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> |
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 |
|
} |
45 |
|
#ifdef IS_MPI |
46 |
|
} |
47 |
|
|
48 |
+ |
//sort the local atoms by global index |
49 |
+ |
sortByGlobalIndex(); |
50 |
+ |
|
51 |
|
sprintf( checkPointMsg, |
52 |
|
"Sucessfully opened output file for dumping.\n"); |
53 |
|
MPIcheckPoint(); |
60 |
|
if(worldRank == 0 ){ |
61 |
|
#endif // is_mpi |
62 |
|
|
63 |
< |
outFile.close(); |
63 |
> |
dumpFile.close(); |
64 |
|
|
65 |
|
#ifdef IS_MPI |
66 |
|
} |
67 |
|
#endif // is_mpi |
68 |
|
} |
69 |
|
|
70 |
< |
void DumpWriter::writeDump( double currentTime ){ |
70 |
> |
#ifdef IS_MPI |
71 |
|
|
72 |
+ |
/** |
73 |
+ |
* A hook function to load balancing |
74 |
+ |
*/ |
75 |
+ |
|
76 |
+ |
void DumpWriter::update(){ |
77 |
+ |
sortByGlobalIndex(); |
78 |
+ |
} |
79 |
+ |
|
80 |
+ |
/** |
81 |
+ |
* Auxiliary sorting function |
82 |
+ |
*/ |
83 |
+ |
|
84 |
+ |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
85 |
+ |
return p1.second < p2.second; |
86 |
+ |
} |
87 |
+ |
|
88 |
+ |
/** |
89 |
+ |
* Sorting the local index by global index |
90 |
+ |
*/ |
91 |
+ |
|
92 |
+ |
void DumpWriter::sortByGlobalIndex(){ |
93 |
+ |
Atom** atoms = entry_plug->atoms; |
94 |
+ |
|
95 |
+ |
indexArray.clear(); |
96 |
+ |
|
97 |
+ |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
98 |
+ |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
99 |
+ |
|
100 |
+ |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
101 |
+ |
} |
102 |
+ |
#endif |
103 |
+ |
|
104 |
+ |
void DumpWriter::writeDump(double currentTime){ |
105 |
+ |
|
106 |
+ |
// write to eor file |
107 |
+ |
writeFinal(currentTime); |
108 |
+ |
|
109 |
+ |
//write to dump file |
110 |
+ |
writeFrame(dumpFile, currentTime); |
111 |
+ |
|
112 |
+ |
} |
113 |
+ |
|
114 |
+ |
void DumpWriter::writeFinal(double currentTime){ |
115 |
+ |
|
116 |
+ |
ofstream finalOut; |
117 |
+ |
|
118 |
+ |
//Open eor file |
119 |
+ |
#ifdef IS_MPI |
120 |
+ |
if(worldRank == 0 ){ |
121 |
+ |
#endif // is_mpi |
122 |
+ |
|
123 |
+ |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
124 |
+ |
if( !finalOut ){ |
125 |
+ |
sprintf( painCave.errMsg, |
126 |
+ |
"Could not open \"%s\" for final dump output.\n", |
127 |
+ |
entry_plug->finalName ); |
128 |
+ |
painCave.isFatal = 1; |
129 |
+ |
simError(); |
130 |
+ |
} |
131 |
+ |
|
132 |
+ |
#ifdef IS_MPI |
133 |
+ |
} |
134 |
+ |
#endif |
135 |
+ |
|
136 |
+ |
//write to eor file |
137 |
+ |
writeFrame(finalOut, currentTime); |
138 |
+ |
|
139 |
+ |
//close eor file |
140 |
+ |
#ifdef IS_MPI |
141 |
+ |
if(worldRank == 0 ){ |
142 |
+ |
finalOut.close(); |
143 |
+ |
} |
144 |
+ |
#endif // is_mpi |
145 |
+ |
|
146 |
+ |
} |
147 |
+ |
|
148 |
+ |
void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ |
149 |
+ |
|
150 |
|
const int BUFFERSIZE = 2000; |
151 |
|
const int MINIBUFFERSIZE = 100; |
152 |
|
|
161 |
|
int myPotato; |
162 |
|
|
163 |
|
int nProc; |
164 |
< |
int j, which_node, done, which_atom, local_index; |
164 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
165 |
|
double atomData6[6]; |
166 |
|
double atomData13[13]; |
