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Annotation of /branches/diaplayground/ripley/src/Brick.cpp

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Revision 4836 - (hide annotations)
Mon Apr 7 05:51:55 2014 UTC (4 years, 11 months ago) by caltinay
Original Path: trunk/ripley/src/Brick.cpp
File size: 165655 byte(s)
"Some" SystemMatrix clean up.....

1 caltinay 3691
2 jfenwick 3981 /*****************************************************************************
3 caltinay 3691 *
4 jfenwick 4657 * Copyright (c) 2003-2014 by University of Queensland
5 jfenwick 3981 * http://www.uq.edu.au
6 caltinay 3691 *
7     * Primary Business: Queensland, Australia
8     * Licensed under the Open Software License version 3.0
9     * http://www.opensource.org/licenses/osl-3.0.php
10     *
11 jfenwick 3981 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 jfenwick 4657 * Development 2012-2013 by School of Earth Sciences
13     * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14 jfenwick 3981 *
15     *****************************************************************************/
16 caltinay 3691
17     #include <ripley/Brick.h>
18 caltinay 3791 #include <paso/SystemMatrix.h>
19 caltinay 4334 #include <esysUtils/esysFileWriter.h>
20 sshaw 4622 #include <ripley/DefaultAssembler3D.h>
21 sshaw 4629 #include <ripley/WaveAssembler3D.h>
22 sshaw 4712 #include <ripley/LameAssembler3D.h>
23     #include <ripley/domainhelpers.h>
24 caltinay 4477 #include <boost/scoped_array.hpp>
25    
26 caltinay 4013 #ifdef USE_NETCDF
27     #include <netcdfcpp.h>
28     #endif
29    
30 caltinay 3691 #if USE_SILO
31     #include <silo.h>
32     #ifdef ESYS_MPI
33     #include <pmpio.h>
34     #endif
35     #endif
36    
37     #include <iomanip>
38    
39 jfenwick 4650 #include "esysUtils/EsysRandom.h"
40     #include "blocktools.h"
41    
42    
43 caltinay 3691 using namespace std;
44 caltinay 4334 using esysUtils::FileWriter;
45 caltinay 3691
46     namespace ripley {
47    
48 sshaw 4712 int indexOfMax(int a, int b, int c) {
49     if (a > b) {
50     if (c > a) {
51     return 2;
52     }
53     return 0;
54     } else if (b > c) {
55     return 1;
56     }
57     return 2;
58     }
59    
60 caltinay 3781 Brick::Brick(int n0, int n1, int n2, double x0, double y0, double z0,
61 sshaw 4622 double x1, double y1, double z1, int d0, int d1, int d2,
62     const std::vector<double>& points, const std::vector<int>& tags,
63 jfenwick 4638 const simap_t& tagnamestonums) :
64 caltinay 4334 RipleyDomain(3)
65 caltinay 3691 {
66 caltinay 3943 // ignore subdivision parameters for serial run
67     if (m_mpiInfo->size == 1) {
68     d0=1;
69     d1=1;
70     d2=1;
71     }
72     bool warn=false;
73 sshaw 4712
74     std::vector<int> factors;
75     int ranks = m_mpiInfo->size;
76     int epr[3] = {n0,n1,n2};
77     int d[3] = {d0,d1,d2};
78     if (d0<=0 || d1<=0 || d2<=0) {
79     for (int i = 0; i < 3; i++) {
80     if (d[i] < 1) {
81     d[i] = 1;
82     continue;
83 caltinay 3943 }
84 sshaw 4712 epr[i] = -1; // can no longer be max
85     if (ranks % d[i] != 0) {
86     throw RipleyException("Invalid number of spatial subdivisions");
87 caltinay 3943 }
88 sshaw 4712 //remove
89     ranks /= d[i];
90 caltinay 3943 }
91 sshaw 4712 factorise(factors, ranks);
92     if (factors.size() != 0) {
93     warn = true;
94 caltinay 3943 }
95 sshaw 4712 }
96     while (factors.size() > 0) {
97     int i = indexOfMax(epr[0],epr[1],epr[2]);
98     int f = factors.back();
99     factors.pop_back();
100     d[i] *= f;
101     epr[i] /= f;
102 caltinay 3943 }
103 sshaw 4712 d0 = d[0]; d1 = d[1]; d2 = d[2];
104 caltinay 3943
105 caltinay 3691 // ensure number of subdivisions is valid and nodes can be distributed
106     // among number of ranks
107 sshaw 4712 if (d0*d1*d2 != m_mpiInfo->size){
108 caltinay 3691 throw RipleyException("Invalid number of spatial subdivisions");
109 sshaw 4712 }
110 caltinay 3943 if (warn) {
111     cout << "Warning: Automatic domain subdivision (d0=" << d0 << ", d1="
112     << d1 << ", d2=" << d2 << "). This may not be optimal!" << endl;
113     }
114 caltinay 3691
115 caltinay 4334 double l0 = x1-x0;
116     double l1 = y1-y0;
117     double l2 = z1-z0;
118     m_dx[0] = l0/n0;
119     m_dx[1] = l1/n1;
120     m_dx[2] = l2/n2;
121    
122     if ((n0+1)%d0 > 0) {
123 caltinay 3943 n0=(int)round((float)(n0+1)/d0+0.5)*d0-1;
124 caltinay 4334 l0=m_dx[0]*n0;
125 caltinay 3943 cout << "Warning: Adjusted number of elements and length. N0="
126 caltinay 4334 << n0 << ", l0=" << l0 << endl;
127 caltinay 3943 }
128 caltinay 4334 if ((n1+1)%d1 > 0) {
129 caltinay 3943 n1=(int)round((float)(n1+1)/d1+0.5)*d1-1;
130 caltinay 4334 l1=m_dx[1]*n1;
131 caltinay 3943 cout << "Warning: Adjusted number of elements and length. N1="
132 caltinay 4334 << n1 << ", l1=" << l1 << endl;
133 caltinay 3943 }
134 caltinay 4334 if ((n2+1)%d2 > 0) {
135 caltinay 3943 n2=(int)round((float)(n2+1)/d2+0.5)*d2-1;
136 caltinay 4334 l2=m_dx[2]*n2;
137 caltinay 3943 cout << "Warning: Adjusted number of elements and length. N2="
138 caltinay 4334 << n2 << ", l2=" << l2 << endl;
139 caltinay 3943 }
140    
141 caltinay 4334 if ((d0 > 1 && (n0+1)/d0<2) || (d1 > 1 && (n1+1)/d1<2) || (d2 > 1 && (n2+1)/d2<2))
142 caltinay 3753 throw RipleyException("Too few elements for the number of ranks");
143    
144 caltinay 4334 m_gNE[0] = n0;
145     m_gNE[1] = n1;
146     m_gNE[2] = n2;
147     m_origin[0] = x0;
148     m_origin[1] = y0;
149     m_origin[2] = z0;
150     m_length[0] = l0;
151     m_length[1] = l1;
152     m_length[2] = l2;
153     m_NX[0] = d0;
154     m_NX[1] = d1;
155     m_NX[2] = d2;
156    
157 caltinay 3753 // local number of elements (including overlap)
158 caltinay 4334 m_NE[0] = m_ownNE[0] = (d0>1 ? (n0+1)/d0 : n0);
159     if (m_mpiInfo->rank%d0>0 && m_mpiInfo->rank%d0<d0-1)
160     m_NE[0]++;
161     else if (d0>1 && m_mpiInfo->rank%d0==d0-1)
162     m_ownNE[0]--;
163 caltinay 3764
164 caltinay 4334 m_NE[1] = m_ownNE[1] = (d1>1 ? (n1+1)/d1 : n1);
165     if (m_mpiInfo->rank%(d0*d1)/d0>0 && m_mpiInfo->rank%(d0*d1)/d0<d1-1)
166     m_NE[1]++;
167     else if (d1>1 && m_mpiInfo->rank%(d0*d1)/d0==d1-1)
168     m_ownNE[1]--;
169 caltinay 3764
170 caltinay 4334 m_NE[2] = m_ownNE[2] = (d2>1 ? (n2+1)/d2 : n2);
171     if (m_mpiInfo->rank/(d0*d1)>0 && m_mpiInfo->rank/(d0*d1)<d2-1)
172     m_NE[2]++;
173     else if (d2>1 && m_mpiInfo->rank/(d0*d1)==d2-1)
174     m_ownNE[2]--;
175 caltinay 3753
176     // local number of nodes
177 caltinay 4334 m_NN[0] = m_NE[0]+1;
178     m_NN[1] = m_NE[1]+1;
179     m_NN[2] = m_NE[2]+1;
180 caltinay 3753
181 caltinay 3691 // bottom-left-front node is at (offset0,offset1,offset2) in global mesh
182 caltinay 4334 m_offset[0] = (n0+1)/d0*(m_mpiInfo->rank%d0);
183     if (m_offset[0] > 0)
184     m_offset[0]--;
185     m_offset[1] = (n1+1)/d1*(m_mpiInfo->rank%(d0*d1)/d0);
186     if (m_offset[1] > 0)
187     m_offset[1]--;
188     m_offset[2] = (n2+1)/d2*(m_mpiInfo->rank/(d0*d1));
189     if (m_offset[2] > 0)
190     m_offset[2]--;
191 caltinay 3753
192 caltinay 3691 populateSampleIds();
193 caltinay 3756 createPattern();
194 sshaw 4622
195     assembler = new DefaultAssembler3D(this, m_dx, m_NX, m_NE, m_NN);
196 sshaw 4629 for (map<string, int>::const_iterator i = tagnamestonums.begin();
197     i != tagnamestonums.end(); i++) {
198     setTagMap(i->first, i->second);
199     }
200 sshaw 4622 addPoints(tags.size(), &points[0], &tags[0]);
201 caltinay 3691 }
202    
203    
204     Brick::~Brick()
205     {
206 sshaw 4622 delete assembler;
207 caltinay 3691 }
208    
209     string Brick::getDescription() const
210     {
211     return "ripley::Brick";
212     }
213    
214     bool Brick::operator==(const AbstractDomain& other) const
215     {
216 caltinay 3744 const Brick* o=dynamic_cast<const Brick*>(&other);
217     if (o) {
218     return (RipleyDomain::operator==(other) &&
219 caltinay 4334 m_gNE[0]==o->m_gNE[0] && m_gNE[1]==o->m_gNE[1] && m_gNE[2]==o->m_gNE[2]
220     && m_origin[0]==o->m_origin[0] && m_origin[1]==o->m_origin[1] && m_origin[2]==o->m_origin[2]
221     && m_length[0]==o->m_length[0] && m_length[1]==o->m_length[1] && m_length[2]==o->m_length[2]
222     && m_NX[0]==o->m_NX[0] && m_NX[1]==o->m_NX[1] && m_NX[2]==o->m_NX[2]);
223 caltinay 3744 }
224 caltinay 3691
225     return false;
226     }
227    
228 caltinay 4013 void Brick::readNcGrid(escript::Data& out, string filename, string varname,
229 caltinay 4618 const ReaderParameters& params) const
230 caltinay 4013 {
231     #ifdef USE_NETCDF
232     // check destination function space
233     int myN0, myN1, myN2;
234     if (out.getFunctionSpace().getTypeCode() == Nodes) {
235 caltinay 4334 myN0 = m_NN[0];
236     myN1 = m_NN[1];
237     myN2 = m_NN[2];
238 caltinay 4013 } else if (out.getFunctionSpace().getTypeCode() == Elements ||
239     out.getFunctionSpace().getTypeCode() == ReducedElements) {
240 caltinay 4334 myN0 = m_NE[0];
241     myN1 = m_NE[1];
242     myN2 = m_NE[2];
243 caltinay 4013 } else
244     throw RipleyException("readNcGrid(): invalid function space for output data object");
245    
246 caltinay 4615 if (params.first.size() != 3)
247 caltinay 4013 throw RipleyException("readNcGrid(): argument 'first' must have 3 entries");
248    
249 caltinay 4615 if (params.numValues.size() != 3)
250 caltinay 4013 throw RipleyException("readNcGrid(): argument 'numValues' must have 3 entries");
251    
252 caltinay 4615 if (params.multiplier.size() != 3)
253 caltinay 4277 throw RipleyException("readNcGrid(): argument 'multiplier' must have 3 entries");
254 caltinay 4615 for (size_t i=0; i<params.multiplier.size(); i++)
255     if (params.multiplier[i]<1)
256 caltinay 4277 throw RipleyException("readNcGrid(): all multipliers must be positive");
257    
258 caltinay 4013 // check file existence and size
259     NcFile f(filename.c_str(), NcFile::ReadOnly);
260     if (!f.is_valid())
261     throw RipleyException("readNcGrid(): cannot open file");
262    
263     NcVar* var = f.get_var(varname.c_str());
264     if (!var)
265     throw RipleyException("readNcGrid(): invalid variable name");
266    
267     // TODO: rank>0 data support
268     const int numComp = out.getDataPointSize();
269     if (numComp > 1)
270     throw RipleyException("readNcGrid(): only scalar data supported");
271    
272     const int dims = var->num_dims();
273 caltinay 4477 boost::scoped_array<long> edges(var->edges());
274 caltinay 4013
275     // is this a slice of the data object (dims!=3)?
