# | Line 3 | Line 3 | |
---|---|---|
3 | #include <string.h> | |
4 | #include <iostream> | |
5 | #include <fstream> | |
6 | + | #include <algorithm> |
7 | + | #include <utility> |
8 | ||
9 | #ifdef IS_MPI | |
10 | #include <mpi.h> | |
# | Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
28 | if(worldRank == 0 ){ | |
29 | #endif // is_mpi | |
30 | ||
29 | – | strcpy( outName, entry_plug->sampleName ); |
31 | ||
32 | < | outFile.open(outName, ios::out | ios::trunc ); |
32 | > | dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 | ||
34 | < | if( !outFile ){ |
34 | > | if( !dumpFile ){ |
35 | ||
36 | sprintf( painCave.errMsg, | |
37 | "Could not open \"%s\" for dump output.\n", | |
38 | < | outName); |
38 | > | entry_plug->sampleName); |
39 | painCave.isFatal = 1; | |
40 | simError(); | |
41 | } | |
42 | ||
43 | < | //outFile.setf( ios::scientific ); |
43 | > | finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
44 | > | if( !finalOut ){ |
45 | > | sprintf( painCave.errMsg, |
46 | > | "Could not open \"%s\" for final dump output.\n", |
47 | > | entry_plug->finalName ); |
48 | > | painCave.isFatal = 1; |
49 | > | simError(); |
50 | > | } |
51 | ||
52 | #ifdef IS_MPI | |
53 | } | |
54 | ||
55 | + | //sort the local atoms by global index |
56 | + | sortByGlobalIndex(); |
57 | + | |
58 | sprintf( checkPointMsg, | |
59 | "Sucessfully opened output file for dumping.\n"); | |
60 | MPIcheckPoint(); | |
# | Line 56 | Line 67 | DumpWriter::~DumpWriter( ){ | |
67 | if(worldRank == 0 ){ | |
68 | #endif // is_mpi | |
69 | ||
70 | < | outFile.close(); |
70 | > | dumpFile.close(); |
71 | > | finalOut.close(); |
72 | ||
73 | #ifdef IS_MPI | |
74 | } | |
75 | #endif // is_mpi | |
76 | } | |
77 | ||
78 | < | void DumpWriter::writeDump( double currentTime ){ |
78 | > | #ifdef IS_MPI |
79 | ||
80 | + | /** |
81 | + | * A hook function to load balancing |
82 | + | */ |
83 | + | |
84 | + | void DumpWriter::update(){ |
85 | + | sortByGlobalIndex(); |
86 | + | } |
87 | + | |
88 | + | /** |
89 | + | * Auxiliary sorting function |
90 | + | */ |
91 | + | |
92 | + | bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
93 | + | return p1.second < p2.second; |
94 | + | } |
95 | + | |
96 | + | /** |
97 | + | * Sorting the local index by global index |
98 | + | */ |
99 | + | |
100 | + | void DumpWriter::sortByGlobalIndex(){ |
101 | + | Atom** atoms = entry_plug->atoms; |
102 | + | |
103 | + | indexArray.clear(); |
104 | + | |
105 | + | for(int i = 0; i < mpiSim->getMyNlocal();i++) |
106 | + | indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
107 | + | |
108 | + | sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
109 | + | } |
110 | + | #endif |
111 | + | |
112 | + | void DumpWriter::writeDump(double currentTime){ |
113 | + | |
114 | + | vector<ofstream*> fileStreams; |
115 | + | |
116 | + | #ifdef IS_MPI |
117 | + | if(worldRank == 0 ){ |
118 | + | finalOut.seekp(0); |
119 | + | } |
120 | + | #endif // is_mpi |
121 | + | |
122 | + | fileStreams.push_back(&finalOut); |
123 | + | fileStreams.push_back(&dumpFile); |
124 | + | |
125 | + | writeFrame(fileStreams, currentTime); |
126 | + | |
127 | + | } |
128 | + | |
129 | + | void DumpWriter::writeFinal(double currentTime){ |
130 | + | |
131 | + | vector<ofstream*> fileStreams; |
132 | + | |
133 | + | #ifdef IS_MPI |
134 | + | if(worldRank == 0 ){ |
135 | + | finalOut.seekp(0); |
136 | + | } |
137 | + | #endif // is_mpi |
138 | + | |
139 | + | fileStreams.push_back(&finalOut); |
140 | + | writeFrame(fileStreams, currentTime); |
141 | + | |
142 | + | } |
143 | + | |
144 | + | void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