167 |
|
int isDirectional; |
177 |
|
Atom** atoms = entry_plug->atoms; |
178 |
|
double pos[3], vel[3]; |
179 |
|
|
98 |
– |
// write current frame to the eor file |
99 |
– |
|
100 |
– |
this->writeFinal( currentTime ); |
101 |
– |
|
180 |
|
#ifndef IS_MPI |
181 |
|
|
182 |
|
outFile << nAtoms << "\n"; |
234 |
|
|
235 |
|
outFile << writeLine; |
236 |
|
} |
159 |
– |
outFile.flush(); |
237 |
|
|
238 |
|
#else // is_mpi |
239 |
|
|
240 |
|
/* code to find maximum tag value */ |
241 |
+ |
|
242 |
|
int *tagub, flag, MAXTAG; |
243 |
|
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
244 |
|
if (flag) { |
282 |
|
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
283 |
|
outFile << endl; |
284 |
|
outFile.flush(); |
285 |
< |
|
285 |
> |
|
286 |
> |
currentIndex = 0; |
287 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
288 |
|
|
289 |
|
// Get the Node number which has this atom; |
306 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
307 |
|
myPotato, MPI_COMM_WORLD, &istatus); |
308 |
|
|
309 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
310 |
< |
|
232 |
< |
// Null terminate the atomTypeString just in case: |
233 |
< |
|
234 |
< |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
235 |
< |
|
309 |
> |
atomTypeString = MPIatomTypeString; |
310 |
> |
|
311 |
|
myPotato++; |
312 |
|
|
313 |
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
330 |
|
|
331 |
|
haveError = 0; |
332 |
|
which_atom = i; |
258 |
– |
local_index=-1; |
333 |
|
|
334 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
335 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
336 |
< |
} |
263 |
< |
|
264 |
< |
if (local_index != -1) { |
334 |
> |
local_index = indexArray[currentIndex].first; |
335 |
> |
|
336 |
> |
if (which_atom == indexArray[currentIndex].second) { |
337 |
|
|
338 |
|
atomTypeString = atoms[local_index]->getType(); |
339 |
|
|
380 |
|
|
381 |
|
if(haveError) DieDieDie(); |
382 |
|
|
383 |
< |
// If we've survived to here, format the line: |
384 |
< |
|
385 |
< |
if (!isDirectional) { |
314 |
< |
|
315 |
< |
sprintf( tempBuffer, |
316 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
317 |
< |
atomTypeString, |
318 |
< |
atomData6[0], |
319 |
< |
atomData6[1], |
320 |
< |
atomData6[2], |
321 |
< |
atomData6[3], |
322 |
< |
atomData6[4], |
323 |
< |
atomData6[5]); |
324 |
< |
|
325 |
< |
strcpy( writeLine, tempBuffer ); |
326 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
327 |
< |
|
328 |
< |
} else { |
329 |
< |
|
330 |
< |
sprintf( tempBuffer, |
331 |
< |
"%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", |
332 |
< |
atomTypeString, |
333 |
< |
atomData13[0], |
334 |
< |
atomData13[1], |
335 |
< |
atomData13[2], |
336 |
< |
atomData13[3], |
337 |
< |
atomData13[4], |
338 |
< |
atomData13[5], |
339 |
< |
atomData13[6], |
340 |
< |
atomData13[7], |
341 |
< |
atomData13[8], |
342 |
< |
atomData13[9], |
343 |
< |
atomData13[10], |
344 |
< |
atomData13[11], |
345 |
< |
atomData13[12]); |
346 |
< |
|
347 |
< |
strcat( writeLine, tempBuffer ); |
348 |
< |
|
349 |
< |
} |
350 |
< |
|
351 |
< |
outFile << writeLine; |
352 |
< |
outFile.flush(); |
353 |
< |