276     // note the expected ordering of edges (as in numpy: z,y,x)
277 caltinay 4615 if ( (dims==3 && (params.numValues[2] > edges[0] ||
278     params.numValues[1] > edges[1] ||
279     params.numValues[0] > edges[2]))
280     || (dims==2 && params.numValues[2]>1)
281     || (dims==1 && (params.numValues[2]>1 || params.numValues[1]>1)) ) {
282 caltinay 4013 throw RipleyException("readNcGrid(): not enough data in file");
283     }
284    
285     // check if this rank contributes anything
286 caltinay 4615 if (params.first[0] >= m_offset[0]+myN0 ||
287     params.first[0]+params.numValues[0]*params.multiplier[0] <= m_offset[0] ||
288     params.first[1] >= m_offset[1]+myN1 ||
289     params.first[1]+params.numValues[1]*params.multiplier[1] <= m_offset[1] ||
290     params.first[2] >= m_offset[2]+myN2 ||
291     params.first[2]+params.numValues[2]*params.multiplier[2] <= m_offset[2]) {
292 caltinay 4013 return;
293     }
294    
295     // now determine how much this rank has to write
296    
297     // first coordinates in data object to write to
298 caltinay 4615 const int first0 = max(0, params.first[0]-m_offset[0]);
299     const int first1 = max(0, params.first[1]-m_offset[1]);
300     const int first2 = max(0, params.first[2]-m_offset[2]);
301 caltinay 4618 // indices to first value in file (not accounting for reverse yet)
302     int idx0 = max(0, m_offset[0]-params.first[0]);
303     int idx1 = max(0, m_offset[1]-params.first[1]);
304     int idx2 = max(0, m_offset[2]-params.first[2]);
305 caltinay 4277 // number of values to read
306 caltinay 4615 const int num0 = min(params.numValues[0]-idx0, myN0-first0);
307     const int num1 = min(params.numValues[1]-idx1, myN1-first1);
308     const int num2 = min(params.numValues[2]-idx2, myN2-first2);
309 caltinay 4013
310 caltinay 4618 // make sure we read the right block if going backwards through file
311     if (params.reverse[0])
312     idx0 = edges[dims-1]-num0-idx0;
313     if (dims>1 && params.reverse[1])
314     idx1 = edges[dims-2]-num1-idx1;
315     if (dims>2 && params.reverse[2])
316     idx2 = edges[dims-3]-num2-idx2;
317    
318    
319 caltinay 4013 vector<double> values(num0*num1*num2);
320     if (dims==3) {
321     var->set_cur(idx2, idx1, idx0);
322     var->get(&values[0], num2, num1, num0);
323     } else if (dims==2) {
324     var->set_cur(idx1, idx0);
325     var->get(&values[0], num1, num0);
326     } else {
327     var->set_cur(idx0);
328     var->get(&values[0], num0);
329     }
330    
331     const int dpp = out.getNumDataPointsPerSample();
332     out.requireWrite();
333    
334 caltinay 4618 // helpers for reversing
335     const int x0 = (params.reverse[0] ? num0-1 : 0);
336     const int x_mult = (params.reverse[0] ? -1 : 1);
337     const int y0 = (params.reverse[1] ? num1-1 : 0);
338     const int y_mult = (params.reverse[1] ? -1 : 1);
339     const int z0 = (params.reverse[2] ? num2-1 : 0);
340     const int z_mult = (params.reverse[2] ? -1 : 1);
341    
342 caltinay 4013 for (index_t z=0; z<num2; z++) {
343     for (index_t y=0; y<num1; y++) {
344     #pragma omp parallel for
345     for (index_t x=0; x<num0; x++) {
346 caltinay 4615 const int baseIndex = first0+x*params.multiplier[0]
347     +(first1+y*params.multiplier[1])*myN0
348     +(first2+z*params.multiplier[2])*myN0*myN1;
349 caltinay 4618 const int srcIndex=(z0+z_mult*z)*num1*num0
350     +(y0+y_mult*y)*num0
351     +(x0+x_mult*x);
352 caltinay 4174 if (!isnan(values[srcIndex])) {
353 caltinay 4615 for (index_t m2=0; m2<params.multiplier[2]; m2++) {
354     for (index_t m1=0; m1<params.multiplier[1]; m1++) {
355     for (index_t m0=0; m0<params.multiplier[0]; m0++) {
356 caltinay 4277 const int dataIndex = baseIndex+m0
357     +m1*myN0
358     +m2*myN0*myN1;
359     double* dest = out.getSampleDataRW(dataIndex);
360     for (index_t q=0; q<dpp; q++) {
361     *dest++ = values[srcIndex];
362     }
363     }
364     }
365 caltinay 4174 }
366 caltinay 4013 }
367     }
368     }
369     }
370     #else
371     throw RipleyException("readNcGrid(): not compiled with netCDF support");
372     #endif
373     }
374    
375 sshaw 4738 #ifdef USE_BOOSTIO
376     void Brick::readBinaryGridFromZipped(escript::Data& out, string filename,
377     const ReaderParameters& params) const
378     {
379     // the mapping is not universally correct but should work on our
380     // supported platforms
381     switch (params.dataType) {
382     case DATATYPE_INT32:
383     readBinaryGridZippedImpl<int>(out, filename, params);
384     break;
385     case DATATYPE_FLOAT32:
386     readBinaryGridZippedImpl<float>(out, filename, params);
387     break;
388     case DATATYPE_FLOAT64:
389     readBinaryGridZippedImpl<double>(out, filename, params);
390     break;
391     default:
392     throw RipleyException("readBinaryGrid(): invalid or unsupported datatype");
393     }
394     }
395     #endif
396    
397 caltinay 4334 void Brick::readBinaryGrid(escript::Data& out, string filename,
398 caltinay 4618 const ReaderParameters& params) const
399 caltinay 4334 {
400 caltinay 4495 // the mapping is not universally correct but should work on our
401     // supported platforms
402 caltinay 4615 switch (params.dataType) {
403 caltinay 4495 case DATATYPE_INT32:
404 caltinay 4615 readBinaryGridImpl<int>(out, filename, params);
405 caltinay 4495 break;
406     case DATATYPE_FLOAT32:
407 caltinay 4615 readBinaryGridImpl<float>(out, filename, params);
408 caltinay 4495 break;
409     case DATATYPE_FLOAT64:
410 caltinay 4615 readBinaryGridImpl<double>(out, filename, params);
411 caltinay 4495 break;
412     default:
413     throw RipleyException("readBinaryGrid(): invalid or unsupported datatype");
414     }
415     }
416    
417     template<typename ValueType>
418     void Brick::readBinaryGridImpl(escript::Data& out, const string& filename,
419 caltinay 4618 const ReaderParameters& params) const
420 caltinay 4495 {
421 caltinay 4334 // check destination function space
422     int myN0, myN1, myN2;
423     if (out.getFunctionSpace().getTypeCode() == Nodes) {
424     myN0 = m_NN[0];
425     myN1 = m_NN[1];
426     myN2 = m_NN[2];
427     } else if (out.getFunctionSpace().getTypeCode() == Elements ||
428     out.getFunctionSpace().getTypeCode() == ReducedElements) {
429     myN0 = m_NE[0];
430     myN1 = m_NE[1];
431     myN2 = m_NE[2];
432     } else
433     throw RipleyException("readBinaryGrid(): invalid function space for output data object");
434    
435 caltinay 4615 if (params.first.size() != 3)
436 caltinay 4334 throw RipleyException("readBinaryGrid(): argument 'first' must have 3 entries");
437    
438 caltinay 4615 if (params.numValues.size() != 3)
439 caltinay 4334 throw RipleyException("readBinaryGrid(): argument 'numValues' must have 3 entries");
440    
441 caltinay 4615 if (params.multiplier.size() != 3)
442 caltinay 4334 throw RipleyException("readBinaryGrid(): argument 'multiplier' must have 3 entries");
443 caltinay 4615 for (size_t i=0; i<params.multiplier.size(); i++)
444     if (params.multiplier[i]<1)
445 caltinay 4334 throw RipleyException("readBinaryGrid(): all multipliers must be positive");
446    
447     // check file existence and size
448     ifstream f(filename.c_str(), ifstream::binary);
449     if (f.fail()) {
450     throw RipleyException("readBinaryGrid(): cannot open file");
451     }
452     f.seekg(0, ios::end);
453     const int numComp = out.getDataPointSize();
454     const int filesize = f.tellg();
455 caltinay 4615 const int reqsize = params.numValues[0]*params.numValues[1]*params.numValues[2]*numComp*sizeof(ValueType);
456 caltinay 4334 if (filesize < reqsize) {
457     f.close();
458     throw RipleyException("readBinaryGrid(): not enough data in file");