145 | + | |
146 | const int BUFFERSIZE = 2000; | |
147 | const int MINIBUFFERSIZE = 100; | |
148 | ||
149 | char tempBuffer[BUFFERSIZE]; | |
150 | char writeLine[BUFFERSIZE]; | |
151 | ||
152 | < | int i; |
152 | > | int i, k; |
153 | ||
154 | #ifdef IS_MPI | |
155 | ||
# | Line 79 | Line 157 | void DumpWriter::writeDump( double currentTime ){ | |
157 | int myPotato; | |
158 | ||
159 | int nProc; | |
160 | < | int j, which_node, done, which_atom, local_index; |
160 | > | int j, which_node, done, which_atom, local_index, currentIndex; |
161 | double atomData6[6]; | |
162 | double atomData13[13]; | |
163 | int isDirectional; | |
# | Line 95 | Line 173 | void DumpWriter::writeDump( double currentTime ){ | |
173 | Atom** atoms = entry_plug->atoms; | |
174 | double pos[3], vel[3]; | |
175 | ||
98 | – | // write current frame to the eor file |
99 | – | |
100 | – | this->writeFinal( currentTime ); |
101 | – | |
176 | #ifndef IS_MPI | |
177 | < | |
178 | < | outFile << nAtoms << "\n"; |
177 | > | |
178 | > | for(k = 0; k < outFile.size(); k++){ |
179 | > | *outFile[k] << nAtoms << "\n"; |
180 | ||
181 | < | outFile << currentTime << ";\t" |
182 | < | << entry_plug->Hmat[0][0] << "\t" |
183 | < | << entry_plug->Hmat[1][0] << "\t" |
184 | < | << entry_plug->Hmat[2][0] << ";\t" |
181 | > | *outFile[k] << currentTime << ";\t" |
182 | > | << entry_plug->Hmat[0][0] << "\t" |
183 | > | << entry_plug->Hmat[1][0] << "\t" |
184 | > | << entry_plug->Hmat[2][0] << ";\t" |
185 | > | |
186 | > | << entry_plug->Hmat[0][1] << "\t" |
187 | > | << entry_plug->Hmat[1][1] << "\t" |
188 | > | << entry_plug->Hmat[2][1] << ";\t" |
189 | ||
190 | < | << entry_plug->Hmat[0][1] << "\t" |
191 | < | << entry_plug->Hmat[1][1] << "\t" |
192 | < | << entry_plug->Hmat[2][1] << ";\t" |
190 | > | << entry_plug->Hmat[0][2] << "\t" |
191 | > | << entry_plug->Hmat[1][2] << "\t" |
192 | > | << entry_plug->Hmat[2][2] << ";"; |
193 | ||
194 | < | << entry_plug->Hmat[0][2] << "\t" |
195 | < | << entry_plug->Hmat[1][2] << "\t" |
196 | < | << entry_plug->Hmat[2][2] << ";"; |
197 | < | //write out additional parameters, such as chi and eta |
119 | < | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
120 | < | outFile << endl; |
121 | < | |
194 | > | //write out additional parameters, such as chi and eta |
195 | > | *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
196 | > | } |
197 | > | |
198 | for( i=0; i<nAtoms; i++ ){ | |
199 | ||
200 | atoms[i]->getPos(pos); | |
# | Line 154 | Line 230 | void DumpWriter::writeDump( double currentTime ){ | |
230 | else | |
231 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
232 | ||
233 | < | outFile << writeLine; |
233 | > | for(k = 0; k < outFile.size(); k++) |
234 | > | *outFile[k] << writeLine; |
235 | } | |
159 | – | outFile.flush(); |
236 | ||
237 | #else // is_mpi | |
238 | ||
# | Line 184 | Line 260 | void DumpWriter::writeDump( double currentTime ){ | |
260 | nProc = mpiSim->getNumberProcessors(); | |
261 | potatoes = new int[nProc]; | |
262 | ||
263 | + | //write out the comment lines |
264 | for (i = 0; i < nProc; i++) | |
265 | potatoes[i] = 0; | |
266 | ||
267 | < | outFile << mpiSim->getTotAtoms() << "\n"; |
267 | > | for(k = 0; k < outFile.size(); k++){ |
268 | > | *outFile[k] << mpiSim->getTotAtoms() << "\n"; |
269 | ||
270 | < | outFile << currentTime << ";\t" |
271 | < | << entry_plug->Hmat[0][0] << "\t" |
272 | < | << entry_plug->Hmat[1][0] << "\t" |
273 | < | << entry_plug->Hmat[2][0] << ";\t" |
270 | > | *outFile[k] << currentTime << ";\t" |
271 | > | << entry_plug->Hmat[0][0] << "\t" |
