrings.back().c_str());
201     }
202     DBPutMultivar(dbfile, "elementId", m_mpiInfo->size, &names[0],
203     &types[0], NULL);
204 caltinay 3691 }
205    
206     if (m_mpiInfo->size > 1) {
207     #ifdef ESYS_MPI
208     PMPIO_HandOffBaton(baton, dbfile);
209     PMPIO_Finish(baton);
210     #endif
211     } else {
212     DBClose(dbfile);
213     }
214    
215     #else // USE_SILO
216     throw RipleyException("dump(): no Silo support");
217     #endif
218     }
219    
220 caltinay 3697 const int* Rectangle::borrowSampleReferenceIDs(int fsType) const
221 caltinay 3691 {
222 caltinay 3697 switch (fsType) {
223 caltinay 3691 case Nodes:
224     return &m_nodeId[0];
225     case Elements:
226     return &m_elementId[0];
227     case FaceElements:
228     return &m_faceId[0];
229     default:
230     break;
231     }
232    
233     stringstream msg;
234     msg << "borrowSampleReferenceIDs() not implemented for function space type "
235 caltinay 3701 << functionSpaceTypeAsString(fsType);
236 caltinay 3691 throw RipleyException(msg.str());
237     }
238    
239     bool Rectangle::ownSample(int fsCode, index_t id) const
240     {
241     #ifdef ESYS_MPI
242     if (fsCode == Nodes) {
243 caltinay 3699 const index_t myFirst=m_nodeDistribution[m_mpiInfo->rank];
244     const index_t myLast=m_nodeDistribution[m_mpiInfo->rank+1]-1;
245 caltinay 3691 return (m_nodeId[id]>=myFirst && m_nodeId[id]<=myLast);
246     } else
247     throw RipleyException("ownSample() only implemented for Nodes");
248     #else
249     return true;
250     #endif
251     }
252    
253 caltinay 3701 void Rectangle::interpolateNodesOnElements(escript::Data& out, escript::Data& in) const
254 caltinay 3691 {
255 caltinay 3701 const dim_t numComp = in.getDataPointSize();
256     /* GENERATOR SNIP_INTERPOLATE_ELEMENTS TOP */
257     const double tmp0_2 = 0.62200846792814621559;
258     const double tmp0_1 = 0.044658198738520451079;
259     const double tmp0_0 = 0.16666666666666666667;
260 caltinay 3697 #pragma omp parallel for
261 caltinay 3701 for (index_t k1=0; k1 < m_NE1; ++k1) {
262     for (index_t k0=0; k0 < m_NE0; ++k0) {
263     const register double* f_10 = in.getSampleDataRO(INDEX2(k0+1,k1, m_N0));
264     const register double* f_11 = in.getSampleDataRO(INDEX2(k0+1,k1+1, m_N0));
265     const register double* f_01 = in.getSampleDataRO(INDEX2(k0,k1+1, m_N0));
266     const register double* f_00 = in.getSampleDataRO(INDEX2(k0,k1, m_N0));
267     double* o = out.getSampleDataRW(INDEX2(k0,k1,m_NE0));
268     for (index_t i=0; i < numComp; ++i) {
269     o[INDEX2(i,numComp,0)] = f_00[i]*tmp0_2 + f_11[i]*tmp0_1 + tmp0_0*(f_01[i] + f_10[i]);
270     o[INDEX2(i,numComp,1)] = f_01[i]*tmp0_1 + f_10[i]*tmp0_2 + tmp0_0*(f_00[i] + f_11[i]);
271     o[INDEX2(i,numComp,2)] = f_01[i]*tmp0_2 + f_10[i]*tmp0_1 + tmp0_0*(f_00[i] + f_11[i]);
272     o[INDEX2(i,numComp,3)] = f_00[i]*tmp0_1 + f_11[i]*tmp0_2 + tmp0_0*(f_01[i] + f_10[i]);
273     } /* end of component loop i */
274     } /* end of k0 loop */
275     } /* end of k1 loop */
276     /* GENERATOR SNIP_INTERPOLATE_ELEMENTS BOTTOM */
277     }
278 caltinay 3697
279 caltinay 3701 void Rectangle::interpolateNodesOnFaces(escript::Data& out, escript::Data& in) const
280     {
281     throw RipleyException("interpolateNodesOnFaces() not implemented");
282 caltinay 3691 }
283    
284 caltinay 3701 void Rectangle::addPDEToSystem(escript::AbstractSystemMatrix& mat,
285     escript::Data& rhs, const escript::Data& A, const escript::Data& B,
286     const escript::Data& C, const escript::Data& D,
287     const escript::Data& X, const escript::Data& Y,