} |
354 |
< |
} |
355 |
< |
|
356 |
< |
outFile.flush(); |
357 |
< |
sprintf( checkPointMsg, |
358 |
< |
"Sucessfully took a dump.\n"); |
359 |
< |
MPIcheckPoint(); |
360 |
< |
|
361 |
< |
} else { |
362 |
< |
|
363 |
< |
// worldRank != 0, so I'm a remote node. |
364 |
< |
|
365 |
< |
// Set my magic potato to 0: |
366 |
< |
|
367 |
< |
myPotato = 0; |
368 |
< |
|
369 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
383 |
> |
currentIndex ++; |
384 |
> |
} |
385 |
> |
// If we've survived to here, format the line: |
386 |
|
|
387 |
< |
// Am I the node which has this atom? |
388 |
< |
|
389 |
< |
if (AtomToProcMap[i] == worldRank) { |
387 |
> |
if (!isDirectional) { |
388 |
> |
|
389 |
> |
sprintf( writeLine, |
390 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
391 |
> |
atomTypeString, |
392 |
> |
atomData6[0], |
393 |
> |
atomData6[1], |
394 |
> |
atomData6[2], |
395 |
> |
atomData6[3], |
396 |
> |
atomData6[4], |
397 |
> |
atomData6[5]); |
398 |
|
|
399 |
< |
if (myPotato + 3 >= MAXTAG) { |
400 |
< |
|
401 |
< |
// The potato was going to exceed the maximum value, |
402 |
< |
// so wrap this processor potato back to 0 (and block until |
403 |
< |
// node 0 says we can go: |
404 |
< |
|
405 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
406 |
< |
|
407 |
< |
} |
408 |
< |
|
409 |
< |
local_index=-1; |
410 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
411 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
412 |
< |
} |
413 |
< |
if (local_index != -1) { |
414 |
< |
|
415 |
< |
atomTypeString = atoms[local_index]->getType(); |
416 |
< |
|
417 |
< |
atoms[local_index]->getPos(pos); |
418 |
< |
atoms[local_index]->getVel(vel); |
395 |
< |
|
396 |
< |
atomData6[0] = pos[0]; |
397 |
< |
atomData6[1] = pos[1]; |
398 |
< |
atomData6[2] = pos[2]; |
399 |
< |
|
400 |
< |
atomData6[3] = vel[0]; |
401 |
< |
atomData6[4] = vel[1]; |
402 |
< |
atomData6[5] = vel[2]; |
403 |
< |
|
404 |
< |
isDirectional = 0; |
405 |
< |
|
406 |
< |
if( atoms[local_index]->isDirectional() ){ |
407 |
< |
|
408 |
< |
isDirectional = 1; |
409 |
< |
|
410 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
411 |
< |
dAtom->getQ( q ); |
412 |
< |
|
413 |
< |
for (int j = 0; j < 6 ; j++) |
414 |
< |
atomData13[j] = atomData6[j]; |
415 |
< |
|
416 |
< |
atomData13[6] = q[0]; |
417 |
< |
atomData13[7] = q[1]; |
418 |
< |
atomData13[8] = q[2]; |
419 |
< |
atomData13[9] = q[3]; |
420 |
< |
|
421 |
< |
atomData13[10] = dAtom->getJx(); |
422 |
< |
atomData13[11] = dAtom->getJy(); |
423 |
< |
atomData13[12] = dAtom->getJz(); |
424 |
< |
} |
425 |
< |
|
426 |
< |
} else { |
427 |
< |
sprintf(painCave.errMsg, |
428 |
< |
"Atom %d not found on processor %d\n", |
429 |
< |
i, worldRank ); |
430 |
< |
haveError= 1; |
431 |
< |
simError(); |
432 |
< |
} |
433 |
< |
|
434 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
435 |
< |
|
436 |
< |
// null terminate the string before sending (just in case): |
437 |
< |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
438 |
< |
|
439 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
440 |
< |
myPotato, MPI_COMM_WORLD); |
399 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