459     }
460    
461     // check if this rank contributes anything
462 caltinay 4615 if (params.first[0] >= m_offset[0]+myN0 ||
463     params.first[0]+params.numValues[0]*params.multiplier[0] <= m_offset[0] ||
464     params.first[1] >= m_offset[1]+myN1 ||
465     params.first[1]+params.numValues[1]*params.multiplier[1] <= m_offset[1] ||
466     params.first[2] >= m_offset[2]+myN2 ||
467     params.first[2]+params.numValues[2]*params.multiplier[2] <= m_offset[2]) {
468 caltinay 4334 f.close();
469     return;
470     }
471    
472     // now determine how much this rank has to write
473    
474     // first coordinates in data object to write to
475 caltinay 4615 const int first0 = max(0, params.first[0]-m_offset[0]);
476     const int first1 = max(0, params.first[1]-m_offset[1]);
477     const int first2 = max(0, params.first[2]-m_offset[2]);
478 caltinay 4334 // indices to first value in file
479 caltinay 4615 const int idx0 = max(0, m_offset[0]-params.first[0]);
480     const int idx1 = max(0, m_offset[1]-params.first[1]);
481     const int idx2 = max(0, m_offset[2]-params.first[2]);
482 caltinay 4334 // number of values to read
483 caltinay 4615 const int num0 = min(params.numValues[0]-idx0, myN0-first0);
484     const int num1 = min(params.numValues[1]-idx1, myN1-first1);
485     const int num2 = min(params.numValues[2]-idx2, myN2-first2);
486 caltinay 4334
487     out.requireWrite();
488 caltinay 4495 vector<ValueType> values(num0*numComp);
489 caltinay 4334 const int dpp = out.getNumDataPointsPerSample();
490    
491 caltinay 4529 for (int z=0; z<num2; z++) {
492     for (int y=0; y<num1; y++) {
493 caltinay 4615 const int fileofs = numComp*(idx0+(idx1+y)*params.numValues[0]
494     +(idx2+z)*params.numValues[0]*params.numValues[1]);
495 caltinay 4495 f.seekg(fileofs*sizeof(ValueType));
496     f.read((char*)&values[0], num0*numComp*sizeof(ValueType));
497 caltinay 4334
498 caltinay 4529 for (int x=0; x<num0; x++) {
499 caltinay 4615 const int baseIndex = first0+x*params.multiplier[0]
500     +(first1+y*params.multiplier[1])*myN0
501     +(first2+z*params.multiplier[2])*myN0*myN1;
502     for (int m2=0; m2<params.multiplier[2]; m2++) {
503     for (int m1=0; m1<params.multiplier[1]; m1++) {
504     for (int m0=0; m0<params.multiplier[0]; m0++) {
505 caltinay 4334 const int dataIndex = baseIndex+m0
506     +m1*myN0
507     +m2*myN0*myN1;
508     double* dest = out.getSampleDataRW(dataIndex);
509 caltinay 4529 for (int c=0; c<numComp; c++) {
510     ValueType val = values[x*numComp+c];
511    
512 caltinay 4615 if (params.byteOrder != BYTEORDER_NATIVE) {
513 caltinay 4529 char* cval = reinterpret_cast<char*>(&val);
514     // this will alter val!!
515     byte_swap32(cval);
516     }
517     if (!std::isnan(val)) {
518     for (int q=0; q<dpp; q++) {
519     *dest++ = static_cast<double>(val);
520 caltinay 4334 }
521     }
522     }
523     }
524     }
525     }
526     }
527     }
528     }
529    
530     f.close();
531     }
532    
533 sshaw 4738 #ifdef USE_BOOSTIO
534     template<typename ValueType>
535     void Brick::readBinaryGridZippedImpl(escript::Data& out, const string& filename,
536     const ReaderParameters& params) const
537     {
538     // check destination function space
539     int myN0, myN1, myN2;
540     if (out.getFunctionSpace().getTypeCode() == Nodes) {
541     myN0 = m_NN[0];
542     myN1 = m_NN[1];
543     myN2 = m_NN[2];
544     } else if (out.getFunctionSpace().getTypeCode() == Elements ||
545     out.getFunctionSpace().getTypeCode() == ReducedElements) {
546     myN0 = m_NE[0];
547     myN1 = m_NE[1];
548     myN2 = m_NE[2];
549     } else
550     throw RipleyException("readBinaryGridFromZipped(): invalid function space for output data object");
551    
552     if (params.first.size() != 3)
553     throw RipleyException("readBinaryGridFromZipped(): argument 'first' must have 3 entries");
554    
555     if (params.numValues.size() != 3)
556     throw RipleyException("readBinaryGridFromZipped(): argument 'numValues' must have 3 entries");
557    
558     if (params.multiplier.size() != 3)
559     throw RipleyException("readBinaryGridFromZipped(): argument 'multiplier' must have 3 entries");
560     for (size_t i=0; i<params.multiplier.size(); i++)
561     if (params.multiplier[i]<1)
562     throw RipleyException("readBinaryGridFromZipped(): all multipliers must be positive");
563    
564     // check file existence and size
565     ifstream f(filename.c_str(), ifstream::binary);
566     if (f.fail()) {
567     throw RipleyException("readBinaryGridFromZipped(): cannot open file");
568     }
569     f.seekg(0, ios::end);
570     const int numComp = out.getDataPointSize();
571     int filesize = f.tellg();
572     f.seekg(0, ios::beg);
573     std::vector<char> compressed(filesize);
574     f.read((char*)&compressed[0], filesize);
575     f.close();
576     std::vector<char> decompressed = unzip(compressed);
577     filesize = decompressed.size();
578     const int reqsize = params.numValues[0]*params.numValues[1]*params.numValues[2]*numComp*sizeof(ValueType);
579     if (filesize < reqsize) {
580     throw RipleyException("readBinaryGridFromZipped(): not enough data in file");
581     }
582    
583     // check if this rank contributes anything
584     if (params.first[0] >= m_offset[0]+myN0 ||
585     params.first[0]+params.numValues[0]*params.multiplier[0] <= m_offset[0] ||
586     params.first[1] >= m_offset[1]+myN1 ||
587     params.first[1]+params.numValues[1]*params.multiplier[1] <= m_offset[1] ||
588     params.first[2] >= m_offset[2]+myN2 ||
589     params.first[2]+params.numValues[2]*params.multiplier[2] <= m_offset[2]) {
590     return;
591     }
592    
593     // now determine how much this rank has to write
594    
595     // first coordinates in data object to write to
596     const int first0 = max(0, params.first[0]-m_offset[0]);
597     const int first1 = max(0, params.first[1]-m_offset[1]);
598     const int first2 = max(0, params.first[2]-m_offset[2]);
599     // indices to first value in file
600     const int idx0 = max(0, m_offset[0]-params.first[0]);
601     const int idx1 = max(0, m_offset[1]-params.first[1]);
602     const int idx2 = max(0, m_offset[2]-params.first[2]);
603     // number of values to read
604     const int num0 = min(params.numValues[0]-idx0, myN0-first0);
605     const int num1 = min(params.numValues[1]-idx1, myN1-first1);
606     const int num2 = min(params.numValues[2]-idx2, myN2-first2);
607    
608     out.requireWrite();
609     vector<ValueType> values(num0*numComp);
610     const int dpp = out.getNumDataPointsPerSample();
611    
612     for (int z=0; z<num2; z++) {
613     for (int y=0; y<num1; y++) {
614     const int fileofs = numComp*(idx0+(idx1+y)*params.numValues[0]
615     +(idx2+z)*params.numValues[0]*params.numValues[1]);
616     memcpy((char*)&values[0], (char*)&decompressed[fileofs*sizeof(ValueType)], num0*numComp*sizeof(ValueType));
617    
618     for (int x=0; x<num0; x++) {
619     const int baseIndex = first0+x*params.multiplier[0]
620     +(first1+y*params.multiplier[1])*myN0
621     +(first2+z*params.multiplier[2])*myN0*myN1;
622     for (int m2=0; m2<params.multiplier[2]; m2++) {
623     for (int m1=0; m1<params.multiplier[1]; m1++) {
624     for (int m0=0; m0<params.multiplier[0]; m0++) {
625     const int dataIndex = baseIndex+m0
626     +m1*myN0
627     +m2*myN0*myN1;
628     double* dest = out.getSampleDataRW(dataIndex);
629     for (int c=0; c<numComp; c++) {
630     ValueType val = values[x*numComp+c];
631    
632     if (params.byteOrder != BYTEORDER_NATIVE) {
633     char* cval = reinterpret_cast<char*>(&val);
634     // this will alter val!!