288     const escript::Data& d, const escript::Data& y,
289     const escript::Data& d_contact, const escript::Data& y_contact,
290     const escript::Data& d_dirac, const escript::Data& y_dirac) const
291     {
292     throw RipleyException("addPDEToSystem() not implemented");
293     }
294    
295 caltinay 3691 Paso_SystemMatrixPattern* Rectangle::getPattern(bool reducedRowOrder,
296     bool reducedColOrder) const
297     {
298     if (reducedRowOrder || reducedColOrder)
299     throw RipleyException("getPattern() not implemented for reduced order");
300    
301 caltinay 3699 // connector
302     RankVector neighbour;
303     IndexVector offsetInShared(1,0);
304     IndexVector sendShared, recvShared;
305     const IndexVector faces=getNumFacesPerBoundary();
306     const index_t left = (m_offset0==0 ? 0 : 1);
307     const index_t bottom = (m_offset1==0 ? 0 : 1);
308     // corner node from bottom-left
309     if (faces[0] == 0 && faces[2] == 0) {
310     neighbour.push_back(m_mpiInfo->rank-m_NX-1);
311     offsetInShared.push_back(offsetInShared.back()+1);
312     sendShared.push_back(m_nodeId[m_N0+left]);
313     recvShared.push_back(m_nodeId[0]);
314     }
315     // bottom edge
316     if (faces[2] == 0) {
317     neighbour.push_back(m_mpiInfo->rank-m_NX);
318     offsetInShared.push_back(offsetInShared.back()+m_N0-left);
319     for (dim_t i=left; i<m_N0; i++) {
320     // easy case, we know the neighbour id's
321     sendShared.push_back(m_nodeId[m_N0+i]);
322     recvShared.push_back(m_nodeId[i]);
323     }
324     }
325     // corner node from bottom-right
326     if (faces[1] == 0 && faces[2] == 0) {
327     neighbour.push_back(m_mpiInfo->rank-m_NX+1);
328     const index_t N0=(neighbour.back()%m_NX == 0 ? m_N0 : m_N0-1);
329     const index_t N1=(neighbour.back()/m_NX == 0 ? m_N1 : m_N1-1);
330     const index_t first=m_nodeDistribution[neighbour.back()];
331     offsetInShared.push_back(offsetInShared.back()+1);
332     sendShared.push_back(m_nodeId[(bottom+1)*m_N0-1]);
333     recvShared.push_back(first+N0*(N1-1));
334     }
335     // left edge
336     if (faces[0] == 0) {
337     neighbour.push_back(m_mpiInfo->rank-1);
338     offsetInShared.push_back(offsetInShared.back()+m_N1-bottom);
339     for (dim_t i=bottom; i<m_N1; i++) {
340     // easy case, we know the neighbour id's
341     sendShared.push_back(m_nodeId[i*m_N0+1]);
342     recvShared.push_back(m_nodeId[i*m_N0]);
343     }
344     }
345     // right edge
346     if (faces[1] == 0) {
347     neighbour.push_back(m_mpiInfo->rank+1);
348     const index_t rightN0=(neighbour.back()%m_NX == 0 ? m_N0 : m_N0-1);
349     const index_t first=m_nodeDistribution[neighbour.back()];
350     offsetInShared.push_back(offsetInShared.back()+m_N1-bottom);
351     for (dim_t i=bottom; i<m_N1; i++) {
352     sendShared.push_back(m_nodeId[(i+1)*m_N0-1]);
353     recvShared.push_back(first+rightN0*(i-bottom));
354     }
355     }
356     // corner node from top-left
357     if (faces[0] == 0 && faces[3] == 0) {
358     neighbour.push_back(m_mpiInfo->rank+m_NX-1);
359     const index_t N0=(neighbour.back()%m_NX == 0 ? m_N0 : m_N0-1);
360     const index_t first=m_nodeDistribution[neighbour.back()];
361     offsetInShared.push_back(offsetInShared.back()+1);
362     sendShared.push_back(m_nodeId[m_N0*(m_N1-1)+left]);
363     recvShared.push_back(first+N0-1);
364     }
365     // top edge
366     if (faces[3] == 0) {
367     neighbour.push_back(m_mpiInfo->rank+m_NX);
368     const index_t first=m_nodeDistribution[neighbour.back()];
369     offsetInShared.push_back(offsetInShared.back()+m_N0-left);
370     for (dim_t i=left; i<m_N0; i++) {