400 |
> |
|
401 |
> |
} else { |
402 |
> |
|
403 |
> |
sprintf( writeLine, |
404 |
> |
"%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", |
405 |
> |
atomTypeString, |
406 |
> |
atomData13[0], |
407 |
> |
atomData13[1], |
408 |
> |
atomData13[2], |
409 |
> |
atomData13[3], |
410 |
> |
atomData13[4], |
411 |
> |
atomData13[5], |
412 |
> |
atomData13[6], |
413 |
> |
atomData13[7], |
414 |
> |
atomData13[8], |
415 |
> |
atomData13[9], |
416 |
> |
atomData13[10], |
417 |
> |
atomData13[11], |
418 |
> |
atomData13[12]); |
419 |
|
|
442 |
– |
myPotato++; |
443 |
– |
|
444 |
– |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
445 |
– |
myPotato, MPI_COMM_WORLD); |
446 |
– |
|
447 |
– |
myPotato++; |
448 |
– |
|
449 |
– |
if (isDirectional) { |
450 |
– |
|
451 |
– |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
452 |
– |
myPotato, MPI_COMM_WORLD); |
453 |
– |
|
454 |
– |
} else { |
455 |
– |
|
456 |
– |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
457 |
– |
myPotato, MPI_COMM_WORLD); |
458 |
– |
} |
459 |
– |
|
460 |
– |
myPotato++; |
420 |
|
} |
421 |
+ |
|
422 |
+ |
outFile << writeLine; |
423 |
|
} |
463 |
– |
|
464 |
– |
sprintf( checkPointMsg, |
465 |
– |
"Sucessfully took a dump.\n"); |
466 |
– |
MPIcheckPoint(); |
424 |
|
|
468 |
– |
} |
469 |
– |
|
470 |
– |
#endif // is_mpi |
471 |
– |
} |
425 |
|
|
426 |
< |
void DumpWriter::writeFinal(double finalTime){ |
474 |
< |
|
475 |
< |
char finalName[500]; |
476 |
< |
ofstream finalOut; |
477 |
< |
|
478 |
< |
const int BUFFERSIZE = 2000; |
479 |
< |
const int MINIBUFFERSIZE = 100; |
480 |
< |
char tempBuffer[BUFFERSIZE]; |
481 |
< |
char writeLine[BUFFERSIZE]; |
482 |
< |
|
483 |
< |
double q[4]; |
484 |
< |
DirectionalAtom* dAtom; |
485 |
< |
Atom** atoms = entry_plug->atoms; |
486 |
< |
int i; |
487 |
< |
#ifdef IS_MPI |
488 |
< |
|
489 |
< |
int *potatoes; |
490 |
< |
int myPotato; |
491 |
< |
|
492 |
< |
int nProc; |
493 |
< |
int j, which_node, done, which_atom, local_index; |
494 |
< |
double atomData6[6]; |
495 |
< |
double atomData13[13]; |
496 |
< |
int isDirectional; |
497 |
< |
char* atomTypeString; |
498 |
< |
char MPIatomTypeString[MINIBUFFERSIZE]; |
499 |
< |
|
500 |
< |
#else //is_mpi |
501 |
< |
int nAtoms = entry_plug->n_atoms; |
502 |
< |
#endif //is_mpi |
503 |
< |
|
504 |
< |
double pos[3], vel[3]; |
505 |
< |
|
506 |
< |
#ifdef IS_MPI |
507 |
< |
if(worldRank == 0 ){ |
508 |
< |
#endif // is_mpi |
509 |
< |
|
510 |
< |
strcpy( finalName, entry_plug->finalName ); |
511 |
< |
|
512 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
513 |
< |
if( !finalOut ){ |
514 |
< |
sprintf( painCave.errMsg, |
515 |
< |
"Could not open \"%s\" for final dump output.\n", |
516 |
< |
finalName ); |
517 |
< |
painCave.isFatal = 1; |
518 |
< |
simError(); |
519 |
< |
} |
520 |
< |
|
521 |
< |
// finalOut.setf( ios::scientific ); |
522 |
< |
|
523 |
< |
#ifdef IS_MPI |
524 |
< |
} |
525 |
< |
|
526 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
527 |
< |
MPIcheckPoint(); |
528 |
< |
|
529 |
< |
#endif //is_mpi |
530 |
< |
|
531 |
< |
|
532 |
< |
#ifndef IS_MPI |
533 |
< |
|
534 |
< |
