62 |
|
#endif |
63 |
|
|
64 |
|
namespace oopse { |
65 |
< |
|
66 |
< |
void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
67 |
< |
|
65 |
> |
|
66 |
> |
void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, |
67 |
> |
Globals* simParams){ |
68 |
> |
|
69 |
|
#ifdef IS_MPI |
70 |
< |
|
70 |
> |
|
71 |
|
if (worldRank == 0) { |
72 |
|
#endif // is_mpi |
73 |
< |
|
73 |
> |
|
74 |
|
simParams->initalize(); |
75 |
|
set_interface_stamps(stamps, simParams); |
76 |
< |
|
76 |
> |
|
77 |
|
#ifdef IS_MPI |
78 |
< |
|
78 |
> |
|
79 |
|
mpiEventInit(); |
80 |
< |
|
80 |
> |
|
81 |
|
#endif |
82 |
< |
|
82 |
> |
|
83 |
|
yacc_BASS(mdFileName.c_str()); |
84 |
< |
|
84 |
> |
|
85 |
|
#ifdef IS_MPI |
86 |
< |
|
86 |
> |
|
87 |
|
throwMPIEvent(NULL); |
88 |
|
} else { |
89 |
|
set_interface_stamps(stamps, simParams); |
91 |
|
MPIcheckPoint(); |
92 |
|
mpiEventLoop(); |
93 |
|
} |
94 |
< |
|
94 |
> |
|
95 |
|
#endif |
96 |
< |
|
96 |
> |
|
97 |
|
} |
98 |
< |
|
99 |
< |
SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
98 |
> |
|
99 |
> |
SimInfo* SimCreator::createSim(const std::string & mdFileName, |
100 |
> |
bool loadInitCoords) { |
101 |
|
|
102 |
|
MakeStamps * stamps = new MakeStamps(); |
103 |
< |
|
103 |
> |
|
104 |
|
Globals * simParams = new Globals(); |
105 |
< |
|
105 |
> |
|
106 |
|
//parse meta-data file |
107 |
|
parseFile(mdFileName, stamps, simParams); |
108 |
< |
|
108 |
> |
|
109 |
|
//create the force field |
110 |
< |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
111 |
< |
simParams->getForceField()); |
110 |
> |
ForceField * ff = ForceFieldFactory::getInstance() |
111 |
> |
->createForceField(simParams->getForceField()); |
112 |
|
|
113 |
|
if (ff == NULL) { |
114 |
< |
sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
114 |
> |
sprintf(painCave.errMsg, |
115 |
> |
"ForceField Factory can not create %s force field\n", |
116 |
|
simParams->getForceField()); |
117 |
|
painCave.isFatal = 1; |
118 |
|
simError(); |
119 |
|
} |
120 |
< |
|
120 |
> |
|
121 |
|
if (simParams->haveForceFieldFileName()) { |
122 |
|
ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
123 |
|
} |
124 |
|
|
125 |
|
std::string forcefieldFileName; |
126 |
|
forcefieldFileName = ff->getForceFieldFileName(); |
127 |
< |
|
127 |
> |
|
128 |
|
if (simParams->haveForceFieldVariant()) { |
129 |
|
//If the force field has variant, the variant force field name will be |
130 |
|
//Base.variant.frc. For exampel EAM.u6.frc |
131 |
< |
|
131 |
> |
|
132 |
|
std::string variant = simParams->getForceFieldVariant(); |
133 |
< |
|
133 |
> |
|
134 |
|
std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
135 |
|
variant = "." + variant; |
136 |
|
if (pos != std::string::npos) { |
146 |
|
//extract the molecule stamps |
147 |
|
std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
148 |
|
compList(stamps, simParams, moleculeStampPairs); |
149 |
< |
|
149 |
> |
|
150 |
|
//create SimInfo |
151 |
< |
SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
152 |
< |
|
151 |
> |
SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
152 |
> |
|
153 |
|
//gather parameters (SimCreator only retrieves part of the parameters) |
154 |
|
gatherParameters(info, mdFileName); |
155 |
< |
|
155 |
> |
|
156 |
|
//divide the molecules and determine the global index of molecules |
157 |
|
#ifdef IS_MPI |
158 |
|
divideMolecules(info); |
159 |
|
#endif |
160 |
< |
|
160 |
> |
|
161 |
|
//create the molecules |
162 |
|
createMolecules(info); |
163 |
< |
|
164 |
< |
|
163 |
> |
|
164 |
> |
|
165 |
|
//allocate memory for DataStorage(circular reference, need to break it) |
166 |
|
info->setSnapshotManager(new SimSnapshotManager(info)); |
167 |
|
|
169 |
|
