1 |
#define _FILE_OFFSET_BITS 64 |
2 |
|
3 |
#include <string.h> |
4 |
#include <iostream> |
5 |
#include <fstream> |
6 |
|
7 |
#ifdef IS_MPI |
8 |
#include <mpi.h> |
9 |
#include "mpiSimulation.hpp" |
10 |
|
11 |
namespace dWrite{ |
12 |
void DieDieDie( void ); |
13 |
} |
14 |
|
15 |
using namespace dWrite; |
16 |
#endif //is_mpi |
17 |
|
18 |
#include "ReadWrite.hpp" |
19 |
#include "simError.h" |
20 |
|
21 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
22 |
|
23 |
entry_plug = the_entry_plug; |
24 |
|
25 |
#ifdef IS_MPI |
26 |
if(worldRank == 0 ){ |
27 |
#endif // is_mpi |
28 |
|
29 |
strcpy( outName, entry_plug->sampleName ); |
30 |
|
31 |
outFile.open(outName, ios::out | ios::trunc ); |
32 |
|
33 |
if( !outFile ){ |
34 |
|
35 |
sprintf( painCave.errMsg, |
36 |
"Could not open \"%s\" for dump output.\n", |
37 |
outName); |
38 |
painCave.isFatal = 1; |
39 |
simError(); |
40 |
} |
41 |
|
42 |
//outFile.setf( ios::scientific ); |
43 |
|
44 |
#ifdef IS_MPI |
45 |
} |
46 |
|
47 |
sprintf( checkPointMsg, |
48 |
"Sucessfully opened output file for dumping.\n"); |
49 |
MPIcheckPoint(); |
50 |
#endif // is_mpi |
51 |
} |
52 |
|
53 |
DumpWriter::~DumpWriter( ){ |
54 |
|
55 |
#ifdef IS_MPI |
56 |
if(worldRank == 0 ){ |
57 |
#endif // is_mpi |
58 |
|
59 |
outFile.close(); |
60 |
|
61 |
#ifdef IS_MPI |
62 |
} |
63 |
#endif // is_mpi |
64 |
} |
65 |
|
66 |
void DumpWriter::writeDump( double currentTime ){ |
67 |
|
68 |
const int BUFFERSIZE = 2000; |
69 |
const int MINIBUFFERSIZE = 10; |
70 |
|
71 |
char tempBuffer[BUFFERSIZE]; |
72 |
char writeLine[BUFFERSIZE]; |
73 |
|
74 |
int i; |
75 |
#ifdef IS_MPI |
76 |
int j, which_node, done, which_atom, local_index; |
77 |
double atomTransData[6]; |
78 |
double atomOrientData[7]; |
79 |
int isDirectional; |
80 |
char* atomTypeString; |
81 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
82 |
int me; |
83 |
int atomTypeTag; |
84 |
int atomIsDirectionalTag; |
85 |
int atomTransDataTag; |
86 |
int atomOrientDataTag; |
87 |
#else //is_mpi |
88 |
int nAtoms = entry_plug->n_atoms; |
89 |
#endif //is_mpi |
90 |
|
91 |
double q[4]; |
92 |
DirectionalAtom* dAtom; |
93 |
Atom** atoms = entry_plug->atoms; |
94 |
double pos[3], vel[3]; |
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|
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// write current frame to the eor file |
97 |
|
98 |
this->writeFinal( currentTime ); |
99 |
|
100 |
#ifndef IS_MPI |
101 |
|
102 |
outFile << nAtoms << "\n"; |
103 |
|
104 |
outFile << currentTime << ";\t" |
105 |
<< entry_plug->Hmat[0][0] << "\t" |
106 |
<< entry_plug->Hmat[1][0] << "\t" |
107 |
<< entry_plug->Hmat[2][0] << ";\t" |
108 |
|
109 |
<< entry_plug->Hmat[0][1] << "\t" |
110 |
<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
112 |
|
113 |
<< entry_plug->Hmat[0][2] << "\t" |
114 |
<< entry_plug->Hmat[1][2] << "\t" |
115 |
<< entry_plug->Hmat[2][2] << ";"; |
116 |
//write out additional parameters, such as chi and eta |
117 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
118 |
outFile << endl; |
119 |
|
120 |
for( i=0; i<nAtoms; i++ ){ |
121 |
|
122 |
atoms[i]->getPos(pos); |
123 |
atoms[i]->getVel(vel); |
124 |
|
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sprintf( tempBuffer, |
126 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
135 |
|
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if( atoms[i]->isDirectional() ){ |
137 |
|
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dAtom = (DirectionalAtom *)atoms[i]; |
139 |
dAtom->getQ( q ); |
140 |
|
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sprintf( tempBuffer, |