finalOut << nAtoms << "\n"; |
535 |
< |
|
536 |
< |
finalOut << finalTime << ";\t" |
537 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
538 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
539 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
540 |
< |
|
541 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
542 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
543 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
544 |
< |
|
545 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
546 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
547 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
548 |
< |
|
549 |
< |
//write out additional parameters, such as chi and eta |
550 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
551 |
< |
finalOut << endl; |
552 |
< |
|
553 |
< |
for( i=0; i<nAtoms; i++ ){ |
554 |
< |
|
555 |
< |
atoms[i]->getPos(pos); |
556 |
< |
atoms[i]->getVel(vel); |
557 |
< |
|
558 |
< |
sprintf( tempBuffer, |
559 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
560 |
< |
atoms[i]->getType(), |
561 |
< |
pos[0], |
562 |
< |
pos[1], |
563 |
< |
pos[2], |
564 |
< |
vel[0], |
565 |
< |
vel[1], |
566 |
< |
vel[2]); |
567 |
< |
strcpy( writeLine, tempBuffer ); |
568 |
< |
|
569 |
< |
if( atoms[i]->isDirectional() ){ |
570 |
< |
|
571 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
572 |
< |
dAtom->getQ( q ); |
573 |
< |
|
574 |
< |
sprintf( tempBuffer, |
575 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
576 |
< |
q[0], |
577 |
< |
q[1], |
578 |
< |
q[2], |
579 |
< |
q[3], |
580 |
< |
dAtom->getJx(), |
581 |
< |
dAtom->getJy(), |
582 |
< |
dAtom->getJz()); |
583 |
< |
strcat( writeLine, tempBuffer ); |
584 |
< |
} |
585 |
< |
else |
586 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
587 |
< |
|
588 |
< |
finalOut << writeLine; |
589 |
< |
} |
590 |
< |
finalOut.flush(); |
591 |
< |
finalOut.close(); |
592 |
< |
|
593 |
< |
#else // is_mpi |
594 |
< |
|
595 |
< |
/* code to find maximum tag value */ |
596 |
< |
int *tagub, flag, MAXTAG; |
597 |
< |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
598 |
< |
if (flag) { |
599 |
< |
MAXTAG = *tagub; |
600 |
< |
} else { |
601 |
< |
MAXTAG = 32767; |
602 |
< |
} |
603 |
< |
|
604 |
< |
int haveError; |
605 |
< |
|
606 |
< |
MPI_Status istatus; |
607 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
608 |
< |
|
609 |
< |
// write out header and node 0's coordinates |
610 |
< |
|
611 |
< |
if( worldRank == 0 ){ |
612 |
< |
|
613 |
< |
// Node 0 needs a list of the magic potatoes for each processor; |
614 |
< |
|
615 |
< |
nProc = mpiSim->getNumberProcessors(); |
616 |
< |
potatoes = new int[nProc]; |
617 |
< |
|
618 |
< |
for (i = 0; i < nProc; i++) |
619 |
< |
potatoes[i] = 0; |
620 |
< |
|
621 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
622 |
< |
|
623 |
< |
finalOut << finalTime << ";\t" |
624 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
625 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
626 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
627 |
< |
|
628 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
629 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