//global index will never change again). Local indices of atoms and rigidbodies are already set by |
170 |
|
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
171 |
|
setGlobalIndex(info); |
172 |
< |
|
172 |
> |
|
173 |
|
//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point |
174 |
|
//atoms don't have the global index yet (their global index are all initialized to -1). |
175 |
|
//Therefore we have to call addExcludePairs explicitly here. A way to work around is that |
180 |
|
info->addExcludePairs(mol); |
181 |
|
} |
182 |
|
|
180 |
– |
|
181 |
– |
//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
182 |
– |
//eta, chi for NPT integrator) |
183 |
|
if (loadInitCoords) |
184 |
|
loadCoordinates(info); |
185 |
|
|
186 |
|
return info; |
187 |
|
} |
188 |
< |
|
188 |
> |
|
189 |
|
void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
190 |
< |
|
190 |
> |
|
191 |
|
//figure out the ouput file names |
192 |
|
std::string prefix; |
193 |
< |
|
193 |
> |
|
194 |
|
#ifdef IS_MPI |
195 |
< |
|
195 |
> |
|
196 |
|
if (worldRank == 0) { |
197 |
|
#endif // is_mpi |
198 |
|
Globals * simParams = info->getSimParams(); |
201 |
|
} else { |
202 |
|
prefix = getPrefix(mdfile); |
203 |
|
} |
204 |
< |
|
204 |
> |
|
205 |
|
info->setFinalConfigFileName(prefix + ".eor"); |
206 |
|
info->setDumpFileName(prefix + ".dump"); |
207 |
|
info->setStatFileName(prefix + ".stat"); |
208 |
< |
|
208 |
> |
info->setRestFileName(prefix + ".zang"); |
209 |
> |
|
210 |
|
#ifdef IS_MPI |
211 |
< |
|
211 |
> |
|
212 |
|
} |
213 |
< |
|
213 |
> |
|
214 |
|
#endif |
215 |
< |
|
215 |
> |
|
216 |
|
} |
217 |
< |
|
217 |
> |
|
218 |
|
#ifdef IS_MPI |
219 |
|
void SimCreator::divideMolecules(SimInfo *info) { |
220 |
|
double numerator; |
238 |
|
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
239 |
|
|
240 |
|
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
241 |
< |
|
241 |
> |
|
242 |
|
if (nProcessors > nGlobalMols) { |
243 |
|
sprintf(painCave.errMsg, |
244 |
|
"nProcessors (%d) > nMol (%d)\n" |
247 |
|
"\tusable division of atoms for force decomposition.\n" |
248 |
|
"\tEither try a smaller number of processors, or run the\n" |
249 |
|
"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
250 |
< |
|
250 |
> |
|
251 |
|
painCave.isFatal = 1; |
252 |
|
simError(); |
253 |
|
} |
254 |
< |
|
254 |
> |
|
255 |
|
int seedValue; |
256 |
|
Globals * simParams = info->getSimParams(); |
257 |
|
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
261 |
|
}else { |
262 |
|
myRandom = new SeqRandNumGen(); |
263 |
|
} |
264 |
< |
|
265 |
< |
|
264 |
> |
|
265 |
> |
|
266 |
|
a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
267 |
< |
|
267 |
> |
|
268 |
|
//initialize atomsPerProc |
269 |
|
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
270 |
< |
|
270 |
> |
|
271 |
|
if (worldRank == 0) { |
272 |
|
numerator = info->getNGlobalAtoms(); |
273 |
|
denominator = nProcessors; |
274 |
|
precast = numerator / denominator; |
275 |
|
nTarget = (int)(precast + 0.5); |
276 |
< |
|
276 |
> |
|
277 |
|
for(i = 0; i < nGlobalMols; i++) { |
278 |
|
done = 0; |
279 |
|
loops = 0; |
280 |
< |
|
280 |
> |
|
281 |
|
while (!done) { |
282 |
|
loops++; |
283 |
< |
|
283 |
> |
|
284 |
|
// Pick a processor at random |
285 |
< |
|
285 |
> |
|
286 |
|
which_proc = (int) (myRandom->rand() * nProcessors); |
287 |
< |
|
287 |
> |
|
288 |
|
//get the molecule stamp first |
289 |
|
int stampId = info->getMoleculeStampId(i); |
290 |
|
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
291 |
< |
|
291 |
> |
|
292 |
|
// How many atoms does this processor have so far? |
293 |
|
old_atoms = atomsPerProc[which_proc]; |
294 |
|
add_atoms = moleculeStamp->getNAtoms(); |