272 | > | << entry_plug->Hmat[1][0] << "\t" |
273 | > | << entry_plug->Hmat[2][0] << ";\t" |
274 | ||
275 | < | << entry_plug->Hmat[0][1] << "\t" |
276 | < | << entry_plug->Hmat[1][1] << "\t" |
277 | < | << entry_plug->Hmat[2][1] << ";\t" |
275 | > | << entry_plug->Hmat[0][1] << "\t" |
276 | > | << entry_plug->Hmat[1][1] << "\t" |
277 | > | << entry_plug->Hmat[2][1] << ";\t" |
278 | ||
279 | < | << entry_plug->Hmat[0][2] << "\t" |
280 | < | << entry_plug->Hmat[1][2] << "\t" |
281 | < | << entry_plug->Hmat[2][2] << ";"; |
279 | > | << entry_plug->Hmat[0][2] << "\t" |
280 | > | << entry_plug->Hmat[1][2] << "\t" |
281 | > | << entry_plug->Hmat[2][2] << ";"; |
282 | > | |
283 | > | *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
284 | > | } |
285 | ||
286 | < | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
206 | < | outFile << endl; |
207 | < | outFile.flush(); |
286 | > | currentIndex = 0; |
287 | ||
288 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
289 | ||
# | Line 228 | Line 307 | void DumpWriter::writeDump( double currentTime ){ | |
307 | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, | |
308 | myPotato, MPI_COMM_WORLD, &istatus); | |
309 | ||
231 | – | //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
232 | – | |
233 | – | // Null terminate the atomTypeString just in case: |
234 | – | |
235 | – | //atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
310 | atomTypeString = MPIatomTypeString; | |
311 | ||
312 | myPotato++; | |
# | Line 255 | Line 329 | void DumpWriter::writeDump( double currentTime ){ | |
329 | ||
330 | } else { | |
331 | ||
332 | < | haveError = 0; |
333 | < | which_atom = i; |
260 | < | local_index=-1; |
332 | > | haveError = 0; |
333 | > | which_atom = i; |
334 | ||
335 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
336 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
337 | < | } |
265 | < | |
266 | < | if (local_index != -1) { |
335 | > | local_index = indexArray[currentIndex].first; |
336 | > | |
337 | > | if (which_atom == indexArray[currentIndex].second) { |
338 | ||
339 | atomTypeString = atoms[local_index]->getType(); | |
340 | ||
341 | < | atoms[local_index]->getPos(pos); |
342 | < | atoms[local_index]->getVel(vel); |
341 | > | atoms[local_index]->getPos(pos); |
342 | > | atoms[local_index]->getVel(vel); |
343 | ||
344 | atomData6[0] = pos[0]; | |
345 | atomData6[1] = pos[1]; | |
# | Line 301 | Line 372 | void DumpWriter::writeDump( double currentTime ){ | |
372 | } | |
373 | ||
374 | } else { | |
375 | < | sprintf(painCave.errMsg, |
376 | < | "Atom %d not found on processor %d\n", |
377 | < | i, worldRank ); |
378 | < | haveError= 1; |
379 | < | simError(); |
380 | < | } |
375 | > | sprintf(painCave.errMsg, |
376 | > | "Atom %d not found on processor %d\n", |
377 | > | i, worldRank ); |
378 | > | haveError= 1; |
379 | > | simError(); |
380 | > | } |
381 | ||
382 | < | if(haveError) DieDieDie(); |
382 | > | if(haveError) DieDieDie(); |
383 | ||
384 | < | // If we've survived to here, format the line: |
314 | < | |
315 | < | if (!isDirectional) { |
316 | < | |
317 | < | sprintf( tempBuffer, |
318 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
319 | < | atomTypeString, |
320 | < | atomData6[0], |
321 | < | atomData6[1], |
322 | < | atomData6[2], |
323 | < | atomData6[3], |
324 | < | atomData6[4], |
325 | < | atomData6[5]); |
326 | < | |
327 | < | strcpy( writeLine, tempBuffer ); |
328 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
329 | < | |
330 | < | } else { |
331 | < | |
332 | < | sprintf( tempBuffer, |
333 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
334 | < | atomTypeString, |