630 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
631 |
< |
|
632 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
633 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
634 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
635 |
< |
|
636 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
637 |
< |
finalOut << endl; |
638 |
< |
finalOut.flush(); |
639 |
< |
|
640 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
641 |
< |
|
642 |
< |
// Get the Node number which has this atom; |
643 |
< |
|
644 |
< |
which_node = AtomToProcMap[i]; |
645 |
< |
|
646 |
< |
if (which_node != 0) { |
647 |
< |
|
648 |
< |
if (potatoes[which_node] + 3 >= MAXTAG) { |
649 |
< |
// The potato was going to exceed the maximum value, |
650 |
< |
// so wrap this processor potato back to 0: |
651 |
< |
|
652 |
< |
potatoes[which_node] = 0; |
653 |
< |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
654 |
< |
|
655 |
< |
} |
656 |
< |
|
657 |
< |
myPotato = potatoes[which_node]; |
658 |
< |
|
659 |
< |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
660 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
661 |
< |
|
662 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
663 |
< |
|
664 |
< |
// Null terminate the atomTypeString just in case: |
665 |
< |
|
666 |
< |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
667 |
< |
|
668 |
< |
myPotato++; |
669 |
< |
|
670 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
671 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
672 |
< |
|
673 |
< |
myPotato++; |
674 |
< |
|
675 |
< |
if (isDirectional) { |
676 |
< |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
677 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
678 |
< |
} else { |
679 |
< |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
680 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
681 |
< |
} |
682 |
< |
|
683 |
< |
myPotato++; |
684 |
< |
potatoes[which_node] = myPotato; |
685 |
< |
|
686 |
< |
} else { |
687 |
< |
|
688 |
< |
haveError = 0; |
689 |
< |
which_atom = i; |
690 |
< |
local_index=-1; |
691 |
< |
|
692 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
693 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
694 |
< |
} |
695 |
< |
|
696 |
< |
if (local_index != -1) { |
697 |
< |
|
698 |
< |
atomTypeString = atoms[local_index]->getType(); |
699 |
< |
|
700 |
< |
atoms[local_index]->getPos(pos); |
701 |
< |
atoms[local_index]->getVel(vel); |
702 |
< |
|
703 |
< |
atomData6[0] = pos[0]; |
704 |
< |
atomData6[1] = pos[1]; |
705 |
< |
atomData6[2] = pos[2]; |
706 |
< |
|
707 |
< |
atomData6[3] = vel[0]; |
708 |
< |
atomData6[4] = vel[1]; |
709 |
< |
atomData6[5] = vel[2]; |
710 |
< |
|
711 |
< |
isDirectional = 0; |
712 |
< |
|
713 |
< |
if( atoms[local_index]->isDirectional() ){ |
714 |
< |
|
715 |
< |
isDirectional = 1; |
716 |
< |
|
717 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
718 |
< |
dAtom->getQ( q ); |
719 |
< |
|
720 |
< |
for (int j = 0; j < 6 ; j++) |
721 |
< |
atomData13[j] = atomData6[j]; |
722 |
< |
|
723 |
< |
atomData13[6] = q[0]; |
724 |
< |
atomData13[7] = q[1]; |
725 |
< |