635     byte_swap32(cval);
636     }
637     if (!std::isnan(val)) {
638     for (int q=0; q<dpp; q++) {
639     *dest++ = static_cast<double>(val);
640     }
641     }
642     }
643     }
644     }
645     }
646     }
647     }
648     }
649     }
650     #endif
651    
652 caltinay 4357 void Brick::writeBinaryGrid(const escript::Data& in, string filename,
653     int byteOrder, int dataType) const
654 caltinay 4334 {
655 caltinay 4357 // the mapping is not universally correct but should work on our
656     // supported platforms
657     switch (dataType) {
658     case DATATYPE_INT32:
659     writeBinaryGridImpl<int>(in, filename, byteOrder);
660     break;
661     case DATATYPE_FLOAT32:
662     writeBinaryGridImpl<float>(in, filename, byteOrder);
663     break;
664     case DATATYPE_FLOAT64:
665     writeBinaryGridImpl<double>(in, filename, byteOrder);
666     break;
667     default:
668     throw RipleyException("writeBinaryGrid(): invalid or unsupported datatype");
669     }
670     }
671    
672     template<typename ValueType>
673     void Brick::writeBinaryGridImpl(const escript::Data& in,
674     const string& filename, int byteOrder) const
675     {
676 caltinay 4334 // check function space and determine number of points
677     int myN0, myN1, myN2;
678     int totalN0, totalN1, totalN2;
679     if (in.getFunctionSpace().getTypeCode() == Nodes) {
680     myN0 = m_NN[0];
681     myN1 = m_NN[1];
682     myN2 = m_NN[2];
683     totalN0 = m_gNE[0]+1;
684     totalN1 = m_gNE[1]+1;
685     totalN2 = m_gNE[2]+1;
686     } else if (in.getFunctionSpace().getTypeCode() == Elements ||
687     in.getFunctionSpace().getTypeCode() == ReducedElements) {
688     myN0 = m_NE[0];
689     myN1 = m_NE[1];
690     myN2 = m_NE[2];
691     totalN0 = m_gNE[0];
692     totalN1 = m_gNE[1];
693     totalN2 = m_gNE[2];
694     } else
695     throw RipleyException("writeBinaryGrid(): invalid function space of data object");
696    
697     const int numComp = in.getDataPointSize();
698     const int dpp = in.getNumDataPointsPerSample();
699 caltinay 4357 const int fileSize = sizeof(ValueType)*numComp*dpp*totalN0*totalN1*totalN2;
700 caltinay 4334
701     if (numComp > 1 || dpp > 1)
702     throw RipleyException("writeBinaryGrid(): only scalar, single-value data supported");
703    
704     // from here on we know that each sample consists of one value
705 caltinay 4482 FileWriter fw;
706     fw.openFile(filename, fileSize);
707 caltinay 4334 MPIBarrier();
708    
709     for (index_t z=0; z<myN2; z++) {
710     for (index_t y=0; y<myN1; y++) {
711     const int fileofs = (m_offset[0]+(m_offset[1]+y)*totalN0
712 caltinay 4357 +(m_offset[2]+z)*totalN0*totalN1)*sizeof(ValueType);
713 caltinay 4334 ostringstream oss;
714    
715     for (index_t x=0; x<myN0; x++) {
716 caltinay 4626 const double* sample = in.getSampleDataRO(z*myN0*myN1+y*myN0+x);
717 caltinay 4357 ValueType fvalue = static_cast<ValueType>(*sample);
718     if (byteOrder == BYTEORDER_NATIVE) {
719 caltinay 4334 oss.write((char*)&fvalue, sizeof(fvalue));
720     } else {
721     char* value = reinterpret_cast<char*>(&fvalue);
722 caltinay 4357 oss.write(byte_swap32(value), sizeof(fvalue));
723 caltinay 4334 }
724     }
725 caltinay 4482 fw.writeAt(oss, fileofs);
726 caltinay 4334 }
727     }
728 caltinay 4482 fw.close();
729 caltinay 4334 }
730    
731 caltinay 3691 void Brick::dump(const string& fileName) const
732     {
733     #if USE_SILO
734     string fn(fileName);
735     if (fileName.length() < 6 || fileName.compare(fileName.length()-5, 5, ".silo") != 0) {
736     fn+=".silo";
737     }
738    
739     int driver=DB_HDF5;
740     string siloPath;
741     DBfile* dbfile = NULL;
742    
743     #ifdef ESYS_MPI
744     PMPIO_baton_t* baton = NULL;
745 gross 3793 const int NUM_SILO_FILES = 1;
746     const char* blockDirFmt = "/block%04d";
747 caltinay 3691 #endif
748    
749     if (m_mpiInfo->size > 1) {
750     #ifdef ESYS_MPI
751     baton = PMPIO_Init(NUM_SILO_FILES, PMPIO_WRITE, m_mpiInfo->comm,
752     0x1337, PMPIO_DefaultCreate, PMPIO_DefaultOpen,
753     PMPIO_DefaultClose, (void*)&driver);
754     // try the fallback driver in case of error
755     if (!baton && driver != DB_PDB) {
756     driver = DB_PDB;
757     baton = PMPIO_Init(NUM_SILO_FILES, PMPIO_WRITE, m_mpiInfo->comm,
758     0x1338, PMPIO_DefaultCreate, PMPIO_DefaultOpen,
759     PMPIO_DefaultClose, (void*)&driver);
760     }
761     if (baton) {
762     char str[64];
763     snprintf(str, 64, blockDirFmt, PMPIO_RankInGroup(baton, m_mpiInfo->rank));
764     siloPath = str;
765     dbfile = (DBfile*) PMPIO_WaitForBaton(baton, fn.c_str(), siloPath.c_str());
766     }
767     #endif
768     } else {
769     dbfile = DBCreate(fn.c_str(), DB_CLOBBER, DB_LOCAL,
770     getDescription().c_str(), driver);
771     // try the fallback driver in case of error
772     if (!dbfile && driver != DB_PDB) {
773     driver = DB_PDB;
774     dbfile = DBCreate(fn.c_str(), DB_CLOBBER, DB_LOCAL,
775     getDescription().c_str(), driver);
776     }
777     }
778    
779     if (!dbfile)
780     throw RipleyException("dump: Could not create Silo file");
781    
782     /*
783     if (driver==DB_HDF5) {
784     // gzip level 1 already provides good compression with minimal
785     // performance penalty. Some tests showed that gzip levels >3 performed
786     // rather badly on escript data both in terms of time and space
787     DBSetCompression("ERRMODE=FALLBACK METHOD=GZIP LEVEL=1");
788     }
789     */
790    
791 caltinay 4334 boost::scoped_ptr<double> x(new double[m_NN[0]]);
792     boost::scoped_ptr<double> y(new double[m_NN[1]]);
793     boost::scoped_ptr<double> z(new double[m_NN[2]]);
794 caltinay 3691 double* coords[3] = { x.get(), y.get(), z.get() };
795     #pragma omp parallel
796     {
797     #pragma omp for
798 caltinay 4334 for (dim_t i0 = 0; i0 < m_NN[0]; i0++) {
799     coords[0][i0]=getLocalCoordinate(i0, 0);
800 caltinay 3691 }
801     #pragma omp for
802 caltinay 4334 for (dim_t i1 = 0; i1 < m_NN[1]; i1++) {
803     coords[1][i1]=getLocalCoordinate(i1, 1);
804 caltinay 3691 }
805     #pragma omp for
806 caltinay 4334 for (dim_t i2 = 0; i2 < m_NN[2]; i2++) {
807     coords[2][i2]=getLocalCoordinate(i2, 2);
808 caltinay 3691 }
809     }
810 caltinay 4334 int* dims = const_cast<int*>(getNumNodesPerDim());
811    
812     // write mesh
813     DBPutQuadmesh(dbfile, "mesh", NULL, coords, dims, 3, DB_DOUBLE,
814 caltinay 3691 DB_COLLINEAR, NULL);
815    
816 caltinay 4334 // write node ids
817     DBPutQuadvar1(dbfile, "nodeId", "mesh", (void*)&m_nodeId[0], dims, 3,
818 caltinay 3698 NULL, 0, DB_INT, DB_NODECENT, NULL);
819 caltinay 3691
820 caltinay 3698 // write element ids
821 caltinay 4334 dims = const_cast<int*>(getNumElementsPerDim());
822 caltinay 3698 DBPutQuadvar1(dbfile, "elementId", "mesh", (void*)&m_elementId[0],
823 caltinay 4334 dims, 3, NULL, 0, DB_INT, DB_ZONECENT, NULL);
824 caltinay 3698
825     // rank 0 writes multimesh and multivar
826 caltinay 3691 if (m_mpiInfo->rank == 0) {
827     vector<string> tempstrings;
828     vector<char*> names;
829     for (dim_t i=0; i<m_mpiInfo->size; i++) {
830     stringstream path;
831     path << "/block" << setw(4) << setfill('0') << right << i << "/mesh";
832     tempstrings.push_back(path.str());
833     names.push_back((char*)tempstrings.back().c_str());
834     }
835     vector<int> types(m_mpiInfo->size, DB_QUAD_RECT);
836     DBSetDir(dbfile, "/");
837     DBPutMultimesh(dbfile, "multimesh", m_mpiInfo->size, &names[0],
838     &types[0], NULL);
839     tempstrings.clear();
840     names.clear();
841     for (dim_t i=0; i<m_mpiInfo->size; i++) {
842     stringstream path;
843     path << "/block" << setw(4) << setfill('0') << right << i << "/nodeId";
844     tempstrings.push_back(path.str());
845     names.push_back((char*)tempstrings.back().c_str());
846     }
847     types.assign(m_mpiInfo->size, DB_QUADVAR);
848     DBPutMultivar(dbfile, "nodeId", m_mpiInfo->size, &names[0],
849     &types[0], NULL);
850 caltinay 3698 tempstrings.clear();
851     names.clear();
852     for (dim_t i=0; i<m_mpiInfo->size; i++) {
853     stringstream path;
854     path << "/block" << setw(4) << setfill('0') << right << i << "/elementId";
855     tempstrings.push_back(path.str());
856     names.push_back((char*)tempstrings.back().c_str());
857     }
858     DBPutMultivar(dbfile, "elementId", m_mpiInfo->size, &names[0],
859     &types[0], NULL);
860 caltinay 3691 }
861    
862     if (m_mpiInfo->size > 1) {
863     #ifdef ESYS_MPI
864     PMPIO_HandOffBaton(baton, dbfile);
865     PMPIO_Finish(baton);
866     #endif
867     } else {
868     DBClose(dbfile);
869     }
870    
871     #else // USE_SILO
872 caltinay 3791 throw RipleyException("dump: no Silo support");
873 caltinay 3691 #endif
874     }
875    
876     const int* Brick::borrowSampleReferenceIDs(int fsType) const
877     {
878 caltinay 3697 switch (fsType) {
879     case Nodes:
880 caltinay 3748 case ReducedNodes: //FIXME: reduced
881 caltinay 3753 return &m_nodeId[0];
882 caltinay 3757 case DegreesOfFreedom:
883     case ReducedDegreesOfFreedom: //FIXME: reduced
884 caltinay 3753 return &m_dofId[0];
885 caltinay 3697 case Elements:
886 caltinay 3733 case ReducedElements:
887 caltinay 3697 return &m_elementId[0];
888 caltinay 3757 case FaceElements:
889 caltinay 3733 case ReducedFaceElements:
890 caltinay 3697 return &m_faceId[0];
891 sshaw 4660 case Points:
892     return &m_diracPointNodeIDs[0];
893 caltinay 3697 default:
894     break;
895     }
896 caltinay 3691
897 caltinay 3697 stringstream msg;
898 caltinay 3791 msg << "borrowSampleReferenceIDs: invalid function space type "<<fsType;
899 caltinay 3697 throw RipleyException(msg.str());
900 caltinay 3691 }
901    
902 caltinay 3757 bool Brick::ownSample(int fsType, index_t id) const
903 caltinay 3691 {
904 caltinay 3759 if (getMPISize()==1)
905     return true;
906    
907 caltinay 3757 switch (fsType) {
908     case Nodes:
909     case ReducedNodes: //FIXME: reduced
910     return (m_dofMap[id] < getNumDOF());
911     case DegreesOfFreedom:
912     case ReducedDegreesOfFreedom:
913     return true;
914     case Elements:
915     case ReducedElements:
916     {
917     // check ownership of element's _last_ node
918 caltinay 4334 const index_t x=id%m_NE[0] + 1;
919     const index_t y=id%(m_NE[0]*m_NE[1])/m_NE[0] + 1;
920     const index_t z=id/(m_NE[0]*m_NE[1]) + 1;
921     return (m_dofMap[x + m_NN[0]*y + m_NN[0]*m_NN[1]*z] < getNumDOF());
922 caltinay 3757 }
923     case FaceElements:
924     case ReducedFaceElements:
925 caltinay 3759 {
926     // check ownership of face element's last node
927     dim_t n=0;
928 caltinay 4334 for (size_t i=0; i<6; i++) {
929     n+=m_faceCount[i];
930 caltinay 3759 if (id<n) {
931 caltinay 4334 const index_t j=id-n+m_faceCount[i];
932 caltinay 3759 if (i>=4) { // front or back
933 caltinay 4334 const index_t first=(i==4 ? 0 : m_NN[0]*m_NN[1]*(m_NN[2]-1));
934     return (m_dofMap[first+j%m_NE[0]+1+(j/m_NE[0]+1)*m_NN[0]] < getNumDOF());
935 caltinay 3759 } else if (i>=2) { // bottom or top
936 caltinay 4334 const index_t first=(i==2 ? 0 : m_NN[0]*(m_NN[1]-1));
937     return (m_dofMap[first+j%m_NE[0]+1+(j/m_NE[0]+1)*m_NN[0]*m_NN[1]] < getNumDOF());
938 caltinay 3759 } else { // left or right
939 caltinay 4334 const index_t first=(i==0 ? 0 : m_NN[0]-1);
940     return (m_dofMap[first+(j%m_NE[1]+1)*m_NN[0]+(j/m_NE[1]+1)*m_NN[0]*m_NN[1]] < getNumDOF());
941 caltinay 3759 }
942     }
943     }
944     return false;
945     }
946 caltinay 3757 default:
947     break;
948 caltinay 3753 }
949 caltinay 3757
950     stringstream msg;
951 caltinay 3791 msg << "ownSample: invalid function space type " << fsType;
952 caltinay 3757 throw RipleyException(msg.str());
953 caltinay 3691 }
954    
955 caltinay 3764 void Brick::setToNormal(escript::Data& out) const
956 caltinay 3703 {
957 caltinay 3764 if (out.getFunctionSpace().getTypeCode() == FaceElements) {
958     out.requireWrite();
959     #pragma omp parallel
960     {
961     if (m_faceOffset[0] > -1) {
962     #pragma omp for nowait
963 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
964     for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
965     double* o = out.getSampleDataRW(m_faceOffset[0]+INDEX2(k1,k2,m_NE[1]));
966 caltinay 3764 // set vector at four quadrature points
967     *o++ = -1.; *o++ = 0.; *o++ = 0.;
968     *o++ = -1.; *o++ = 0.; *o++ = 0.;
969     *o++ = -1.; *o++ = 0.; *o++ = 0.;
970     *o++ = -1.; *o++ = 0.; *o = 0.;
971     }
972     }
973     }
974    
975     if (m_faceOffset[1] > -1) {
976     #pragma omp for nowait
977 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
978     for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
979     double* o = out.getSampleDataRW(m_faceOffset[1]+INDEX2(k1,k2,m_NE[1]));
980 caltinay 3764 // set vector at four quadrature points
981     *o++ = 1.; *o++ = 0.; *o++ = 0.;
982     *o++ = 1.; *o++ = 0.; *o++ = 0.;
983     *o++ = 1.; *o++ = 0.; *o++ = 0.;
984     *o++ = 1.; *o++ = 0.; *o = 0.;
985     }
986     }
987     }
988    
989     if (m_faceOffset[2] > -1) {
990     #pragma omp for nowait
991 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
992     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
993     double* o = out.getSampleDataRW(m_faceOffset[2]+INDEX2(k0,k2,m_NE[0]));
994 caltinay 3764 // set vector at four quadrature points
995     *o++ = 0.; *o++ = -1.; *o++ = 0.;
996     *o++ = 0.; *o++ = -1.; *o++ = 0.;
997     *o++ = 0.; *o++ = -1.; *o++ = 0.;
998     *o++ = 0.; *o++ = -1.; *o = 0.;
999     }
1000     }
1001     }
1002    
1003     if (m_faceOffset[3] > -1) {
1004     #pragma omp for nowait
1005 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1006     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1007     double* o = out.getSampleDataRW(m_faceOffset[3]+INDEX2(k0,k2,m_NE[0]));
1008 caltinay 3764 // set vector at four quadrature points
1009     *o++ = 0.; *o++ = 1.; *o++ = 0.;
1010     *o++ = 0.; *o++ = 1.; *o++ = 0.;
1011     *o++ = 0.; *o++ = 1.; *o++ = 0.;
1012     *o++ = 0.; *o++ = 1.; *o = 0.;
1013     }
1014     }
1015     }
1016    
1017     if (m_faceOffset[4] > -1) {
1018     #pragma omp for nowait
1019 caltinay 4334 for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1020     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1021     double* o = out.getSampleDataRW(m_faceOffset[4]+INDEX2(k0,k1,m_NE[0]));
1022 caltinay 3764 // set vector at four quadrature points
1023     *o++ = 0.; *o++ = 0.; *o++ = -1.;
1024     *o++ = 0.; *o++ = 0.; *o++ = -1.;
1025     *o++ = 0.; *o++ = 0.; *o++ = -1.;
1026     *o++ = 0.; *o++ = 0.; *o = -1.;
1027     }
1028     }
1029     }
1030    
1031     if (m_faceOffset[5] > -1) {
1032     #pragma omp for nowait
1033 caltinay 4334 for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1034     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1035     double* o = out.getSampleDataRW(m_faceOffset[5]+INDEX2(k0,k1,m_NE[0]));
1036 caltinay 3764 // set vector at four quadrature points
1037     *o++ = 0.; *o++ = 0.; *o++ = 1.;
1038     *o++ = 0.; *o++ = 0.; *o++ = 1.;
1039     *o++ = 0.; *o++ = 0.; *o++ = 1.;
1040     *o++ = 0.; *o++ = 0.; *o = 1.;
1041     }
1042     }
1043     }
1044     } // end of parallel section
1045     } else if (out.getFunctionSpace().getTypeCode() == ReducedFaceElements) {
1046     out.requireWrite();
1047     #pragma omp parallel
1048     {
1049     if (m_faceOffset[0] > -1) {
1050     #pragma omp for nowait
1051 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1052     for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1053     double* o = out.getSampleDataRW(m_faceOffset[0]+INDEX2(k1,k2,m_NE[1]));
1054 caltinay 3764 *o++ = -1.;
1055     *o++ = 0.;
1056     *o = 0.;
1057     }
1058     }
1059     }
1060    
1061     if (m_faceOffset[1] > -1) {
1062     #pragma omp for nowait
1063 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1064     for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1065     double* o = out.getSampleDataRW(m_faceOffset[1]+INDEX2(k1,k2,m_NE[1]));
1066 caltinay 3764 *o++ = 1.;
1067     *o++ = 0.;
1068     *o = 0.;
1069     }
1070     }
1071     }
1072    
1073     if (m_faceOffset[2] > -1) {
1074     #pragma omp for nowait
1075 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1076     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1077     double* o = out.getSampleDataRW(m_faceOffset[2]+INDEX2(k0,k2,m_NE[0]));
1078 caltinay 3764 *o++ = 0.;
1079     *o++ = -1.;
1080     *o = 0.;
1081     }
1082     }
1083     }
1084    
1085     if (m_faceOffset[3] > -1) {
1086     #pragma omp for nowait
1087 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1088     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1089     double* o = out.getSampleDataRW(m_faceOffset[3]+INDEX2(k0,k2,m_NE[0]));
1090 caltinay 3764 *o++ = 0.;
1091     *o++ = 1.;
1092     *o = 0.;
1093     }
1094     }
1095     }
1096    
1097     if (m_faceOffset[4] > -1) {
1098     #pragma omp for nowait
1099 caltinay 4334 for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1100     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1101     double* o = out.getSampleDataRW(m_faceOffset[4]+INDEX2(k0,k1,m_NE[0]));
1102 caltinay 3764 *o++ = 0.;
1103     *o++ = 0.;
1104     *o = -1.;
1105     }
1106     }
1107     }
1108    
1109     if (m_faceOffset[5] > -1) {
1110     #pragma omp for nowait
1111 caltinay 4334 for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1112     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1113     double* o = out.getSampleDataRW(m_faceOffset[5]+INDEX2(k0,k1,m_NE[0]));
1114 caltinay 3764 *o++ = 0.;
1115     *o++ = 0.;
1116     *o = 1.;
1117     }
1118     }
1119     }
1120     } // end of parallel section
1121    
1122     } else {
1123     stringstream msg;
1124 caltinay 3791 msg << "setToNormal: invalid function space type "
1125     << out.getFunctionSpace().getTypeCode();
1126 caltinay 3764 throw RipleyException(msg.str());
1127     }
1128     }
1129    
1130     void Brick::setToSize(escript::Data& out) const
1131     {
1132     if (out.getFunctionSpace().getTypeCode() == Elements
1133     || out.getFunctionSpace().getTypeCode() == ReducedElements) {
1134     out.requireWrite();
1135     const dim_t numQuad=out.getNumDataPointsPerSample();
1136 caltinay 4334 const double size=sqrt(m_dx[0]*m_dx[0]+m_dx[1]*m_dx[1]+m_dx[2]*m_dx[2]);
1137 caltinay 3764 #pragma omp parallel for
1138     for (index_t k = 0; k < getNumElements(); ++k) {
1139     double* o = out.getSampleDataRW(k);
1140     fill(o, o+numQuad, size);
1141     }
1142     } else if (out.getFunctionSpace().getTypeCode() == FaceElements
1143     || out.getFunctionSpace().getTypeCode() == ReducedFaceElements) {
1144     out.requireWrite();
1145     const dim_t numQuad=out.getNumDataPointsPerSample();
1146     #pragma omp parallel
1147     {
1148     if (m_faceOffset[0] > -1) {
1149 caltinay 4334 const double size=min(m_dx[1],m_dx[2]);