142 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
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q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
148 |
dAtom->getJy(), |
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dAtom->getJz()); |
150 |
strcat( writeLine, tempBuffer ); |
151 |
} |
152 |
else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
154 |
|
155 |
outFile << writeLine; |
156 |
} |
157 |
outFile.flush(); |
158 |
|
159 |
#else // is_mpi |
160 |
|
161 |
// first thing first, suspend fatalities. |
162 |
painCave.isEventLoop = 1; |
163 |
|
164 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
165 |
int haveError; |
166 |
|
167 |
MPI_Status istatus; |
168 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
169 |
|
170 |
// write out header and node 0's coordinates |
171 |
|
172 |
if( worldRank == 0 ){ |
173 |
outFile << mpiSim->getTotAtoms() << "\n"; |
174 |
|
175 |
outFile << currentTime << ";\t" |
176 |
<< entry_plug->Hmat[0][0] << "\t" |
177 |
<< entry_plug->Hmat[1][0] << "\t" |
178 |
<< entry_plug->Hmat[2][0] << ";\t" |
179 |
|
180 |
<< entry_plug->Hmat[0][1] << "\t" |
181 |
<< entry_plug->Hmat[1][1] << "\t" |
182 |
<< entry_plug->Hmat[2][1] << ";\t" |
183 |
|
184 |
<< entry_plug->Hmat[0][2] << "\t" |
185 |
<< entry_plug->Hmat[1][2] << "\t" |
186 |
<< entry_plug->Hmat[2][2] << ";"; |
187 |
|
188 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
189 |
outFile << endl; |
190 |
outFile.flush(); |
191 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
192 |
// Get the Node number which has this atom; |
193 |
|
194 |
which_node = AtomToProcMap[i]; |
195 |
|
196 |
if (which_node != 0) { |
197 |
|
198 |
atomTypeTag = 4*i; |
199 |
atomIsDirectionalTag = 4*i + 1; |
200 |
atomTransDataTag = 4*i + 2; |
201 |
atomOrientDataTag = 4*i + 3; |
202 |
|
203 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
204 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
205 |
|
206 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
207 |
|
208 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
209 |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
210 |
|
211 |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
212 |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
213 |
|
214 |
if (isDirectional) { |
215 |
|
216 |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
217 |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
218 |
|
219 |
} |
220 |
|
221 |
} else { |
222 |
|
223 |
haveError = 0; |
224 |
which_atom = i; |
225 |
local_index=-1; |
226 |
|
227 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
228 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
229 |
} |
230 |
|
231 |
if (local_index != -1) { |
232 |
|
233 |
atomTypeString = atoms[local_index]->getType(); |
234 |
|
235 |
atoms[local_index]->getPos(pos); |
236 |
atoms[local_index]->getVel(vel); |
237 |
|
238 |
atomTransData[0] = pos[0]; |
239 |
atomTransData[1] = pos[1]; |
240 |
atomTransData[2] = pos[2]; |
241 |
|
242 |
atomTransData[3] = vel[0]; |
243 |
atomTransData[4] = vel[1]; |
244 |
atomTransData[5] = vel[2]; |
245 |
|
246 |
isDirectional = 0; |
247 |
|
248 |
if( atoms[local_index]->isDirectional() ){ |
249 |
|
250 |
isDirectional = 1; |
251 |
|
252 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
253 |
dAtom->getQ( q ); |
254 |
|
255 |
atomOrientData[0] = q[0]; |
256 |
atomOrientData[1] = q[1]; |
257 |
atomOrientData[2] = q[2]; |
258 |
atomOrientData[3] = q[3]; |
259 |
|
260 |
atomOrientData[4] = dAtom->getJx(); |
261 |
atomOrientData[5] = dAtom->getJy(); |
262 |