335 | < | atomData13[0], |
336 | < | atomData13[1], |
337 | < | atomData13[2], |
338 | < | atomData13[3], |
339 | < | atomData13[4], |
340 | < | atomData13[5], |
341 | < | atomData13[6], |
342 | < | atomData13[7], |
343 | < | atomData13[8], |
344 | < | atomData13[9], |
345 | < | atomData13[10], |
346 | < | atomData13[11], |
347 | < | atomData13[12]); |
348 | < | |
349 | < | strcat( writeLine, tempBuffer ); |
350 | < | |
351 | < | } |
352 | < | |
353 | < | outFile << writeLine; |
354 | < | outFile.flush(); |
384 | > | currentIndex ++; |
385 | } | |
386 | < | } |
357 | < | |
358 | < | outFile.flush(); |
359 | < | sprintf( checkPointMsg, |
360 | < | "Sucessfully took a dump.\n"); |
361 | < | MPIcheckPoint(); |
362 | < | delete[] potatoes; |
363 | < | } else { |
364 | < | |
365 | < | // worldRank != 0, so I'm a remote node. |
366 | < | |
367 | < | // Set my magic potato to 0: |
368 | < | |
369 | < | myPotato = 0; |
370 | < | |
371 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
386 | > | // If we've survived to here, format the line: |
387 | ||
388 | < | // Am I the node which has this atom? |
389 | < | |
390 | < | if (AtomToProcMap[i] == worldRank) { |
391 | < | |
392 | < | if (myPotato + 3 >= MAXTAG) { |
393 | < | |
394 | < | // The potato was going to exceed the maximum value, |
395 | < | // so wrap this processor potato back to 0 (and block until |
396 | < | // node 0 says we can go: |
397 | < | |
398 | < | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
384 | < | |
385 | < | } |
386 | < | which_atom = i; |
387 | < | local_index=-1; |
388 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
389 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
390 | < | } |
391 | < | if (local_index != -1) { |
392 | < | |
393 | < | atomTypeString = atoms[local_index]->getType(); |
394 | < | |
395 | < | atoms[local_index]->getPos(pos); |
396 | < | atoms[local_index]->getVel(vel); |
397 | < | |
398 | < | atomData6[0] = pos[0]; |
399 | < | atomData6[1] = pos[1]; |
400 | < | atomData6[2] = pos[2]; |
401 | < | |
402 | < | atomData6[3] = vel[0]; |
403 | < | atomData6[4] = vel[1]; |
404 | < | atomData6[5] = vel[2]; |
405 | < | |
406 | < | isDirectional = 0; |
407 | < | |
408 | < | if( atoms[local_index]->isDirectional() ){ |
409 | < | |
410 | < | isDirectional = 1; |
411 | < | |
412 | < | dAtom = (DirectionalAtom *)atoms[local_index]; |
413 | < | dAtom->getQ( q ); |
414 | < | |
415 | < | for (int j = 0; j < 6 ; j++) |
416 | < | atomData13[j] = atomData6[j]; |
417 | < | |
418 | < | atomData13[6] = q[0]; |
419 | < | atomData13[7] = q[1]; |
420 | < | atomData13[8] = q[2]; |
421 | < | atomData13[9] = q[3]; |
422 | < | |
423 | < | atomData13[10] = dAtom->getJx(); |
424 | < | atomData13[11] = dAtom->getJy(); |
425 | < | atomData13[12] = dAtom->getJz(); |
426 | < | } |
427 | < | |
428 | < | } else { |
429 | < | sprintf(painCave.errMsg, |
430 | < | "Atom %d not found on processor %d\n", |
431 | < | i, worldRank ); |
432 | < | haveError= 1; |
433 | < | simError(); |
434 | < | } |
435 | < | |
436 | < | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
437 | < | |
438 | < | // null terminate the string before sending (just in case): |
439 | < | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
440 | < | |
441 | < | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
442 | < | myPotato, MPI_COMM_WORLD); |
443 | < | |
444 | < | myPotato++; |
445 | < | |
446 | < | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
447 | < | myPotato, MPI_COMM_WORLD); |
448 | < | |
449 | < | myPotato++; |
450 | < | |
451 | < | if (isDirectional) { |
452 | < | |