1150 caltinay 3764 #pragma omp for nowait
1151 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1152     for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1153     double* o = out.getSampleDataRW(m_faceOffset[0]+INDEX2(k1,k2,m_NE[1]));
1154 caltinay 3764 fill(o, o+numQuad, size);
1155     }
1156     }
1157     }
1158    
1159     if (m_faceOffset[1] > -1) {
1160 caltinay 4334 const double size=min(m_dx[1],m_dx[2]);
1161 caltinay 3764 #pragma omp for nowait
1162 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1163     for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1164     double* o = out.getSampleDataRW(m_faceOffset[1]+INDEX2(k1,k2,m_NE[1]));
1165 caltinay 3764 fill(o, o+numQuad, size);
1166     }
1167     }
1168     }
1169    
1170     if (m_faceOffset[2] > -1) {
1171 caltinay 4334 const double size=min(m_dx[0],m_dx[2]);
1172 caltinay 3764 #pragma omp for nowait
1173 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1174     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1175     double* o = out.getSampleDataRW(m_faceOffset[2]+INDEX2(k0,k2,m_NE[0]));
1176 caltinay 3764 fill(o, o+numQuad, size);
1177     }
1178     }
1179     }
1180    
1181     if (m_faceOffset[3] > -1) {
1182 caltinay 4334 const double size=min(m_dx[0],m_dx[2]);
1183 caltinay 3764 #pragma omp for nowait
1184 caltinay 4334 for (index_t k2 = 0; k2 < m_NE[2]; ++k2) {
1185     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1186     double* o = out.getSampleDataRW(m_faceOffset[3]+INDEX2(k0,k2,m_NE[0]));
1187 caltinay 3764 fill(o, o+numQuad, size);
1188     }
1189     }
1190     }
1191    
1192     if (m_faceOffset[4] > -1) {
1193 caltinay 4334 const double size=min(m_dx[0],m_dx[1]);
1194 caltinay 3764 #pragma omp for nowait
1195 caltinay 4334 for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1196     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1197     double* o = out.getSampleDataRW(m_faceOffset[4]+INDEX2(k0,k1,m_NE[0]));
1198 caltinay 3764 fill(o, o+numQuad, size);
1199     }
1200     }
1201     }
1202    
1203     if (m_faceOffset[5] > -1) {
1204 caltinay 4334 const double size=min(m_dx[0],m_dx[1]);
1205 caltinay 3764 #pragma omp for nowait
1206 caltinay 4334 for (index_t k1 = 0; k1 < m_NE[1]; ++k1) {
1207     for (index_t k0 = 0; k0 < m_NE[0]; ++k0) {
1208     double* o = out.getSampleDataRW(m_faceOffset[5]+INDEX2(k0,k1,m_NE[0]));
1209 caltinay 3764 fill(o, o+numQuad, size);
1210     }
1211     }
1212     }
1213     } // end of parallel section
1214    
1215     } else {
1216     stringstream msg;
1217 caltinay 3791 msg << "setToSize: invalid function space type "
1218     << out.getFunctionSpace().getTypeCode();
1219 caltinay 3764 throw RipleyException(msg.str());
1220     }
1221     }
1222    
1223     void Brick::Print_Mesh_Info(const bool full) const
1224     {
1225     RipleyDomain::Print_Mesh_Info(full);
1226     if (full) {
1227     cout << " Id Coordinates" << endl;
1228     cout.precision(15);
1229     cout.setf(ios::scientific, ios::floatfield);
1230     for (index_t i=0; i < getNumNodes(); i++) {
1231     cout << " " << setw(5) << m_nodeId[i]
1232 caltinay 4334 << " " << getLocalCoordinate(i%m_NN[0], 0)
1233     << " " << getLocalCoordinate(i%(m_NN[0]*m_NN[1])/m_NN[0], 1)
1234     << " " << getLocalCoordinate(i/(m_NN[0]*m_NN[1]), 2) << endl;
1235 caltinay 3764 }
1236     }
1237     }
1238    
1239    
1240     //protected
1241     void Brick::assembleCoordinates(escript::Data& arg) const
1242     {
1243     escriptDataC x = arg.getDataC();
1244     int numDim = m_numDim;
1245     if (!isDataPointShapeEqual(&x, 1, &numDim))
1246     throw RipleyException("setToX: Invalid Data object shape");
1247     if (!numSamplesEqual(&x, 1, getNumNodes()))
1248     throw RipleyException("setToX: Illegal number of samples in Data object");
1249    
1250     arg.requireWrite();
1251     #pragma omp parallel for
1252 caltinay 4334 for (dim_t i2 = 0; i2 < m_NN[2]; i2++) {
1253     for (dim_t i1 = 0; i1 < m_NN[1]; i1++) {
1254     for (dim_t i0 = 0; i0 < m_NN[0]; i0++) {
1255     double* point = arg.getSampleDataRW(i0+m_NN[0]*i1+m_NN[0]*m_NN[1]*i2);
1256     point[0] = getLocalCoordinate(i0, 0);
1257     point[1] = getLocalCoordinate(i1, 1);
1258     point[2] = getLocalCoordinate(i2, 2);
1259 caltinay 3764 }
1260     }
1261     }
1262     }
1263    
1264     //protected
1265 caltinay 4626 void Brick::assembleGradient(escript::Data& out, const escript::Data& in) const
1266 caltinay 3764 {
1267 caltinay 3703 const dim_t numComp = in.getDataPointSize();
1268 caltinay 3731 const double C0 = .044658198738520451079;
1269     const double C1 = .16666666666666666667;
1270     const double C2 = .21132486540518711775;
1271     const double C3 = .25;
1272     const double C4 = .5;
1273     const double C5 = .62200846792814621559;
1274     const double C6 = .78867513459481288225;
1275    
1276 caltinay 3703 if (out.getFunctionSpace().getTypeCode() == Elements) {
1277 caltinay 3760 out.requireWrite();
1278 caltinay 3913 #pragma omp parallel
1279     {
1280     vector<double> f_000(numComp);
1281     vector<double> f_001(numComp);
1282     vector<double> f_010(numComp);
1283     vector<double> f_011(numComp);
1284     vector<double> f_100(numComp);
1285     vector<double> f_101(numComp);
1286     vector<double> f_110(numComp);
1287     vector<double> f_111(numComp);
1288     #pragma omp for
1289 caltinay 4334 for (index_t k2=0; k2 < m_NE[2]; ++k2) {
1290     for (index_t k1=0; k1 < m_NE[1]; ++k1) {
1291     for (index_t k0=0; k0 < m_NE[0]; ++k0) {
1292     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(k0,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1293     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(k0,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1294     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(k0,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1295     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(k0,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1296     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(k0+1,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1297     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(k0+1,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1298     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1299     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1300     double* o = out.getSampleDataRW(INDEX3(k0,k1,k2,m_NE[0],m_NE[1]));
1301 caltinay 3913 for (index_t i=0; i < numComp; ++i) {
1302 caltinay 4375 const double V0=((f_100[i]-f_000[i])*C5 + (f_111[i]-f_011[i])*C0 + (f_101[i]+f_110[i]-f_001[i]-f_010[i])*C1) / m_dx[0];
1303     const double V1=((f_110[i]-f_010[i])*C5 + (f_101[i]-f_001[i])*C0 + (f_100[i]+f_111[i]-f_000[i]-f_011[i])*C1) / m_dx[0];
1304     const double V2=((f_101[i]-f_001[i])*C5 + (f_110[i]-f_010[i])*C0 + (f_100[i]+f_111[i]-f_000[i]-f_011[i])*C1) / m_dx[0];
1305     const double V3=((f_111[i]-f_011[i])*C5 + (f_100[i]-f_000[i])*C0 + (f_101[i]+f_110[i]-f_001[i]-f_010[i])*C1) / m_dx[0];
1306     const double V4=((f_010[i]-f_000[i])*C5 + (f_111[i]-f_101[i])*C0 + (f_011[i]+f_110[i]-f_001[i]-f_100[i])*C1) / m_dx[1];
1307     const double V5=((f_110[i]-f_100[i])*C5 + (f_011[i]-f_001[i])*C0 + (f_010[i]+f_111[i]-f_000[i]-f_101[i])*C1) / m_dx[1];
1308     const double V6=((f_011[i]-f_001[i])*C5 + (f_110[i]-f_100[i])*C0 + (f_010[i]+f_111[i]-f_000[i]-f_101[i])*C1) / m_dx[1];
1309     const double V7=((f_111[i]-f_101[i])*C5 + (f_010[i]-f_000[i])*C0 + (f_011[i]+f_110[i]-f_001[i]-f_100[i])*C1) / m_dx[1];
1310     const double V8=((f_001[i]-f_000[i])*C5 + (f_111[i]-f_110[i])*C0 + (f_011[i]+f_101[i]-f_010[i]-f_100[i])*C1) / m_dx[2];
1311     const double V9=((f_101[i]-f_100[i])*C5 + (f_011[i]-f_010[i])*C0 + (f_001[i]+f_111[i]-f_000[i]-f_110[i])*C1) / m_dx[2];
1312     const double V10=((f_011[i]-f_010[i])*C5 + (f_101[i]-f_100[i])*C0 + (f_001[i]+f_111[i]-f_000[i]-f_110[i])*C1) / m_dx[2];
1313     const double V11=((f_111[i]-f_110[i])*C5 + (f_001[i]-f_000[i])*C0 + (f_011[i]+f_101[i]-f_010[i]-f_100[i])*C1) / m_dx[2];
1314 caltinay 3913 o[INDEX3(i,0,0,numComp,3)] = V0;
1315     o[INDEX3(i,1,0,numComp,3)] = V4;
1316     o[INDEX3(i,2,0,numComp,3)] = V8;
1317     o[INDEX3(i,0,1,numComp,3)] = V0;
1318     o[INDEX3(i,1,1,numComp,3)] = V5;
1319     o[INDEX3(i,2,1,numComp,3)] = V9;
1320     o[INDEX3(i,0,2,numComp,3)] = V1;
1321     o[INDEX3(i,1,2,numComp,3)] = V4;
1322     o[INDEX3(i,2,2,numComp,3)] = V10;
1323     o[INDEX3(i,0,3,numComp,3)] = V1;
1324     o[INDEX3(i,1,3,numComp,3)] = V5;
1325     o[INDEX3(i,2,3,numComp,3)] = V11;
1326     o[INDEX3(i,0,4,numComp,3)] = V2;
1327     o[INDEX3(i,1,4,numComp,3)] = V6;
1328     o[INDEX3(i,2,4,numComp,3)] = V8;
1329     o[INDEX3(i,0,5,numComp,3)] = V2;
1330     o[INDEX3(i,1,5,numComp,3)] = V7;
1331     o[INDEX3(i,2,5,numComp,3)] = V9;
1332     o[INDEX3(i,0,6,numComp,3)] = V3;
1333     o[INDEX3(i,1,6,numComp,3)] = V6;
1334     o[INDEX3(i,2,6,numComp,3)] = V10;
1335     o[INDEX3(i,0,7,numComp,3)] = V3;
1336     o[INDEX3(i,1,7,numComp,3)] = V7;
1337     o[INDEX3(i,2,7,numComp,3)] = V11;
1338     } // end of component loop i
1339     } // end of k0 loop
1340     } // end of k1 loop
1341     } // end of k2 loop
1342     } // end of parallel section
1343 caltinay 3711 } else if (out.getFunctionSpace().getTypeCode() == ReducedElements) {
1344 caltinay 3760 out.requireWrite();
1345 caltinay 3913 #pragma omp parallel
1346     {
1347     vector<double> f_000(numComp);