atomOrientData[6] = dAtom->getJz(); |
263 |
} |
264 |
|
265 |
} else { |
266 |
sprintf(painCave.errMsg, |
267 |
"Atom %d not found on processor %d\n", |
268 |
i, worldRank ); |
269 |
haveError= 1; |
270 |
simError(); |
271 |
} |
272 |
|
273 |
if(haveError) DieDieDie(); |
274 |
|
275 |
// If we've survived to here, format the line: |
276 |
|
277 |
sprintf( tempBuffer, |
278 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
279 |
atomTypeString, |
280 |
atomTransData[0], |
281 |
atomTransData[1], |
282 |
atomTransData[2], |
283 |
atomTransData[3], |
284 |
atomTransData[4], |
285 |
atomTransData[5]); |
286 |
|
287 |
strcpy( writeLine, tempBuffer ); |
288 |
|
289 |
if (isDirectional) { |
290 |
|
291 |
sprintf( tempBuffer, |
292 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
293 |
atomOrientData[0], |
294 |
atomOrientData[1], |
295 |
atomOrientData[2], |
296 |
atomOrientData[3], |
297 |
atomOrientData[4], |
298 |
atomOrientData[5], |
299 |
atomOrientData[6]); |
300 |
strcat( writeLine, tempBuffer ); |
301 |
|
302 |
} else { |
303 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
304 |
} |
305 |
|
306 |
outFile << writeLine; |
307 |
outFile.flush(); |
308 |
} |
309 |
} |
310 |
|
311 |
outFile.flush(); |
312 |
sprintf( checkPointMsg, |
313 |
"Sucessfully took a dump.\n"); |
314 |
MPIcheckPoint(); |
315 |
|
316 |
} else { |
317 |
|
318 |
// worldRank != 0, so I'm a remote node. |
319 |
|
320 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
321 |
|
322 |
// Am I the node which has this atom? |
323 |
|
324 |
if (AtomToProcMap[i] == worldRank) { |
325 |
|
326 |
local_index=-1; |
327 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
328 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
329 |
} |
330 |
if (local_index != -1) { |
331 |
|
332 |
atomTypeString = atoms[local_index]->getType(); |
333 |
|
334 |
atoms[local_index]->getPos(pos); |
335 |
atoms[local_index]->getVel(vel); |
336 |
|
337 |
atomTransData[0] = pos[0]; |
338 |
atomTransData[1] = pos[1]; |
339 |
atomTransData[2] = pos[2]; |
340 |
|
341 |
atomTransData[3] = vel[0]; |
342 |
atomTransData[4] = vel[1]; |
343 |
atomTransData[5] = vel[2]; |
344 |
|
345 |
isDirectional = 0; |
346 |
|
347 |
if( atoms[local_index]->isDirectional() ){ |
348 |
|
349 |
isDirectional = 1; |
350 |
|
351 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
352 |
dAtom->getQ( q ); |
353 |
|
354 |
atomOrientData[0] = q[0]; |
355 |
atomOrientData[1] = q[1]; |
356 |
atomOrientData[2] = q[2]; |
357 |
atomOrientData[3] = q[3]; |
358 |
|
359 |
atomOrientData[4] = dAtom->getJx(); |
360 |
atomOrientData[5] = dAtom->getJy(); |
361 |
atomOrientData[6] = dAtom->getJz(); |
362 |
} |
363 |
|
364 |
} else { |
365 |
sprintf(painCave.errMsg, |
366 |
"Atom %d not found on processor %d\n", |
367 |
i, worldRank ); |
368 |
haveError= 1; |
369 |
simError(); |
370 |
} |
371 |
|
372 |
// I've survived this far, so send off the data! |
373 |
|
374 |
atomTypeTag = 4*i; |
375 |
atomIsDirectionalTag = 4*i + 1; |
376 |
atomTransDataTag = 4*i + 2; |
377 |
atomOrientDataTag = 4*i + 3; |
378 |
|
379 |
|
380 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
381 |
|
382 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
383 |
atomTypeTag, MPI_COMM_WORLD); |
384 |
|
385 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
386 |
atomIsDirectionalTag, MPI_COMM_WORLD); |
387 |
|
388 |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
389 |
atomTransDataTag, MPI_COMM_WORLD); |
390 |
|
391 |
if (isDirectional) { |
392 |
|
393 |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
394 |