atomData13[8] = q[2]; |
726 |
< |
atomData13[9] = q[3]; |
727 |
< |
|
728 |
< |
atomData13[10] = dAtom->getJx(); |
729 |
< |
atomData13[11] = dAtom->getJy(); |
730 |
< |
atomData13[12] = dAtom->getJz(); |
731 |
< |
} |
732 |
< |
|
733 |
< |
} else { |
734 |
< |
sprintf(painCave.errMsg, |
735 |
< |
"Atom %d not found on processor %d\n", |
736 |
< |
i, worldRank ); |
737 |
< |
haveError= 1; |
738 |
< |
simError(); |
739 |
< |
} |
740 |
< |
|
741 |
< |
if(haveError) DieDieDie(); |
742 |
< |
|
743 |
< |
// If we've survived to here, format the line: |
744 |
< |
|
745 |
< |
if (!isDirectional) { |
746 |
< |
|
747 |
< |
sprintf( tempBuffer, |
748 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
749 |
< |
atomTypeString, |
750 |
< |
atomData6[0], |
751 |
< |
atomData6[1], |
752 |
< |
atomData6[2], |
753 |
< |
atomData6[3], |
754 |
< |
atomData6[4], |
755 |
< |
atomData6[5]); |
756 |
< |
|
757 |
< |
strcpy( writeLine, tempBuffer ); |
758 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
759 |
< |
|
760 |
< |
} else { |
761 |
< |
|
762 |
< |
sprintf( tempBuffer, |
763 |
< |
"%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", |
764 |
< |
atomTypeString, |
765 |
< |
atomData13[0], |
766 |
< |
atomData13[1], |
767 |
< |
atomData13[2], |
768 |
< |
atomData13[3], |
769 |
< |
atomData13[4], |
770 |
< |
atomData13[5], |
771 |
< |
atomData13[6], |
772 |
< |
atomData13[7], |
773 |
< |
atomData13[8], |
774 |
< |
atomData13[9], |
775 |
< |
atomData13[10], |
776 |
< |
atomData13[11], |
777 |
< |
atomData13[12]); |
778 |
< |
|
779 |
< |
strcat( writeLine, tempBuffer ); |
780 |
< |
|
781 |
< |
} |
782 |
< |
|
783 |
< |
finalOut << writeLine; |
784 |
< |
finalOut.flush(); |
785 |
< |
} |
786 |
< |
} |
787 |
< |
|
788 |
< |
finalOut.flush(); |
426 |
> |
outFile.flush(); |
427 |
|
sprintf( checkPointMsg, |
428 |
|
"Sucessfully took a dump.\n"); |
429 |
|
MPIcheckPoint(); |
430 |
< |
|
430 |
> |
delete[] potatoes; |
431 |
|
} else { |
432 |
|
|
433 |
|
// worldRank != 0, so I'm a remote node. |
435 |
|
// Set my magic potato to 0: |
436 |
|
|
437 |
|
myPotato = 0; |
438 |
+ |
currentIndex = 0; |
439 |
|
|
440 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
441 |
|
|
452 |
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
453 |
|
|
454 |
|
} |
455 |
< |
|
456 |
< |
local_index=-1; |
457 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
458 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
820 |
< |
} |
821 |
< |
if (local_index != -1) { |
455 |
> |
which_atom = i; |
456 |
> |
local_index = indexArray[currentIndex].first; |
457 |
> |
|
458 |
> |
if (which_atom == indexArray[currentIndex].second) { |
459 |
|
|
460 |
|
atomTypeString = atoms[local_index]->getType(); |
461 |
|
|
526 |
|
myPotato, MPI_COMM_WORLD); |
527 |
|
} |
528 |
|
|
529 |
< |
myPotato++; |
529 |
> |
myPotato++; |
530 |
> |
currentIndex++; |
531 |
|
} |
532 |
|
} |
533 |
|
|
537 |
|
|
538 |
|
} |
539 |
|
|
902 |
– |
if( worldRank == 0 ) finalOut.close(); |
540 |
|
#endif // is_mpi |
541 |
|
} |
542 |
|
|
906 |
– |
|
907 |
– |
|
543 |
|
#ifdef IS_MPI |
544 |
|
|
545 |
|
// a couple of functions to let us escape the write loop |