453 | < | MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
454 | < | myPotato, MPI_COMM_WORLD); |
455 | < | |
456 | < | } else { |
457 | < | |
458 | < | MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
459 | < | myPotato, MPI_COMM_WORLD); |
460 | < | } |
461 | < | |
462 | < | myPotato++; |
463 | < | } |
464 | < | } |
465 | < | |
466 | < | sprintf( checkPointMsg, |
467 | < | "Sucessfully took a dump.\n"); |
468 | < | MPIcheckPoint(); |
469 | < | |
470 | < | } |
471 | < | |
472 | < | #endif // is_mpi |
473 | < | } |
474 | < | |
475 | < | void DumpWriter::writeFinal(double finalTime){ |
476 | < | |
477 | < | char finalName[500]; |
478 | < | ofstream finalOut; |
479 | < | |
480 | < | const int BUFFERSIZE = 2000; |
481 | < | const int MINIBUFFERSIZE = 100; |
482 | < | char tempBuffer[BUFFERSIZE]; |
483 | < | char writeLine[BUFFERSIZE]; |
484 | < | |
485 | < | double q[4]; |
486 | < | DirectionalAtom* dAtom; |
487 | < | Atom** atoms = entry_plug->atoms; |
488 | < | int i; |
489 | < | #ifdef IS_MPI |
490 | < | |
491 | < | int *potatoes; |
492 | < | int myPotato; |
493 | < | |
494 | < | int nProc; |
495 | < | int j, which_node, done, which_atom, local_index; |
496 | < | double atomData6[6]; |
497 | < | double atomData13[13]; |
498 | < | int isDirectional; |
499 | < | char* atomTypeString; |
500 | < | char MPIatomTypeString[MINIBUFFERSIZE]; |
501 | < | |
502 | < | #else //is_mpi |
503 | < | int nAtoms = entry_plug->n_atoms; |
504 | < | #endif //is_mpi |
505 | < | |
506 | < | double pos[3], vel[3]; |
507 | < | |
508 | < | #ifdef IS_MPI |
509 | < | if(worldRank == 0 ){ |
510 | < | #endif // is_mpi |
511 | < | |
512 | < | strcpy( finalName, entry_plug->finalName ); |
513 | < | |
514 | < | finalOut.open( finalName, ios::out | ios::trunc ); |
515 | < | if( !finalOut ){ |
516 | < | sprintf( painCave.errMsg, |
517 | < | "Could not open \"%s\" for final dump output.\n", |
518 | < | finalName ); |
519 | < | painCave.isFatal = 1; |
520 | < | simError(); |
521 | < | } |
522 | < | |
523 | < | // finalOut.setf( ios::scientific ); |
524 | < | |
525 | < | #ifdef IS_MPI |
526 | < | } |
527 | < | |
528 | < | sprintf(checkPointMsg,"Opened file for final configuration\n"); |
529 | < | MPIcheckPoint(); |
530 | < | |
531 | < | #endif //is_mpi |
532 | < | |
533 | < | |
534 | < | #ifndef IS_MPI |
535 | < | |
536 | < | finalOut << nAtoms << "\n"; |
537 | < | |
538 | < | finalOut << finalTime << ";\t" |
539 | < | << entry_plug->Hmat[0][0] << "\t" |
540 | < | << entry_plug->Hmat[1][0] << "\t" |
541 | < | << entry_plug->Hmat[2][0] << ";\t" |
542 | < | |
543 | < | << entry_plug->Hmat[0][1] << "\t" |
544 | < | << entry_plug->Hmat[1][1] << "\t" |
545 | < | << entry_plug->Hmat[2][1] << ";\t" |
546 | < | |
547 | < | << entry_plug->Hmat[0][2] << "\t" |
548 | < | << entry_plug->Hmat[1][2] << "\t" |
549 | < | << entry_plug->Hmat[2][2] << ";"; |
550 | < | |
551 | < | //write out additional parameters, such as chi and eta |
552 | < | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
553 | < | finalOut << endl; |
554 | < | |
555 | < | for( i=0; i<nAtoms; i++ ){ |
556 | < | |
557 | < | atoms[i]->getPos(pos); |
558 | < | atoms[i]->getVel(vel); |
559 | < | |
560 | < | sprintf( tempBuffer, |
561 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
562 | < | atoms[i]->getType(), |
563 | < | pos[0], |
564 | < | pos[1], |
565 | < | pos[2], |
566 | < | vel[0], |
567 | < | vel[1], |
568 | < | vel[2]); |
569 | < | strcpy( writeLine, tempBuffer ); |
570 | < | |
571 | < | if( atoms[i]->isDirectional() ){ |
572 | < | |
573 | < | dAtom = (DirectionalAtom *)atoms[i]; |
574 | < | dAtom->getQ( q ); |