atomOrientDataTag, MPI_COMM_WORLD); |
395 |
|
396 |
} |
397 |
|
398 |
} |
399 |
} |
400 |
|
401 |
sprintf( checkPointMsg, |
402 |
"Sucessfully took a dump.\n"); |
403 |
MPIcheckPoint(); |
404 |
|
405 |
} |
406 |
|
407 |
painCave.isEventLoop = 0; |
408 |
|
409 |
#endif // is_mpi |
410 |
} |
411 |
|
412 |
void DumpWriter::writeFinal(double finalTime){ |
413 |
|
414 |
char finalName[500]; |
415 |
ofstream finalOut; |
416 |
|
417 |
const int BUFFERSIZE = 2000; |
418 |
const int MINIBUFFERSIZE = 10; |
419 |
char tempBuffer[BUFFERSIZE]; |
420 |
char writeLine[BUFFERSIZE]; |
421 |
|
422 |
double q[4]; |
423 |
DirectionalAtom* dAtom; |
424 |
Atom** atoms = entry_plug->atoms; |
425 |
int i; |
426 |
#ifdef IS_MPI |
427 |
int j, which_node, done, which_atom, local_index; |
428 |
double atomTransData[6]; |
429 |
double atomOrientData[7]; |
430 |
int isDirectional; |
431 |
char* atomTypeString; |
432 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
433 |
int atomTypeTag; |
434 |
int atomIsDirectionalTag; |
435 |
int atomTransDataTag; |
436 |
int atomOrientDataTag; |
437 |
#else //is_mpi |
438 |
int nAtoms = entry_plug->n_atoms; |
439 |
#endif //is_mpi |
440 |
|
441 |
double pos[3], vel[3]; |
442 |
|
443 |
#ifdef IS_MPI |
444 |
if(worldRank == 0 ){ |
445 |
#endif // is_mpi |
446 |
|
447 |
strcpy( finalName, entry_plug->finalName ); |
448 |
|
449 |
finalOut.open( finalName, ios::out | ios::trunc ); |
450 |
if( !finalOut ){ |
451 |
sprintf( painCave.errMsg, |
452 |
"Could not open \"%s\" for final dump output.\n", |
453 |
finalName ); |
454 |
painCave.isFatal = 1; |
455 |
simError(); |
456 |
} |
457 |
|
458 |
// finalOut.setf( ios::scientific ); |
459 |
|
460 |
#ifdef IS_MPI |
461 |
} |
462 |
|
463 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
464 |
MPIcheckPoint(); |
465 |
|
466 |
#endif //is_mpi |
467 |
|
468 |
|
469 |
#ifndef IS_MPI |
470 |
|
471 |
finalOut << nAtoms << "\n"; |
472 |
|
473 |
finalOut << finalTime << ";\t" |
474 |
<< entry_plug->Hmat[0][0] << "\t" |
475 |
<< entry_plug->Hmat[1][0] << "\t" |
476 |
<< entry_plug->Hmat[2][0] << ";\t" |
477 |
|
478 |
<< entry_plug->Hmat[0][1] << "\t" |
479 |
<< entry_plug->Hmat[1][1] << "\t" |
480 |
<< entry_plug->Hmat[2][1] << ";\t" |
481 |
|
482 |
<< entry_plug->Hmat[0][2] << "\t" |
483 |
<< entry_plug->Hmat[1][2] << "\t" |
484 |
<< entry_plug->Hmat[2][2] << ";"; |
485 |
|
486 |
//write out additional parameters, such as chi and eta |
487 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
488 |
finalOut << endl; |
489 |
|
490 |
for( i=0; i<nAtoms; i++ ){ |
491 |
|
492 |
atoms[i]->getPos(pos); |
493 |
atoms[i]->getVel(vel); |
494 |
|
495 |
sprintf( tempBuffer, |
496 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
497 |
atoms[i]->getType(), |
498 |
pos[0], |
499 |
pos[1], |
500 |
pos[2], |
501 |
vel[0], |
502 |
vel[1], |
503 |
vel[2]); |
504 |
strcpy( writeLine, tempBuffer ); |
505 |
|
506 |
if( atoms[i]->isDirectional() ){ |
507 |
|
508 |
dAtom = (DirectionalAtom *)atoms[i]; |
509 |
dAtom->getQ( q ); |
510 |
|
511 |
sprintf( tempBuffer, |
512 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
513 |
q[0], |
514 |
q[1], |
515 |
q[2], |
516 |
q[3], |
517 |
dAtom->getJx(), |
518 |
dAtom->getJy(), |
519 |
dAtom->getJz()); |
520 |
strcat( writeLine, tempBuffer ); |
521 |
} |
522 |
else |
523 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
524 |
|
525 |
finalOut << writeLine; |
526 |
} |
527 |
finalOut.flush(); |
528 |
finalOut.close(); |
529 |
|
530 |
#else // is_mpi |
531 |
|
532 |
// first thing first, suspend fatalities. |
533 |
painCave.isEventLoop = 1; |