1348     vector<double> f_001(numComp);
1349     vector<double> f_010(numComp);
1350     vector<double> f_011(numComp);
1351     vector<double> f_100(numComp);
1352     vector<double> f_101(numComp);
1353     vector<double> f_110(numComp);
1354     vector<double> f_111(numComp);
1355     #pragma omp for
1356 caltinay 4334 for (index_t k2=0; k2 < m_NE[2]; ++k2) {
1357     for (index_t k1=0; k1 < m_NE[1]; ++k1) {
1358     for (index_t k0=0; k0 < m_NE[0]; ++k0) {
1359     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(k0,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1360     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(k0,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1361     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(k0,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1362     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(k0,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1363     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(k0+1,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1364     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(k0+1,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1365     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1366     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1367     double* o = out.getSampleDataRW(INDEX3(k0,k1,k2,m_NE[0],m_NE[1]));
1368 caltinay 3913 for (index_t i=0; i < numComp; ++i) {
1369 caltinay 4375 o[INDEX3(i,0,0,numComp,3)] = (f_100[i]+f_101[i]+f_110[i]+f_111[i]-f_000[i]-f_001[i]-f_010[i]-f_011[i])*C3 / m_dx[0];
1370     o[INDEX3(i,1,0,numComp,3)] = (f_010[i]+f_011[i]+f_110[i]+f_111[i]-f_000[i]-f_001[i]-f_100[i]-f_101[i])*C3 / m_dx[1];
1371     o[INDEX3(i,2,0,numComp,3)] = (f_001[i]+f_011[i]+f_101[i]+f_111[i]-f_000[i]-f_010[i]-f_100[i]-f_110[i])*C3 / m_dx[2];
1372 caltinay 3913 } // end of component loop i
1373     } // end of k0 loop
1374     } // end of k1 loop
1375     } // end of k2 loop
1376     } // end of parallel section
1377 caltinay 3707 } else if (out.getFunctionSpace().getTypeCode() == FaceElements) {
1378 caltinay 3760 out.requireWrite();
1379 caltinay 3722 #pragma omp parallel
1380     {
1381 caltinay 3913 vector<double> f_000(numComp);
1382     vector<double> f_001(numComp);
1383     vector<double> f_010(numComp);
1384     vector<double> f_011(numComp);
1385     vector<double> f_100(numComp);
1386     vector<double> f_101(numComp);
1387     vector<double> f_110(numComp);
1388     vector<double> f_111(numComp);
1389 caltinay 3722 if (m_faceOffset[0] > -1) {
1390     #pragma omp for nowait
1391 caltinay 4334 for (index_t k2=0; k2 < m_NE[2]; ++k2) {
1392     for (index_t k1=0; k1 < m_NE[1]; ++k1) {
1393     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(0,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1394     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(0,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1395     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(0,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1396     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(0,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1397     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(1,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1398     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(1,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1399     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(1,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1400     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(1,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1401     double* o = out.getSampleDataRW(m_faceOffset[0]+INDEX2(k1,k2,m_NE[1]));
1402 caltinay 3722 for (index_t i=0; i < numComp; ++i) {
1403 caltinay 4375 const double V0=((f_010[i]-f_000[i])*C6 + (f_011[i]-f_001[i])*C2) / m_dx[1];
1404     const double V1=((f_010[i]-f_000[i])*C2 + (f_011[i]-f_001[i])*C6) / m_dx[1];
1405     const double V2=((f_001[i]-f_000[i])*C6 + (f_010[i]-f_011[i])*C2) / m_dx[2];
1406     const double V3=((f_001[i]-f_000[i])*C2 + (f_011[i]-f_010[i])*C6) / m_dx[2];
1407     o[INDEX3(i,0,0,numComp,3)] = ((f_100[i]-f_000[i])*C5 + (f_111[i]-f_011[i])*C0 + (f_101[i]+f_110[i]-f_001[i]-f_010[i])*C1) / m_dx[0];
1408 caltinay 3731 o[INDEX3(i,1,0,numComp,3)] = V0;
1409     o[INDEX3(i,2,0,numComp,3)] = V2;
1410 caltinay 4375 o[INDEX3(i,0,1,numComp,3)] = ((f_110[i]-f_010[i])*C5 + (f_101[i]-f_001[i])*C0 + (f_100[i]+f_111[i]-f_000[i]-f_011[i])*C1) / m_dx[0];
1411 caltinay 3731 o[INDEX3(i,1,1,numComp,3)] = V0;
1412     o[INDEX3(i,2,1,numComp,3)] = V3;
1413 caltinay 4375 o[INDEX3(i,0,2,numComp,3)] = ((f_101[i]-f_001[i])*C5 + (f_110[i]-f_010[i])*C0 + (f_100[i]+f_111[i]-f_000[i]-f_011[i])*C1) / m_dx[0];
1414 caltinay 3731 o[INDEX3(i,1,2,numComp,3)] = V1;
1415     o[INDEX3(i,2,2,numComp,3)] = V2;
1416 caltinay 4375 o[INDEX3(i,0,3,numComp,3)] = ((f_111[i]-f_011[i])*C5 + (f_100[i]-f_000[i])*C0 + (f_101[i]+f_110[i]-f_001[i]-f_010[i])*C1) / m_dx[0];
1417 caltinay 3731 o[INDEX3(i,1,3,numComp,3)] = V1;
1418     o[INDEX3(i,2,3,numComp,3)] = V3;
1419 caltinay 3764 } // end of component loop i
1420     } // end of k1 loop
1421     } // end of k2 loop
1422     } // end of face 0
1423 caltinay 3722 if (m_faceOffset[1] > -1) {
1424     #pragma omp for nowait
1425 caltinay 4334 for (index_t k2=0; k2 < m_NE[2]; ++k2) {
1426     for (index_t k1=0; k1 < m_NE[1]; ++k1) {
1427     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(m_NN[0]-2,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1428     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(m_NN[0]-2,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1429     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(m_NN[0]-2,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1430     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(m_NN[0]-2,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1431     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(m_NN[0]-1,k1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1432     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(m_NN[0]-1,k1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1433     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(m_NN[0]-1,k1+1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1434     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(m_NN[0]-1,k1+1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1435     double* o = out.getSampleDataRW(m_faceOffset[1]+INDEX2(k1,k2,m_NE[1]));
1436 caltinay 3722 for (index_t i=0; i < numComp; ++i) {
1437 caltinay 4375 const double V0=((f_110[i]-f_100[i])*C6 + (f_111[i]-f_101[i])*C2) / m_dx[1];
1438     const double V1=((f_110[i]-f_100[i])*C2 + (f_111[i]-f_101[i])*C6) / m_dx[1];
1439     const double V2=((f_101[i]-f_100[i])*C6 + (f_111[i]-f_110[i])*C2) / m_dx[2];
1440     const double V3=((f_101[i]-f_100[i])*C2 + (f_111[i]-f_110[i])*C6) / m_dx[2];
1441     o[INDEX3(i,0,0,numComp,3)] = ((f_100[i]-f_000[i])*C5 + (f_111[i]-f_011[i])*C0 + (f_101[i]+f_110[i]-f_001[i]-f_010[i])*C1) / m_dx[0];
1442 caltinay 3731 o[INDEX3(i,1,0,numComp,3)] = V0;
1443     o[INDEX3(i,2,0,numComp,3)] = V2;
1444 caltinay 4375 o[INDEX3(i,0,1,numComp,3)] = ((f_110[i]-f_010[i])*C5 + (f_101[i]-f_001[i])*C0 + (f_100[i]+f_111[i]-f_000[i]-f_011[i])*C1) / m_dx[0];
1445 caltinay 3731 o[INDEX3(i,1,1,numComp,3)] = V0;
1446     o[INDEX3(i,2,1,numComp,3)] = V3;
1447 caltinay 4375 o[INDEX3(i,0,2,numComp,3)] = ((f_101[i]-f_001[i])*C5 + (f_110[i]-f_010[i])*C0 + (f_100[i]+f_111[i]-f_000[i]-f_011[i])*C1) / m_dx[0];
1448 caltinay 3731 o[INDEX3(i,1,2,numComp,3)] = V1;
1449     o[INDEX3(i,2,2,numComp,3)] = V2;
1450 caltinay 4375 o[INDEX3(i,0,3,numComp,3)] = ((f_111[i]-f_011[i])*C5 + (f_100[i]-f_000[i])*C0 + (f_101[i]+f_110[i]-f_001[i]-f_010[i])*C1) / m_dx[0];
1451 caltinay 3731 o[INDEX3(i,1,3,numComp,3)] = V1;
1452     o[INDEX3(i,2,3,numComp,3)] = V3;
1453 caltinay 3764 } // end of component loop i
1454     } // end of k1 loop
1455     } // end of k2 loop
1456     } // end of face 1
1457 caltinay 3722 if (m_faceOffset[2] > -1) {
1458     #pragma omp for nowait
1459 caltinay 4334 for (index_t k2=0; k2 < m_NE[2]; ++k2) {
1460     for (index_t k0=0; k0 < m_NE[0]; ++k0) {
1461     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(k0,0,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1462     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(k0,0,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1463     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(k0,1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1464     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(k0,1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1465     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(k0+1,0,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1466     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(k0+1,0,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1467     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(k0+1,1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1468     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(k0+1,1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1469     double* o = out.getSampleDataRW(m_faceOffset[2]+INDEX2(k0,k2,m_NE[0]));
1470 caltinay 3722 for (index_t i=0; i < numComp; ++i) {
1471 caltinay 4375 const double V0=((f_100[i]-f_000[i])*C6 + (f_101[i]-f_001[i])*C2) / m_dx[0];
1472     const double V1=((f_001[i]-f_000[i])*C6 + (f_101[i]-f_100[i])*C2) / m_dx[2];