575 | < | |
576 | < | sprintf( tempBuffer, |
577 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
578 | < | q[0], |
579 | < | q[1], |
580 | < | q[2], |
581 | < | q[3], |
582 | < | dAtom->getJx(), |
583 | < | dAtom->getJy(), |
584 | < | dAtom->getJz()); |
585 | < | strcat( writeLine, tempBuffer ); |
586 | < | } |
587 | < | else |
588 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
589 | < | |
590 | < | finalOut << writeLine; |
591 | < | } |
592 | < | finalOut.flush(); |
593 | < | finalOut.close(); |
594 | < | |
595 | < | #else // is_mpi |
596 | < | |
597 | < | /* code to find maximum tag value */ |
598 | < | int *tagub, flag, MAXTAG; |
599 | < | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
600 | < | if (flag) { |
601 | < | MAXTAG = *tagub; |
602 | < | } else { |
603 | < | MAXTAG = 32767; |
604 | < | } |
605 | < | |
606 | < | int haveError; |
607 | < | |
608 | < | MPI_Status istatus; |
609 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
610 | < | |
611 | < | // write out header and node 0's coordinates |
612 | < | |
613 | < | if( worldRank == 0 ){ |
614 | < | |
615 | < | // Node 0 needs a list of the magic potatoes for each processor; |
616 | < | |
617 | < | nProc = mpiSim->getNumberProcessors(); |
618 | < | potatoes = new int[nProc]; |
619 | < | |
620 | < | for (i = 0; i < nProc; i++) |
621 | < | potatoes[i] = 0; |
622 | < | |
623 | < | finalOut << mpiSim->getTotAtoms() << "\n"; |
624 | < | |
625 | < | finalOut << finalTime << ";\t" |
626 | < | << entry_plug->Hmat[0][0] << "\t" |
627 | < | << entry_plug->Hmat[1][0] << "\t" |
628 | < | << entry_plug->Hmat[2][0] << ";\t" |
629 | < | |
630 | < | << entry_plug->Hmat[0][1] << "\t" |
631 | < | << entry_plug->Hmat[1][1] << "\t" |
632 | < | << entry_plug->Hmat[2][1] << ";\t" |
633 | < | |
634 | < | << entry_plug->Hmat[0][2] << "\t" |
635 | < | << entry_plug->Hmat[1][2] << "\t" |
636 | < | << entry_plug->Hmat[2][2] << ";"; |
637 | < | |
638 | < | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
639 | < | finalOut << endl; |
640 | < | finalOut.flush(); |
641 | < | |
642 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
643 | < | |
644 | < | // Get the Node number which has this atom; |
645 | < | |
646 | < | which_node = AtomToProcMap[i]; |
647 | < | |
648 | < | if (which_node != 0) { |
649 | < | |
650 | < | if (potatoes[which_node] + 3 >= MAXTAG) { |
651 | < | // The potato was going to exceed the maximum value, |
652 | < | // so wrap this processor potato back to 0: |
653 | < | |
654 | < | potatoes[which_node] = 0; |
655 | < | MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
656 | < | |
657 | < | } |
658 | < | |
659 | < | myPotato = potatoes[which_node]; |
660 | < | |
661 | < | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
662 | < | myPotato, MPI_COMM_WORLD, &istatus); |
663 | < | |
664 | < | atomTypeString = MPIatomTypeString; |
665 | < | |
666 | < | myPotato++; |
667 | < | |
668 | < | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
669 | < | myPotato, MPI_COMM_WORLD, &istatus); |
670 | < | |
671 | < | myPotato++; |
672 | < | |
673 | < | if (isDirectional) { |
674 | < | MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
675 | < | myPotato, MPI_COMM_WORLD, &istatus); |
676 | < | } else { |
677 | < | MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
678 | < | myPotato, MPI_COMM_WORLD, &istatus); |
679 | < | } |
680 | < | |
681 | < | myPotato++; |
682 | < | potatoes[which_node] = myPotato; |
388 | > | if (!isDirectional) { |
389 | > | |
390 | > | sprintf( writeLine, |
391 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
392 | > | atomTypeString, |