534 |
|
535 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
536 |
int haveError; |
537 |
|
538 |
MPI_Status istatus; |
539 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
540 |
|
541 |
// write out header and node 0's coordinates |
542 |
|
543 |
if( worldRank == 0 ){ |
544 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
545 |
|
546 |
finalOut << finalTime << ";\t" |
547 |
<< entry_plug->Hmat[0][0] << "\t" |
548 |
<< entry_plug->Hmat[1][0] << "\t" |
549 |
<< entry_plug->Hmat[2][0] << ";\t" |
550 |
|
551 |
<< entry_plug->Hmat[0][1] << "\t" |
552 |
<< entry_plug->Hmat[1][1] << "\t" |
553 |
<< entry_plug->Hmat[2][1] << ";\t" |
554 |
|
555 |
<< entry_plug->Hmat[0][2] << "\t" |
556 |
<< entry_plug->Hmat[1][2] << "\t" |
557 |
<< entry_plug->Hmat[2][2] << ";"; |
558 |
|
559 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
560 |
finalOut << endl; |
561 |
finalOut.flush(); |
562 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
563 |
// Get the Node number which has this atom; |
564 |
|
565 |
which_node = AtomToProcMap[i]; |
566 |
|
567 |
if (which_node != 0) { |
568 |
|
569 |
atomTypeTag = 4*i; |
570 |
atomIsDirectionalTag = 4*i + 1; |
571 |
atomTransDataTag = 4*i + 2; |
572 |
atomOrientDataTag = 4*i + 3; |
573 |
|
574 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
575 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
576 |
|
577 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
578 |
|
579 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
580 |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
581 |
|
582 |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
583 |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
584 |
|
585 |
if (isDirectional) { |
586 |
|
587 |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
588 |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
589 |
|
590 |
} |
591 |
|
592 |
} else { |
593 |
|
594 |
haveError = 0; |
595 |
which_atom = i; |
596 |
local_index=-1; |
597 |
|
598 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
599 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
600 |
} |
601 |
|
602 |
if (local_index != -1) { |
603 |
|
604 |
atomTypeString = atoms[local_index]->getType(); |
605 |
|
606 |
atoms[local_index]->getPos(pos); |
607 |
atoms[local_index]->getVel(vel); |
608 |
|
609 |
atomTransData[0] = pos[0]; |
610 |
atomTransData[1] = pos[1]; |
611 |
atomTransData[2] = pos[2]; |
612 |
|
613 |
atomTransData[3] = vel[0]; |
614 |
atomTransData[4] = vel[1]; |
615 |
atomTransData[5] = vel[2]; |
616 |
|
617 |
isDirectional = 0; |
618 |
|
619 |
if( atoms[local_index]->isDirectional() ){ |
620 |
|
621 |
isDirectional = 1; |
622 |
|
623 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
624 |
dAtom->getQ( q ); |
625 |
|
626 |
atomOrientData[0] = q[0]; |
627 |
atomOrientData[1] = q[1]; |
628 |
atomOrientData[2] = q[2]; |
629 |
atomOrientData[3] = q[3]; |
630 |
|
631 |
atomOrientData[4] = dAtom->getJx(); |
632 |
atomOrientData[5] = dAtom->getJy(); |
633 |
atomOrientData[6] = dAtom->getJz(); |
634 |
} |
635 |
|
636 |
} else { |
637 |
sprintf(painCave.errMsg, |
638 |
"Atom %d not found on processor %d\n", |
639 |
i, worldRank ); |
640 |
haveError= 1; |
641 |
simError(); |
642 |
} |
643 |
|
644 |
if(haveError) DieDieDie(); |
645 |
|
646 |
// If we've survived to here, format the line: |
647 |
|
648 |
sprintf( tempBuffer, |
649 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
650 |
atomTypeString, |
651 |
atomTransData[0], |
652 |
atomTransData[1], |
653 |
atomTransData[2], |
654 |
atomTransData[3], |
655 |
atomTransData[4], |
656 |