371     sendShared.push_back(m_nodeId[m_N0*(m_N1-1)+i]);
372     recvShared.push_back(first+i-left);
373     }
374     }
375     // corner node from top-right
376     if (faces[1] == 0 && faces[3] == 0) {
377     neighbour.push_back(m_mpiInfo->rank+m_NX+1);
378     const index_t first=m_nodeDistribution[neighbour.back()];
379     offsetInShared.push_back(offsetInShared.back()+1);
380     sendShared.push_back(m_nodeId[m_N0*m_N1-1]);
381     recvShared.push_back(first);
382     }
383     const int numDOF=m_nodeDistribution[m_mpiInfo->rank+1]-m_nodeDistribution[m_mpiInfo->rank];
384     cout << "--- rcv_shcomp ---" << endl;
385     cout << "numDOF=" << numDOF << ", numNeighbors=" << neighbour.size() << endl;
386     for (size_t i=0; i<neighbour.size(); i++) {
387     cout << "neighbor[" << i << "]=" << neighbour[i]
388     << " offsetInShared[" << i+1 << "]=" << offsetInShared[i+1] << endl;
389     }
390     for (size_t i=0; i<recvShared.size(); i++) {
391     cout << "shared[" << i << "]=" << recvShared[i] << endl;
392     }
393     cout << "--- snd_shcomp ---" << endl;
394     for (size_t i=0; i<sendShared.size(); i++) {
395     cout << "shared[" << i << "]=" << sendShared[i] << endl;
396     }
397 caltinay 3691
398     Paso_SharedComponents *snd_shcomp = Paso_SharedComponents_alloc(
399 caltinay 3699 numDOF, neighbour.size(), &neighbour[0], &sendShared[0],
400 caltinay 3697 &offsetInShared[0], 1, 0, m_mpiInfo);
401 caltinay 3691 Paso_SharedComponents *rcv_shcomp = Paso_SharedComponents_alloc(
402 caltinay 3699 numDOF, neighbour.size(), &neighbour[0], &recvShared[0],
403 caltinay 3697 &offsetInShared[0], 1, 0, m_mpiInfo);
404 caltinay 3691 Paso_Connector* connector = Paso_Connector_alloc(snd_shcomp, rcv_shcomp);
405 caltinay 3699 Paso_SharedComponents_free(snd_shcomp);
406     Paso_SharedComponents_free(rcv_shcomp);
407 caltinay 3691
408     // create patterns
409 caltinay 3699 dim_t M, N;
410     IndexVector ptr(1,0);
411     IndexVector index;
412    
413     // main pattern
414     for (index_t i=0; i<numDOF; i++) {
415     // always add the node itself
416     index.push_back(i);
417     int num=insertNeighbours(index, i);
418     ptr.push_back(ptr.back()+num+1);
419     }
420     M=N=ptr.size()-1;
421     // paso will manage the memory
422     index_t* indexC = MEMALLOC(index.size(),index_t);
423     index_t* ptrC = MEMALLOC(ptr.size(), index_t);
424     copy(index.begin(), index.end(), indexC);
425     copy(ptr.begin(), ptr.end(), ptrC);
426 caltinay 3691 Paso_Pattern *mainPattern = Paso_Pattern_alloc(MATRIX_FORMAT_DEFAULT,
427 caltinay 3699 M, N, ptrC, indexC);
428 caltinay 3691
429 caltinay 3699 cout << "--- main_pattern ---" << endl;
430     cout << "M=" << M << ", N=" << N << endl;
431     for (size_t i=0; i<ptr.size(); i++) {
432     cout << "ptr[" << i << "]=" << ptr[i] << endl;
433     }
434     for (size_t i=0; i<index.size(); i++) {
435     cout << "index[" << i << "]=" << index[i] << endl;
436     }
437    
438     ptr.clear();
439     index.clear();
440    
441     // column & row couple patterns
442     Paso_Pattern *colCouplePattern, *rowCouplePattern;
443     generateCouplePatterns(&colCouplePattern, &rowCouplePattern);
444    
445     // allocate paso distribution
446     Paso_Distribution* distribution = Paso_Distribution_alloc(m_mpiInfo,
447     const_cast<index_t*>(&m_nodeDistribution[0]), 1, 0);
448    
449 caltinay 3691 Paso_SystemMatrixPattern* pattern = Paso_SystemMatrixPattern_alloc(
450     MATRIX_FORMAT_DEFAULT, distribution, distribution,
451     mainPattern, colCouplePattern, rowCouplePattern,
452     connector, connector);
453     Paso_Pattern_free(mainPattern);