1473     const double V2=((f_001[i]-f_000[i])*C2 + (f_101[i]-f_100[i])*C6) / m_dx[2];
1474 caltinay 3731 o[INDEX3(i,0,0,numComp,3)] = V0;
1475 caltinay 4375 o[INDEX3(i,1,0,numComp,3)] = ((f_010[i]-f_000[i])*C5 + (f_111[i]-f_101[i])*C0 + (f_011[i]+f_110[i]-f_001[i]-f_100[i])*C1) / m_dx[1];
1476 caltinay 3731 o[INDEX3(i,2,0,numComp,3)] = V1;
1477     o[INDEX3(i,0,1,numComp,3)] = V0;
1478 caltinay 4375 o[INDEX3(i,1,1,numComp,3)] = ((f_110[i]-f_100[i])*C5 + (f_011[i]-f_001[i])*C0 + (f_010[i]+f_111[i]-f_000[i]-f_101[i])*C1) / m_dx[1];
1479 caltinay 3731 o[INDEX3(i,2,1,numComp,3)] = V2;
1480     o[INDEX3(i,0,2,numComp,3)] = V0;
1481 caltinay 4375 o[INDEX3(i,1,2,numComp,3)] = ((f_011[i]-f_001[i])*C5 + (f_110[i]-f_100[i])*C0 + (f_010[i]+f_111[i]-f_000[i]-f_101[i])*C1) / m_dx[1];
1482 caltinay 3731 o[INDEX3(i,2,2,numComp,3)] = V1;
1483     o[INDEX3(i,0,3,numComp,3)] = V0;
1484 caltinay 4375 o[INDEX3(i,1,3,numComp,3)] = ((f_111[i]-f_101[i])*C5 + (f_010[i]-f_000[i])*C0 + (f_011[i]+f_110[i]-f_001[i]-f_100[i])*C1) / m_dx[1];
1485 caltinay 3731 o[INDEX3(i,2,3,numComp,3)] = V2;
1486 caltinay 3764 } // end of component loop i
1487     } // end of k0 loop
1488     } // end of k2 loop
1489     } // end of face 2
1490 caltinay 3722 if (m_faceOffset[3] > -1) {
1491     #pragma omp for nowait
1492 caltinay 4334 for (index_t k2=0; k2 < m_NE[2]; ++k2) {
1493     for (index_t k0=0; k0 < m_NE[0]; ++k0) {
1494     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(k0,m_NN[1]-2,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1495     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(k0,m_NN[1]-2,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1496     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(k0,m_NN[1]-1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1497     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(k0,m_NN[1]-1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1498     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(k0+1,m_NN[1]-2,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1499     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(k0+1,m_NN[1]-2,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1500     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(k0+1,m_NN[1]-1,k2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1501     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(k0+1,m_NN[1]-1,k2+1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1502     double* o = out.getSampleDataRW(m_faceOffset[3]+INDEX2(k0,k2,m_NE[0]));
1503 caltinay 3722 for (index_t i=0; i < numComp; ++i) {
1504 caltinay 4375 const double V0=((f_110[i]-f_010[i])*C6 + (f_111[i]-f_011[i])*C2) / m_dx[0];
1505     const double V1=((f_110[i]-f_010[i])*C2 + (f_111[i]-f_011[i])*C6) / m_dx[0];
1506     const double V2=((f_011[i]-f_010[i])*C6 + (f_111[i]-f_110[i])*C2) / m_dx[2];
1507     const double V3=((f_011[i]-f_010[i])*C2 + (f_111[i]-f_110[i])*C6) / m_dx[2];
1508 caltinay 3731 o[INDEX3(i,0,0,numComp,3)] = V0;
1509 caltinay 4375 o[INDEX3(i,1,0,numComp,3)] = ((f_010[i]-f_000[i])*C5 + (f_111[i]-f_101[i])*C0 + (f_011[i]+f_110[i]-f_001[i]-f_100[i])*C1) / m_dx[1];
1510 caltinay 3731 o[INDEX3(i,2,0,numComp,3)] = V2;
1511     o[INDEX3(i,0,1,numComp,3)] = V0;
1512 caltinay 4375 o[INDEX3(i,1,1,numComp,3)] = ((f_110[i]-f_100[i])*C5 + (f_011[i]-f_001[i])*C0 + (f_010[i]+f_111[i]-f_000[i]-f_101[i])*C1) / m_dx[1];
1513 caltinay 3731 o[INDEX3(i,2,1,numComp,3)] = V3;
1514     o[INDEX3(i,0,2,numComp,3)] = V1;
1515 caltinay 4375 o[INDEX3(i,1,2,numComp,3)] = ((f_011[i]-f_001[i])*C5 + (f_110[i]-f_100[i])*C0 + (f_010[i]+f_111[i]-f_000[i]-f_101[i])*C1) / m_dx[1];
1516 caltinay 3731 o[INDEX3(i,2,2,numComp,3)] = V2;
1517     o[INDEX3(i,0,3,numComp,3)] = V1;
1518 caltinay 4375 o[INDEX3(i,1,3,numComp,3)] = ((f_111[i]-f_101[i])*C5 + (f_010[i]-f_000[i])*C0 + (f_011[i]+f_110[i]-f_001[i]-f_100[i])*C1) / m_dx[1];
1519 caltinay 3731 o[INDEX3(i,2,3,numComp,3)] = V3;
1520 caltinay 3764 } // end of component loop i
1521     } // end of k0 loop
1522     } // end of k2 loop
1523     } // end of face 3
1524 caltinay 3722 if (m_faceOffset[4] > -1) {
1525     #pragma omp for nowait
1526 caltinay 4334 for (index_t k1=0; k1 < m_NE[1]; ++k1) {
1527     for (index_t k0=0; k0 < m_NE[0]; ++k0) {
1528     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(k0,k1,0, m_NN[0],m_NN[1])), numComp*sizeof(double));
1529     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(k0,k1,1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1530     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(k0,k1+1,0, m_NN[0],m_NN[1])), numComp*sizeof(double));
1531     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(k0,k1+1,1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1532     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(k0+1,k1,0, m_NN[0],m_NN[1])), numComp*sizeof(double));
1533     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(k0+1,k1,1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1534     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,0, m_NN[0],m_NN[1])), numComp*sizeof(double));
1535     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1536     double* o = out.getSampleDataRW(m_faceOffset[4]+INDEX2(k0,k1,m_NE[0]));
1537 caltinay 3722 for (index_t i=0; i < numComp; ++i) {
1538 caltinay 4375 const double V0=((f_100[i]-f_000[i])*C6 + (f_110[i]-f_010[i])*C2) / m_dx[0];
1539     const double V1=((f_100[i]-f_000[i])*C2 + (f_110[i]-f_010[i])*C6) / m_dx[0];
1540     const double V2=((f_010[i]-f_000[i])*C6 + (f_110[i]-f_100[i])*C2) / m_dx[1];
1541     const double V3=((f_010[i]-f_000[i])*C2 + (f_110[i]-f_100[i])*C6) / m_dx[1];
1542 caltinay 3731 o[INDEX3(i,0,0,numComp,3)] = V0;
1543     o[INDEX3(i,1,0,numComp,3)] = V2;
1544 caltinay 4375 o[INDEX3(i,2,0,numComp,3)] = ((f_001[i]-f_000[i])*C5 + (f_111[i]-f_110[i])*C0 + (f_011[i]+f_101[i]-f_010[i]-f_100[i])*C1) / m_dx[2];
1545 caltinay 3731 o[INDEX3(i,0,1,numComp,3)] = V0;
1546     o[INDEX3(i,1,1,numComp,3)] = V3;
1547 caltinay 4375 o[INDEX3(i,2,1,numComp,3)] = ((f_101[i]-f_100[i])*C5 + (f_011[i]-f_010[i])*C0 + (f_001[i]+f_111[i]-f_000[i]-f_110[i])*C1) / m_dx[2];
1548 caltinay 3731 o[INDEX3(i,0,2,numComp,3)] = V1;
1549     o[INDEX3(i,1,2,numComp,3)] = V2;
1550 caltinay 4375 o[INDEX3(i,2,2,numComp,3)] = ((f_011[i]-f_010[i])*C5 + (f_101[i]-f_100[i])*C0 + (f_001[i]+f_111[i]-f_000[i]-f_110[i])*C1) / m_dx[2];
1551 caltinay 3731 o[INDEX3(i,0,3,numComp,3)] = V1;
1552     o[INDEX3(i,1,3,numComp,3)] = V3;
1553 caltinay 4375 o[INDEX3(i,2,3,numComp,3)] = ((f_111[i]-f_110[i])*C5 + (f_001[i]-f_000[i])*C0 + (f_011[i]+f_101[i]-f_010[i]-f_100[i])*C1) / m_dx[2];
1554 caltinay 3764 } // end of component loop i
1555     } // end of k0 loop
1556     } // end of k1 loop
1557     } // end of face 4
1558 caltinay 3722 if (m_faceOffset[5] > -1) {
1559     #pragma omp for nowait
1560 caltinay 4334 for (index_t k1=0; k1 < m_NE[1]; ++k1) {
1561     for (index_t k0=0; k0 < m_NE[0]; ++k0) {
1562     memcpy(&f_000[0], in.getSampleDataRO(INDEX3(k0,k1,m_NN[2]-2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1563     memcpy(&f_001[0], in.getSampleDataRO(INDEX3(k0,k1,m_NN[2]-1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1564     memcpy(&f_010[0], in.getSampleDataRO(INDEX3(k0,k1+1,m_NN[2]-2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1565     memcpy(&f_011[0], in.getSampleDataRO(INDEX3(k0,k1+1,m_NN[2]-1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1566     memcpy(&f_100[0], in.getSampleDataRO(INDEX3(k0+1,k1,m_NN[2]-2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1567     memcpy(&f_101[0], in.getSampleDataRO(INDEX3(k0+1,k1,m_NN[2]-1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1568     memcpy(&f_110[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,m_NN[2]-2, m_NN[0],m_NN[1])), numComp*sizeof(double));
1569     memcpy(&f_111[0], in.getSampleDataRO(INDEX3(k0+1,k1+1,m_NN[2]-1, m_NN[0],m_NN[1])), numComp*sizeof(double));
1570     double* o = out.getSampleDataRW(m_faceOffset[5]+INDEX2(k0,k1,m_NE[0]));
1571 caltinay 3722 for (index_t i=0; i < numComp; ++i) {
1572 caltinay 4375 const double V0=((f_101[i]-f_001[i])*C6 + (f_111[i]-f_011[i])*C2) / m_dx[0];
1573     const double V1=((f_101[i]-f_001[i])*C2 + (f_111[i]-f_011[i])*C6) / m_dx[0];
1574     const double V2=((f_011[i]-f_001[i])*C6 + (f_111[i]-f_101[i])*C2) / m_dx[1];
1575     const double V3=((f_011[i]-f_001[i])*C2 + (f_111[i]-f_101[i])*C6) / m_dx[1];
1576 caltinay 3731 o[INDEX3(i,0,0,numComp,3)] = V0;
1577     o[INDEX3(i,1,0,numComp,3)] = V2;
1578 caltinay 4375 o[INDEX3(i,2,0,numComp,3)] = ((f_001[i]-f_000[i])*C5 + (f_111[i]-f_110[i])*C0 + (f_011[i]+f_101[i]-f_010[i]-f_100[i])*C1) / m_dx[2];
1579 caltinay 3731 o[INDEX3(i,0,1,numComp,3)] = V0;
1580     o[INDEX3(i,1,1,numComp,3)] = V3;
1581 caltinay 4375 o[INDEX3(i,2,1,numComp,3)] = ((f_011[i]-f_010[i])*C0 + (f_101[i]-f_100[i])*C5 + (f_001[i]+f_111[i]-f_000[i]-f_110[i])*C1) / m_dx[2];
1582 caltinay 3731 o[INDEX3(i,0,2,numComp,3)] = V1;
1583     o[INDEX3(i,1,2,numComp,3)] = V2;
1584 caltinay 4375 o[INDEX3(i,2,2,numComp,3)] = ((f_011[i]-f_010[i])*C5 + (f_101[i]-f_100[i])*C0 + (f_001[i]+f_111[i]-f_000[i]-f_110[i])*C1) / m_dx[2];
1585 caltinay 3731 o[INDEX3(i,0,3,numComp,3)] = V1;
1586     o[INDEX3(i,1,3,numComp,3)] = V3;
1587 caltinay 4375 o[INDEX3(i,2,3,numComp,3)] = ((f_001[i]-f_000[i])*C0 + (f_111[i]-f_110[i])*C5 + (f_011[i]+f_101[i]-f_010[i]-f_100[i])*C1) / m_dx[2];
1588 caltinay 3764 } // end of component loop i
1589     } // end of k0 loop
1590