atomTransData[5]); |
657 |
|
658 |
strcpy( writeLine, tempBuffer ); |
659 |
|
660 |
if (isDirectional) { |
661 |
|
662 |
sprintf( tempBuffer, |
663 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
664 |
atomOrientData[0], |
665 |
atomOrientData[1], |
666 |
atomOrientData[2], |
667 |
atomOrientData[3], |
668 |
atomOrientData[4], |
669 |
atomOrientData[5], |
670 |
atomOrientData[6]); |
671 |
strcat( writeLine, tempBuffer ); |
672 |
|
673 |
} else { |
674 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
675 |
} |
676 |
|
677 |
finalOut << writeLine; |
678 |
finalOut.flush(); |
679 |
} |
680 |
} |
681 |
|
682 |
finalOut.flush(); |
683 |
sprintf( checkPointMsg, |
684 |
"Sucessfully took a dump.\n"); |
685 |
MPIcheckPoint(); |
686 |
|
687 |
} else { |
688 |
|
689 |
// worldRank != 0, so I'm a remote node. |
690 |
|
691 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
692 |
|
693 |
// Am I the node which has this atom? |
694 |
|
695 |
if (AtomToProcMap[i] == worldRank) { |
696 |
|
697 |
local_index=-1; |
698 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
699 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
700 |
} |
701 |
if (local_index != -1) { |
702 |
|
703 |
atomTypeString = atoms[local_index]->getType(); |
704 |
|
705 |
atoms[local_index]->getPos(pos); |
706 |
atoms[local_index]->getVel(vel); |
707 |
|
708 |
atomTransData[0] = pos[0]; |
709 |
atomTransData[1] = pos[1]; |
710 |
atomTransData[2] = pos[2]; |
711 |
|
712 |
atomTransData[3] = vel[0]; |
713 |
atomTransData[4] = vel[1]; |
714 |
atomTransData[5] = vel[2]; |
715 |
|
716 |
isDirectional = 0; |
717 |
|
718 |
if( atoms[local_index]->isDirectional() ){ |
719 |
|
720 |
isDirectional = 1; |
721 |
|
722 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
723 |
dAtom->getQ( q ); |
724 |
|
725 |
atomOrientData[0] = q[0]; |
726 |
atomOrientData[1] = q[1]; |
727 |
atomOrientData[2] = q[2]; |
728 |
atomOrientData[3] = q[3]; |
729 |
|
730 |
atomOrientData[4] = dAtom->getJx(); |
731 |
atomOrientData[5] = dAtom->getJy(); |
732 |
atomOrientData[6] = dAtom->getJz(); |
733 |
} |
734 |
|
735 |
} else { |
736 |
sprintf(painCave.errMsg, |
737 |
"Atom %d not found on processor %d\n", |
738 |
i, worldRank ); |
739 |
haveError= 1; |
740 |
simError(); |
741 |
} |
742 |
|
743 |
// I've survived this far, so send off the data! |
744 |
|
745 |
atomTypeTag = 4*i; |
746 |
atomIsDirectionalTag = 4*i + 1; |
747 |
atomTransDataTag = 4*i + 2; |
748 |
atomOrientDataTag = 4*i + 3; |
749 |
|
750 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
751 |
|
752 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
753 |
atomTypeTag, MPI_COMM_WORLD); |
754 |
|
755 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
756 |
atomIsDirectionalTag, MPI_COMM_WORLD); |
757 |
|
758 |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
759 |
atomTransDataTag, MPI_COMM_WORLD); |
760 |
|
761 |
if (isDirectional) { |
762 |
|
763 |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
764 |
atomOrientDataTag, MPI_COMM_WORLD); |
765 |
|
766 |
} |
767 |
|
768 |
} |
769 |
} |
770 |
|
771 |
sprintf( checkPointMsg, |
772 |
"Sucessfully wrote final file.\n"); |
773 |
MPIcheckPoint(); |
774 |
|
775 |
} |
776 |
|
777 |
painCave.isEventLoop = 0; |
778 |
|
779 |
if( worldRank == 0 ) finalOut.close(); |
780 |
#endif // is_mpi |
781 |
} |
782 |
|
783 |
|
784 |
|
785 |
#ifdef IS_MPI |
786 |
|
787 |
// a couple of functions to let us escape the write loop |
788 |
|
789 |
void dWrite::DieDieDie( void ){ |
790 |
|
791 |
MPI_Finalize(); |
792 |
exit (0); |
793 |
} |
794 |
|
795 |
#endif //is_mpi |