454     Paso_Pattern_free(colCouplePattern);
455     Paso_Pattern_free(rowCouplePattern);
456     Paso_Distribution_free(distribution);
457 caltinay 3697 return pattern;
458 caltinay 3691 }
459    
460     void Rectangle::Print_Mesh_Info(const bool full) const
461     {
462     RipleyDomain::Print_Mesh_Info(full);
463     if (full) {
464     cout << " Id Coordinates" << endl;
465     cout.precision(15);
466     cout.setf(ios::scientific, ios::floatfield);
467 caltinay 3697 pair<double,double> xdx = getFirstCoordAndSpacing(0);
468     pair<double,double> ydy = getFirstCoordAndSpacing(1);
469 caltinay 3691 for (index_t i=0; i < getNumNodes(); i++) {
470     cout << " " << setw(5) << m_nodeId[i]
471 caltinay 3697 << " " << xdx.first+(i%m_N0)*xdx.second
472     << " " << ydy.first+(i/m_N0)*ydy.second << endl;
473 caltinay 3691 }
474     }
475     }
476    
477 caltinay 3697 IndexVector Rectangle::getNumNodesPerDim() const
478     {
479     IndexVector ret;
480     ret.push_back(m_N0);
481     ret.push_back(m_N1);
482     return ret;
483     }
484    
485     IndexVector Rectangle::getNumElementsPerDim() const
486     {
487     IndexVector ret;
488     ret.push_back(m_NE0);
489     ret.push_back(m_NE1);
490     return ret;
491     }
492    
493     IndexVector Rectangle::getNumFacesPerBoundary() const
494     {
495     IndexVector ret(4, 0);
496     //left
497     if (m_offset0==0)
498     ret[0]=m_NE1;
499     //right
500     if (m_mpiInfo->rank%m_NX==m_NX-1)
501     ret[1]=m_NE1;
502     //bottom
503     if (m_offset1==0)
504     ret[2]=m_NE0;
505     //top
506     if (m_mpiInfo->rank/m_NX==m_NY-1)
507     ret[3]=m_NE0;
508     return ret;
509     }
510    
511     pair<double,double> Rectangle::getFirstCoordAndSpacing(dim_t dim) const
512     {
513     if (dim==0) {
514     return pair<double,double>((m_l0*m_offset0)/m_gNE0, m_l0/m_gNE0);
515     } else if (dim==1) {
516     return pair<double,double>((m_l1*m_offset1)/m_gNE1, m_l1/m_gNE1);
517     }
518     throw RipleyException("getFirstCoordAndSpacing(): invalid argument");
519     }
520    
521 caltinay 3691 //protected
522     dim_t Rectangle::getNumFaceElements() const
523     {
524 caltinay 3699 const IndexVector faces = getNumFacesPerBoundary();
525 caltinay 3691 dim_t n=0;
526 caltinay 3699 for (size_t i=0; i<faces.size(); i++)
527     n+=faces[i];
528 caltinay 3691 return n;
529     }
530    
531     //protected
532     void Rectangle::assembleCoordinates(escript::Data& arg) const
533     {
534     escriptDataC x = arg.getDataC();
535     int numDim = m_numDim;
536     if (!isDataPointShapeEqual(&x, 1, &numDim))
537     throw RipleyException("setToX: Invalid Data object shape");
538     if (!numSamplesEqual(&x, 1, getNumNodes()))
539     throw RipleyException("setToX: Illegal number of samples in Data object");
540    
541 caltinay 3697 pair<double,double> xdx = getFirstCoordAndSpacing(0);
542     pair<double,double> ydy = getFirstCoordAndSpacing(1);
543 caltinay 3691 arg.requireWrite();
544     #pragma omp parallel for
545     for (dim_t i1 = 0; i1 < m_N1; i1++) {
546     for (dim_t i0 = 0; i0 < m_N0; i0++) {
547     double* point = arg.getSampleDataRW(i0+m_N0*i1);
548 caltinay 3697 point[0] = xdx.first+i0*xdx.second;
549     point[1] = ydy.first+i1*ydy.second;
550 caltinay 3691 }
551     }
552     }
553    
554     //private
555     void Rectangle::populateSampleIds()
556     {
557 caltinay 3697 // identifiers are ordered from left to right, bottom to top on each rank,
558     // except for the shared nodes which are owned by the rank below / to the
559     // left of the current rank
560    
561     // build node distribution vector first.