295 |
|
new_atoms = old_atoms + add_atoms; |
296 |
< |
|
296 |
> |
|
297 |
|
// If we've been through this loop too many times, we need |
298 |
|
// to just give up and assign the molecule to this processor |
299 |
|
// and be done with it. |
300 |
< |
|
300 |
> |
|
301 |
|
if (loops > 100) { |
302 |
|
sprintf(painCave.errMsg, |
303 |
|
"I've tried 100 times to assign molecule %d to a " |
304 |
|
" processor, but can't find a good spot.\n" |
305 |
|
"I'm assigning it at random to processor %d.\n", |
306 |
|
i, which_proc); |
307 |
< |
|
307 |
> |
|
308 |
|
painCave.isFatal = 0; |
309 |
|
simError(); |
310 |
< |
|
310 |
> |
|
311 |
|
molToProcMap[i] = which_proc; |
312 |
|
atomsPerProc[which_proc] += add_atoms; |
313 |
< |
|
313 |
> |
|
314 |
|
done = 1; |
315 |
|
continue; |
316 |
|
} |
317 |
< |
|
317 |
> |
|
318 |
|
// If we can add this molecule to this processor without sending |
319 |
|
// it above nTarget, then go ahead and do it: |
320 |
< |
|
320 |
> |
|
321 |
|
if (new_atoms <= nTarget) { |
322 |
|
molToProcMap[i] = which_proc; |
323 |
|
atomsPerProc[which_proc] += add_atoms; |
324 |
< |
|
324 |
> |
|
325 |
|
done = 1; |
326 |
|
continue; |
327 |
|
} |
328 |
< |
|
328 |
> |
|
329 |
|
// The only situation left is when new_atoms > nTarget. We |
330 |
|
// want to accept this with some probability that dies off the |
331 |
|
// farther we are from nTarget |
332 |
< |
|
332 |
> |
|
333 |
|
// roughly: x = new_atoms - nTarget |
334 |
|
// Pacc(x) = exp(- a * x) |
335 |
|
// where a = penalty / (average atoms per molecule) |
336 |
< |
|
336 |
> |
|
337 |
|
x = (double)(new_atoms - nTarget); |
338 |
|
y = myRandom->rand(); |
339 |
< |
|
339 |
> |
|
340 |
|
if (y < exp(- a * x)) { |
341 |
|
molToProcMap[i] = which_proc; |
342 |
|
atomsPerProc[which_proc] += add_atoms; |
343 |
< |
|
343 |
> |
|
344 |
|
done = 1; |
345 |
|
continue; |
346 |
|
} else { |
348 |
|
} |
349 |
|
} |
350 |
|
} |
351 |
< |
|
351 |
> |
|
352 |
|
delete myRandom; |
353 |
< |
|
353 |
> |
|
354 |
|
// Spray out this nonsense to all other processors: |
355 |
< |
|
355 |
> |
|
356 |
|
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
357 |
|
} else { |
358 |
< |
|
358 |
> |
|
359 |
|
// Listen to your marching orders from processor 0: |
360 |
< |
|
360 |
> |
|
361 |
|
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
362 |
|
} |
363 |
< |
|
363 |
> |
|
364 |
|
info->setMolToProcMap(molToProcMap); |
365 |
|
sprintf(checkPointMsg, |
366 |
|
"Successfully divided the molecules among the processors.\n"); |
367 |
|
MPIcheckPoint(); |
368 |
|
} |
369 |
< |
|
369 |
> |
|
370 |
|
#endif |
371 |
< |
|
371 |
> |
|
372 |
|
void SimCreator::createMolecules(SimInfo *info) { |
373 |
|
MoleculeCreator molCreator; |
374 |
|
int stampId; |
375 |
< |
|
375 |
> |
|
376 |
|
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
377 |
< |
|
377 |
> |
|
378 |
|
#ifdef IS_MPI |
379 |
< |
|
379 |
> |
|
380 |
|
if (info->getMolToProc(i) == worldRank) { |
381 |
|
#endif |
382 |
< |
|
382 |
> |
|
383 |
|
stampId = info->getMoleculeStampId(i); |
384 |
|
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
385 |
|
stampId, i, info->getLocalIndexManager()); |
386 |
< |
|
386 |
> |
|
387 |
|
info->addMolecule(mol); |
388 |
< |
|
388 |
> |
|
389 |
|
#ifdef IS_MPI |
390 |
< |
|
390 |
> |
|
391 |
|
} |
392 |
< |
|
392 |
> |
|
393 |
|
#endif |
394 |
< |
|
394 |
> |
|
395 |
|
} //end for(int i=0) |
396 |
|
} |
397 |
< |
|
397 |
> |
|
398 |
|
void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
399 |
|
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
400 |
|
int i; |
401 |
|
char * id; |
401 |
– |
LinkedMolStamp* extractedStamp = NULL; |
402 |
|
MoleculeStamp * currentStamp; |
403 |