393 | > | atomData6[0], |
394 | > | atomData6[1], |
395 | > | atomData6[2], |
396 | > | atomData6[3], |
397 | > | atomData6[4], |
398 | > | atomData6[5]); |
399 | ||
400 | + | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
401 | + | |
402 | } else { | |
403 | + | |
404 | + | sprintf( writeLine, |
405 | + | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
406 | + | atomTypeString, |
407 | + | atomData13[0], |
408 | + | atomData13[1], |
409 | + | atomData13[2], |
410 | + | atomData13[3], |
411 | + | atomData13[4], |
412 | + | atomData13[5], |
413 | + | atomData13[6], |
414 | + | atomData13[7], |
415 | + | atomData13[8], |
416 | + | atomData13[9], |
417 | + | atomData13[10], |
418 | + | atomData13[11], |
419 | + | atomData13[12]); |
420 | ||
686 | – | haveError = 0; |
687 | – | which_atom = i; |
688 | – | local_index=-1; |
689 | – | |
690 | – | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
691 | – | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
692 | – | } |
693 | – | |
694 | – | if (local_index != -1) { |
695 | – | |
696 | – | atomTypeString = atoms[local_index]->getType(); |
697 | – | |
698 | – | atoms[local_index]->getPos(pos); |
699 | – | atoms[local_index]->getVel(vel); |
700 | – | |
701 | – | atomData6[0] = pos[0]; |
702 | – | atomData6[1] = pos[1]; |
703 | – | atomData6[2] = pos[2]; |
704 | – | |
705 | – | atomData6[3] = vel[0]; |
706 | – | atomData6[4] = vel[1]; |
707 | – | atomData6[5] = vel[2]; |
708 | – | |
709 | – | isDirectional = 0; |
710 | – | |
711 | – | if( atoms[local_index]->isDirectional() ){ |
712 | – | |
713 | – | isDirectional = 1; |
714 | – | |
715 | – | dAtom = (DirectionalAtom *)atoms[local_index]; |
716 | – | dAtom->getQ( q ); |
717 | – | |
718 | – | for (int j = 0; j < 6 ; j++) |
719 | – | atomData13[j] = atomData6[j]; |
720 | – | |
721 | – | atomData13[6] = q[0]; |
722 | – | atomData13[7] = q[1]; |
723 | – | atomData13[8] = q[2]; |
724 | – | atomData13[9] = q[3]; |
725 | – | |
726 | – | atomData13[10] = dAtom->getJx(); |
727 | – | atomData13[11] = dAtom->getJy(); |
728 | – | atomData13[12] = dAtom->getJz(); |
729 | – | } |
730 | – | |
731 | – | } else { |
732 | – | sprintf(painCave.errMsg, |
733 | – | "Atom %d not found on processor %d\n", |
734 | – | i, worldRank ); |
735 | – | haveError= 1; |
736 | – | simError(); |
737 | – | } |
738 | – | |
739 | – | if(haveError) DieDieDie(); |
740 | – | |
741 | – | // If we've survived to here, format the line: |
742 | – | |
743 | – | if (!isDirectional) { |
744 | – | |
745 | – | sprintf( tempBuffer, |
746 | – | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
747 | – | atomTypeString, |
748 | – | atomData6[0], |
749 | – | atomData6[1], |
750 | – | atomData6[2], |
751 | – | atomData6[3], |
752 | – | atomData6[4], |
753 | – | atomData6[5]); |
754 | – | |
755 | – | strcpy( writeLine, tempBuffer ); |
756 | – | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
757 | – | |
758 | – | } else { |
759 | – | |
760 | – | sprintf( tempBuffer, |
761 | – | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
762 | – | atomTypeString, |
763 | – | atomData13[0], |
764 | – | atomData13[1], |
765 | – | atomData13[2], |
766 | – | atomData13[3], |
767 | – | atomData13[4], |
768 | – | atomData13[5], |
769 | – | atomData13[6], |
770 | – | atomData13[7], |
771 | – | atomData13[8], |
772 | – | atomData13[9], |
773 | – | atomData13[10], |
774 | – | atomData13[11], |
775 | – | atomData13[12]); |
776 | – | |
777 | – | strcat( writeLine, tempBuffer ); |
778 | – | |
779 | – | } |
780 | – | |
781 | – | finalOut << writeLine; |
782 | – | finalOut.flush(); |
421 | } | |
422 | + | |