562     // m_nodeDistribution[i] is the first node id on rank i, that is
563     // rank i owns m_nodeDistribution[i+1]-nodeDistribution[i] nodes
564     m_nodeDistribution.assign(m_mpiInfo->size+1, 0);
565     m_nodeDistribution[1]=getNumNodes();
566     for (dim_t k=1; k<m_mpiInfo->size-1; k++) {
567     const index_t x=k%m_NX;
568     const index_t y=k/m_NX;
569     index_t numNodes=getNumNodes();
570     if (x>0)
571     numNodes-=m_N1;
572     if (y>0)
573     numNodes-=m_N0;
574     if (x>0 && y>0)
575     numNodes++; // subtracted corner twice -> fix that
576     m_nodeDistribution[k+1]=m_nodeDistribution[k]+numNodes;
577     }
578     m_nodeDistribution[m_mpiInfo->size]=getNumDataPointsGlobal();
579    
580 caltinay 3691 m_nodeId.resize(getNumNodes());
581 caltinay 3697
582     // the bottom row and left column are not owned by this rank so the
583     // identifiers need to be computed accordingly
584     const index_t left = (m_offset0==0 ? 0 : 1);
585     const index_t bottom = (m_offset1==0 ? 0 : 1);
586     if (left>0) {
587     const int neighbour=m_mpiInfo->rank-1;
588     const index_t leftN0=(neighbour%m_NX == 0 ? m_N0 : m_N0-1);
589 caltinay 3691 #pragma omp parallel for
590 caltinay 3697 for (dim_t i1=bottom; i1<m_N1; i1++) {
591     m_nodeId[i1*m_N0]=m_nodeDistribution[neighbour]
592     + (i1-bottom+1)*leftN0-1;
593     }
594     }
595     if (bottom>0) {
596     const int neighbour=m_mpiInfo->rank-m_NX;
597     const index_t bottomN0=(neighbour%m_NX == 0 ? m_N0 : m_N0-1);
598     const index_t bottomN1=(neighbour/m_NX == 0 ? m_N1 : m_N1-1);
599     #pragma omp parallel for
600     for (dim_t i0=left; i0<m_N0; i0++) {
601     m_nodeId[i0]=m_nodeDistribution[neighbour]
602     + (bottomN1-1)*bottomN0 + i0 - left;
603     }
604     }
605     if (left>0 && bottom>0) {
606     const int neighbour=m_mpiInfo->rank-m_NX-1;
607 caltinay 3699 const index_t N0=(neighbour%m_NX == 0 ? m_N0 : m_N0-1);
608     const index_t N1=(neighbour/m_NX == 0 ? m_N1 : m_N1-1);
609     m_nodeId[0]=m_nodeDistribution[neighbour]+N0*N1-1;
610 caltinay 3697 }
611    
612     // the rest of the id's are contiguous
613     const index_t firstId=m_nodeDistribution[m_mpiInfo->rank];
614     #pragma omp parallel for
615     for (dim_t i1=bottom; i1<m_N1; i1++) {
616     for (dim_t i0=left; i0<m_N0; i0++) {
617     m_nodeId[i0+i1*m_N0] = firstId+i0-left+(i1-bottom)*(m_N0-left);
618     }
619     }
620    
621     // elements
622     m_elementId.resize(getNumElements());
623     #pragma omp parallel for
624     for (dim_t k=0; k<getNumElements(); k++) {
625     m_elementId[k]=k;
626     }
627    
628     // face elements
629     m_faceId.resize(getNumFaceElements());
630     #pragma omp parallel for
631     for (dim_t k=0; k<getNumFaceElements(); k++) {
632     m_faceId[k]=k;
633     }
634 caltinay 3691 }
635    
636 caltinay 3699 //private
637     int Rectangle::insertNeighbours(IndexVector& index, index_t node) const
638     {
639     const dim_t myN0 = (m_offset0==0 ? m_N0 : m_N0-1);
640     const dim_t myN1 = (m_offset1==0 ? m_N1 : m_N1-1);
641     const int x=node%myN0;
642     const int y=node/myN0;
643     int num=0;
644     if (y>0) {
645     if (x>0) {
646     // bottom-left
647     index.push_back(node-myN0-1);
648     num++;
649     }
650     // bottom
651     index.push_back(node-myN0);
652     num++;
653     if (x<myN0-1) {
654     // bottom-right
655     index.push_back(node-myN0+1);
656     num++;
657     }
658     }
659     if (x<myN0-1) {
660     // right
661     index.push_back(node+1);
662     num++;
663     if (y<myN1-1) {
664     // top-right
665     index.push_back(node+myN0+1);
666     num++;
667     }
668     }
669     if (y<myN1-1) {
670     // top
671     index.push_back(node+myN0);
672     num++;
673     if (x>0) {
674     // top-left
675     index.push_back(node+myN0-1);
676     num++;
677     }
678     }
679     if (x>0) {
680     // left
681     index.push_back(node-1);
682     num++;
683     }
684    
685     return num;
686     }
687    
688     //private
689     void Rectangle::generateCouplePatterns(Paso_Pattern** colPattern, Paso_Pattern** rowPattern) const
690     {
691     IndexVector ptr(1,0);
692     IndexVector index;
693     const dim_t myN0 = (m_offset0==0 ? m_N0 : m_N0-1);
694     const dim_t myN1 = (m_offset1==0 ? m_N1 : m_N1-1);
695     const IndexVector faces=getNumFacesPerBoundary();
696    
697     // bottom edge
698     dim_t n=0;
699     if (faces[0] == 0) {
700     index.push_back(2*(myN0+myN1+1));
701     index.push_back(2*(myN0+myN1+1)+1);
702     n+=2;
703     if (faces[2] == 0) {
704     index.push_back(0);
705     index.push_back(1);
706     index.push_back(2);
707     n+=3;
708     }
709     } else if (faces[2] == 0) {
710     index.push_back(1);
711     index.push_back(2);
712     n+=2;
713     }
714     // n=neighbours of bottom-left corner node
715     ptr.push_back(ptr.back()+n);
716     n=0;
717     if (faces[2] == 0) {
718     for (dim_t i=1; i<myN0-1; i++) {
719     index.push_back(i);
720     index.push_back(i+1);
721     index.push_back(i+2);
722     ptr.push_back(ptr.back()+3);
723     }
724     index.push_back(myN0-1);
725     index.push_back(myN0);
726     n+=2;
727     if (faces[1] == 0) {
728     index.push_back(myN0+1);
729     index.push_back(myN0+2);
730     index.push_back(myN0+3);
731     n+=3;
732     }
733     } else {
734     for (dim_t i=1; i<myN0-1; i++) {
735     ptr.push_back(ptr.back());
736     }
737     if (faces[1] == 0) {
738     index.push_back(myN0+2);
739     index.push_back(myN0+3);
740     n+=2;
741     }
742     }
743     // n=neighbours of bottom-right corner node
744     ptr.push_back(ptr.back()+n);
745    
746     // 2nd row to 2nd last row
747     for (dim_t i=1; i<myN1-1; i++) {
748     // left edge
749     if (faces[0] == 0) {
750     index.push_back(2*(myN0+myN1+2)-i);
751     index.push_back(2*(myN0+myN1+2)-i-1);
752     index.push_back(2*(myN0+myN1+2)-i-2);
753     ptr.push_back(ptr.back()+3);
754     } else {
755     ptr.push_back(ptr.back());
756     }
757     for (dim_t j=1; j<myN0-1; j++) {
758     ptr.push_back(ptr.back());
759     }
760     // right edge
761     if (faces[1] == 0) {
762     index.push_back(myN0+i+1);
763     index.push_back(myN0+i+2);
764     index.push_back(myN0+i+3);
765     ptr.push_back(ptr.back()+3);
766     } else {
767     ptr.push_back(ptr.back());
768     }
769     }
770    
771     // top edge
772     n=0;
773     if (faces[0] == 0) {
774     index.push_back(2*myN0+myN1+5);
775     index.push_back(2*myN0+myN1+4);
776     n+=2;
777     if (faces[3] == 0) {
778     index.push_back(2*myN0+myN1+3);
779     index.push_back(2*myN0+myN1+2);
780     index.push_back(2*myN0+myN1+1);
781     n+=3;
782     }
783     } else if (faces[3] == 0) {
784     index.push_back(2*myN0+myN1+2);
785     index.push_back(2*myN0+myN1+1);
786     n+=2;
787     }
788     // n=neighbours of top-left corner node
789     ptr.push_back(ptr.back()+n);
790     n=0;
791     if (faces[3] == 0) {
792     for (dim_t i=1; i<myN0-1; i++) {
793     index.push_back(2*myN0+myN1+i+1);
794     index.push_back(2*myN0+myN1+i);
795     index.push_back(2*myN0+myN1+i-1);
796     ptr.push_back(ptr.back()+3);
797     }
798     index.push_back(myN0+myN1+4);
799     index.push_back(myN0+myN1+3);
800     n+=2;
801     if (faces[1] == 0) {
802     index.push_back(myN0+myN1+2);
803     index.push_back(myN0+myN1+1);
804     index.push_back(myN0+myN1);
805     n+=3;
806     }
807     } else {
808     for (dim_t i=1; i<myN0-1; i++) {
809     ptr.push_back(ptr.back());
810     }
811     if (faces[1] == 0) {
812     index.push_back(myN0+myN1+1);
813     index.push_back(myN0+myN1);
814     n+=2;
815     }
816     }
817     // n=neighbours of top-right corner node
818     ptr.push_back(ptr.back()+n);
819    
820     dim_t M=ptr.size()-1;
821     map<index_t,index_t> idMap;
822     dim_t N=0;
823     for (IndexVector::iterator it=index.begin(); it!=index.end(); it++) {
824     if (idMap.find(*it)==idMap.end()) {
825     idMap[*it]=N;
826     *it=N++;
827     } else {
828     *it=idMap[*it];
829     }
830     }
831    
832     cout << "--- colCouple_pattern ---" << endl;
833     cout << "M=" << M << ", N=" << N << endl;
834     for (size_t i=0; i<ptr.size(); i++) {
835     cout << "ptr[" << i << "]=" << ptr[i] << endl;
836     }
837     for (size_t i=0; i<index.size(); i++) {
838     cout << "index[" << i << "]=" << index[i] << endl;
839     }
840    
841     // now build the row couple pattern
842     IndexVector ptr2(1,0);
843     IndexVector index2;
844     for (dim_t id=0; id<N; id++) {
845     n=0;
846     for (dim_t i=0; i<M; i++) {
847     for (dim_t j=ptr[i]; j<ptr[i+1]; j++) {
848     if (index[j]==id) {
849     index2.push_back(i);
850     n++;
851     break;
852     }
853     }
854     }
855     ptr2.push_back(ptr2.back()+n);
856     }
857    
858     cout << "--- rowCouple_pattern ---" << endl;
859     cout << "M=" << N << ", N=" << M << endl;
860     for (size_t i=0; i<ptr2.size(); i++) {
861     cout << "ptr[" << i << "]=" << ptr2[i] << endl;
862     }
863     for (size_t i=0; i<index2.size(); i++) {
864     cout << "index[" << i << "]=" << index2[i] << endl;
865     }
866    
867     // paso will manage the memory
868     index_t* indexC = MEMALLOC(index.size(), index_t);
869     index_t* ptrC = MEMALLOC(ptr.size(), index_t);
870     copy(index.begin(), index.end(), indexC);
871     copy(ptr.begin(), ptr.end(), ptrC);
872     *colPattern=Paso_Pattern_alloc(MATRIX_FORMAT_DEFAULT, M, N, ptrC, indexC);
873    
874     // paso will manage the memory
875     indexC = MEMALLOC(index2.size(), index_t);
876     ptrC = MEMALLOC(ptr2.size(), index_t);
877     copy(index2.begin(), index2.end(), indexC);
878     copy(ptr2.begin(), ptr2.end(), ptrC);
879     *rowPattern=Paso_Pattern_alloc(MATRIX_FORMAT_DEFAULT, N, M, ptrC, indexC);
880     }
881    
882 caltinay 3691 } // end of namespace ripley
883    

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