|
Component** the_components = simParams->getComponents(); |
404 |
|
int n_components = simParams->getNComponents(); |
405 |
< |
|
405 |
> |
|
406 |
|
if (!simParams->haveNMol()) { |
407 |
|
// we don't have the total number of molecules, so we assume it is |
408 |
|
// given in each component |
409 |
< |
|
409 |
> |
|
410 |
|
for(i = 0; i < n_components; i++) { |
411 |
|
if (!the_components[i]->haveNMol()) { |
412 |
|
// we have a problem |
413 |
|
sprintf(painCave.errMsg, |
414 |
|
"SimCreator Error. No global NMol or component NMol given.\n" |
415 |
|
"\tCannot calculate the number of atoms.\n"); |
416 |
< |
|
416 |
> |
|
417 |
|
painCave.isFatal = 1; |
418 |
|
simError(); |
419 |
|
} |
420 |
< |
|
420 |
> |
|
421 |
|
id = the_components[i]->getType(); |
422 |
|
|
423 |
< |
extractedStamp = stamps->extractMolStamp(id); |
424 |
< |
if (extractedStamp == NULL) { |
423 |
> |
currentStamp = stamps->getMolStamp(id); |
424 |
> |
if (currentStamp == NULL) { |
425 |
|
sprintf(painCave.errMsg, |
426 |
|
"SimCreator error: Component \"%s\" was not found in the " |
427 |
|
"list of declared molecules\n", id); |
428 |
< |
|
428 |
> |
|
429 |
|
painCave.isFatal = 1; |
430 |
|
simError(); |
431 |
|
} |
432 |
< |
|
433 |
< |
currentStamp = extractedStamp->getStamp(); |
434 |
< |
|
435 |
< |
|
432 |
> |
|
433 |
|
moleculeStampPairs.push_back( |
434 |
|
std::make_pair(currentStamp, the_components[i]->getNMol())); |
435 |
|
} //end for (i = 0; i < n_components; i++) |
439 |
|
" nMols and then give molfractions in the components\n" |
440 |
|
"\tis not currently supported." |
441 |
|
" Please give nMol in the components.\n"); |
442 |
< |
|
442 |
> |
|
443 |
|
painCave.isFatal = 1; |
444 |
|
simError(); |
445 |
|
} |
446 |
< |
|
446 |
> |
|
447 |
|
#ifdef IS_MPI |
448 |
< |
|
448 |
> |
|
449 |
|
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
450 |
|
MPIcheckPoint(); |
451 |
< |
|
451 |
> |
|
452 |
|
#endif // is_mpi |
453 |
< |
|
453 |
> |
|
454 |
|
} |
455 |
< |
|
455 |
> |
|
456 |
|
void SimCreator::setGlobalIndex(SimInfo *info) { |
457 |
|
SimInfo::MoleculeIterator mi; |
458 |
|
Molecule::AtomIterator ai; |
468 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
469 |
|
|
470 |
|
#ifndef IS_MPI |
471 |
< |
|
471 |
> |
|
472 |
|
beginAtomIndex = 0; |
473 |
|
beginRigidBodyIndex = 0; |
474 |
|
beginCutoffGroupIndex = 0; |
475 |
< |
|
475 |
> |
|
476 |
|
#else |
477 |
< |
|
477 |
> |
|
478 |
|
int nproc; |
479 |
|
int myNode; |
480 |
< |
|
480 |
> |
|
481 |
|
myNode = worldRank; |
482 |
|
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
483 |
< |
|
483 |
> |
|
484 |
|
std::vector < int > tmpAtomsInProc(nproc, 0); |
485 |
|
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
486 |
|
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
487 |
|
std::vector < int > NumAtomsInProc(nproc, 0); |
488 |
|
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
489 |
|
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
490 |
< |
|
490 |
> |
|
491 |
|
tmpAtomsInProc[myNode] = info->getNAtoms(); |
492 |
|
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
493 |
|
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
494 |
< |
|
494 |
> |
|
495 |
|
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
496 |
|
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
497 |
|
MPI_SUM, MPI_COMM_WORLD); |
499 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
500 |
|
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
501 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
502 |
< |
|
502 |
> |
|
503 |
|
beginAtomIndex = 0; |
504 |
|
beginRigidBodyIndex = 0; |
505 |
|
beginCutoffGroupIndex = 0; |
506 |
< |
|
506 |
> |
|
507 |
|
for(int i = 0; i < myNode; i++) { |
508 |
|
beginAtomIndex += NumAtomsInProc[i]; |
509 |
|
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
510 |
|
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
511 |
|
} |
512 |
< |
|
512 |
> |
|
513 |
|
#endif |
514 |
< |
|
514 |
> |
|
515 |
|
//rigidbody's index begins right after atom's |
516 |
|
beginRigidBodyIndex += info->getNGlobalAtoms(); |
517 |
< |
|
517 |
> |
|
518 |
|
for(mol = info->beginMolecule(mi); mol != NULL; |
519 |
|
mol = info->nextMolecule(mi)) { |
520 |
< |
|
520 |
> |
|
521 |
|
//local index(index in DataStorge) of atom is important |
522 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
523 |
|
atom->setGlobalIndex(beginAtomIndex++); |
524 |
|
} |
525 |
< |
|
525 |
> |
|
526 |
|
for(rb = mol->beginRigidBody(ri); rb != NULL; |
527 |
|
rb = mol->nextRigidBody(ri)) { |
528 |
|
rb->setGlobalIndex(beginRigidBodyIndex++); |
529 |
|
} |
530 |
< |
|
530 |
> |
|
531 |
|
//local index of cutoff group is trivial, it only depends on the order of travesing |
532 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
533 |
|
cg = mol->nextCutoffGroup(ci)) { |
534 |
|
cg->setGlobalIndex(beginCutoffGroupIndex++); |
535 |
|
} |
536 |
|
} |
537 |
< |
|
537 |
> |
|
538 |
|
//fill globalGroupMembership |
539 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
540 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
541 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
542 |
< |
|
542 |
> |
|
543 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
544 |
|
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
545 |
|
} |
546 |
< |
|
546 |
> |
|
547 |
|
} |
548 |
|
} |
549 |
< |
|
549 |
> |
|
550 |
|
#ifdef IS_MPI |
551 |
|
// Since the globalGroupMembership has been zero filled and we've only |
552 |
|
// poked values into the atoms we know, we can do an Allreduce |
560 |
|
#else |
561 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
562 |
|
#endif |
563 |
< |
|
563 |
> |
|
564 |
|
//fill molMembership |
565 |
|
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
566 |
|
|
567 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
568 |
< |
|
568 |
> |
|
569 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
570 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
571 |
|
} |
572 |
|
} |
573 |
< |
|
573 |
> |
|
574 |
|
#ifdef IS_MPI |
575 |
|
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
576 |
< |
|
576 |
> |
|
577 |
|
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
578 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
579 |
|
|
581 |
|
#else |
582 |
|
info->setGlobalMolMembership(globalMolMembership); |
583 |
|
#endif |
584 |
< |
|
584 |
> |
|
585 |
|
} |
586 |
< |
|
586 |
> |
|
587 |
|
void SimCreator::loadCoordinates(SimInfo* info) { |
588 |
|
Globals* simParams; |
589 |
|
simParams = info->getSimParams(); |
594 |
|
painCave.isFatal = 1;; |
595 |
|
simError(); |
596 |
|
} |
597 |
< |
|
597 |
> |
|
598 |
|
DumpReader reader(info, simParams->getInitialConfig()); |
599 |
|
int nframes = reader.getNFrames(); |
600 |
< |
|
600 |
> |
|
601 |
|
if (nframes > 0) { |
602 |
|
reader.readFrame(nframes - 1); |
603 |
|
} else { |
604 |
|
//invalid initial coordinate file |
605 |
< |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
605 |
> |
sprintf(painCave.errMsg, |
606 |
> |
"Initial configuration file %s should at least contain one frame\n", |
607 |
|
simParams->getInitialConfig()); |
608 |
|
painCave.isFatal = 1; |
609 |
|
simError(); |
610 |
|
} |
611 |
< |
|
611 |
> |
|
612 |
|
//copy the current snapshot to previous snapshot |
613 |
|
info->getSnapshotManager()->advance(); |
614 |
|
} |
615 |
< |
|
615 |
> |
|
616 |
|
} //end namespace oopse |
617 |
|
|
618 |
|
|