423 | + | for(k = 0; k < outFile.size(); k++) |
424 | + | *outFile[k] << writeLine; |
425 | } | |
426 | < | |
427 | < | finalOut.flush(); |
426 | > | |
427 | > | for(k = 0; k < outFile.size(); k++) |
428 | > | outFile[k]->flush(); |
429 | > | |
430 | sprintf( checkPointMsg, | |
431 | "Sucessfully took a dump.\n"); | |
432 | < | delete[] potatoes; |
790 | < | |
432 | > | |
433 | MPIcheckPoint(); | |
434 | < | |
434 | > | |
435 | > | delete[] potatoes; |
436 | > | |
437 | } else { | |
438 | ||
439 | // worldRank != 0, so I'm a remote node. | |
# | Line 797 | Line 441 | void DumpWriter::writeFinal(double finalTime){ | |
441 | // Set my magic potato to 0: | |
442 | ||
443 | myPotato = 0; | |
444 | + | currentIndex = 0; |
445 | ||
446 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
447 | ||
# | Line 813 | Line 458 | void DumpWriter::writeFinal(double finalTime){ | |
458 | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); | |
459 | ||
460 | } | |
461 | < | which_atom = i; |
462 | < | local_index=-1; |
463 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
464 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
820 | < | } |
821 | < | if (local_index != -1) { |
461 | > | which_atom = i; |
462 | > | local_index = indexArray[currentIndex].first; |
463 | > | |
464 | > | if (which_atom == indexArray[currentIndex].second) { |
465 | ||
466 | atomTypeString = atoms[local_index]->getType(); | |
467 | ||
468 | < | atoms[local_index]->getPos(pos); |
469 | < | atoms[local_index]->getVel(vel); |
468 | > | atoms[local_index]->getPos(pos); |
469 | > | atoms[local_index]->getVel(vel); |
470 | ||
471 | atomData6[0] = pos[0]; | |
472 | atomData6[1] = pos[1]; | |
# | Line 849 | Line 492 | void DumpWriter::writeFinal(double finalTime){ | |
492 | atomData13[7] = q[1]; | |
493 | atomData13[8] = q[2]; | |
494 | atomData13[9] = q[3]; | |
495 | < | |
495 | > | |
496 | atomData13[10] = dAtom->getJx(); | |
497 | atomData13[11] = dAtom->getJy(); | |
498 | atomData13[12] = dAtom->getJz(); | |
499 | } | |
500 | ||
501 | } else { | |
502 | < | sprintf(painCave.errMsg, |
503 | < | "Atom %d not found on processor %d\n", |
504 | < | i, worldRank ); |
505 | < | haveError= 1; |
506 | < | simError(); |
507 | < | } |
502 | > | sprintf(painCave.errMsg, |
503 | > | "Atom %d not found on processor %d\n", |
504 | > | i, worldRank ); |
505 | > | haveError= 1; |
506 | > | simError(); |
507 | > | } |
508 | ||
509 | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); | |
510 | ||
# | Line 869 | Line 512 | void DumpWriter::writeFinal(double finalTime){ | |
512 | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; | |
513 | ||
514 | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, | |
515 | < | myPotato, MPI_COMM_WORLD); |
515 | > | myPotato, MPI_COMM_WORLD); |
516 | ||
517 | myPotato++; | |
518 | ||
519 | MPI_Send(&isDirectional, 1, MPI_INT, 0, | |
520 | < | myPotato, MPI_COMM_WORLD); |
520 | > | myPotato, MPI_COMM_WORLD); |
521 | ||
522 | myPotato++; | |
523 | ||
# | Line 889 | Line 532 | void DumpWriter::writeFinal(double finalTime){ | |
532 | myPotato, MPI_COMM_WORLD); | |
533 | } | |
534 | ||
535 | < | myPotato++; |
535 | > | myPotato++; |
536 | > | currentIndex++; |
537 | } | |
538 | } | |
539 | ||
# | Line 899 | Line 543 | void DumpWriter::writeFinal(double finalTime){ | |
543 | ||
544 | } | |
545 | ||
902 | – | if( worldRank == 0 ) finalOut.close(); |
546 | #endif // is_mpi | |
547 | } | |
548 | ||
906 | – | |
907 | – | |
549 | #ifdef IS_MPI | |
550 | ||
551 | // a couple of functions to let us escape the write loop |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |