31 |
|
*/ |
32 |
|
|
33 |
|
#include <algorithm> |
34 |
< |
|
34 |
> |
#include <set> |
35 |
|
#include "brains/SimInfo.hpp" |
36 |
+ |
#include "primitives/Molecule.hpp" |
37 |
+ |
#include "UseTheForce/doForces_interface.h" |
38 |
+ |
#include "UseTheForce/notifyCutoffs_interface.h" |
39 |
|
#include "utils/MemoryUtils.hpp" |
40 |
+ |
#include "utils/simError.h" |
41 |
|
|
42 |
|
namespace oopse { |
43 |
|
|
44 |
< |
SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
45 |
< |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){ |
44 |
> |
SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
45 |
> |
ForceField* ff, Globals* simParams) : |
46 |
> |
forceField_(ff), simParams_(simParams), |
47 |
> |
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
48 |
> |
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
49 |
> |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
50 |
> |
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
51 |
> |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
52 |
> |
sman_(NULL), fortranInitialized_(false) { |
53 |
|
|
54 |
+ |
|
55 |
+ |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
56 |
+ |
MoleculeStamp* molStamp; |
57 |
+ |
int nMolWithSameStamp; |
58 |
+ |
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
59 |
+ |
int nGroups = 0; //total cutoff groups defined in meta-data file |
60 |
+ |
CutoffGroupStamp* cgStamp; |
61 |
+ |
RigidBodyStamp* rbStamp; |
62 |
+ |
int nRigidAtoms = 0; |
63 |
+ |
|
64 |
+ |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
65 |
+ |
molStamp = i->first; |
66 |
+ |
nMolWithSameStamp = i->second; |
67 |
+ |
|
68 |
+ |
addMoleculeStamp(molStamp, nMolWithSameStamp); |
69 |
+ |
|
70 |
+ |
//calculate atoms in molecules |
71 |
+ |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
72 |
+ |
|
73 |
+ |
|
74 |
+ |
//calculate atoms in cutoff groups |
75 |
+ |
int nAtomsInGroups = 0; |
76 |
+ |
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
77 |
+ |
|
78 |
+ |
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
79 |
+ |
cgStamp = molStamp->getCutoffGroup(j); |
80 |
+ |
nAtomsInGroups += cgStamp->getNMembers(); |
81 |
+ |
} |
82 |
+ |
|
83 |
+ |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
84 |
+ |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
85 |
+ |
|
86 |
+ |
//calculate atoms in rigid bodies |
87 |
+ |
int nAtomsInRigidBodies = 0; |
88 |
+ |
int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
89 |
+ |
|
90 |
+ |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
91 |
+ |
rbStamp = molStamp->getRigidBody(j); |
92 |
+ |
nAtomsInRigidBodies += rbStamp->getNMembers(); |
93 |
+ |
} |
94 |
+ |
|
95 |
+ |
nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
96 |
+ |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
97 |
+ |
|
98 |
+ |
} |
99 |
+ |
|
100 |
+ |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
101 |
+ |
//therefore the total number of cutoff groups in the system is equal to |
102 |
+ |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
103 |
+ |
//file plus the number of cutoff groups defined in meta-data file |
104 |
+ |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
105 |
+ |
|
106 |
+ |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
107 |
+ |
//therefore the total number of integrable objects in the system is equal to |
108 |
+ |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
109 |
+ |
//file plus the number of rigid bodies defined in meta-data file |
110 |
+ |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
111 |
+ |
|
112 |
+ |
nGlobalMols_ = molStampIds_.size(); |
113 |
+ |
|
114 |
+ |
#ifdef IS_MPI |
115 |
+ |
molToProcMap_.resize(nGlobalMols_); |
116 |
+ |
#endif |
117 |
+ |
|
118 |
|
} |
119 |
|
|
120 |
|
SimInfo::~SimInfo() { |
121 |
< |
MemoryUtils::deleteVectorOfPointer(molecules_); |
121 |
> |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
122 |
> |
|
123 |
> |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
124 |
> |
|
125 |
|
delete sman_; |
126 |
+ |
delete simParams_; |
127 |
+ |
delete forceField_; |
128 |
|
|
129 |
|
} |
130 |
|
|
131 |
|
|
132 |
|
bool SimInfo::addMolecule(Molecule* mol) { |
133 |
< |
std::vector<Molecule*>::iterator i; |
54 |
< |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
55 |
< |
if (i != molecules_.end() ) { |
56 |
< |
molecules_.push_back(mol); |
133 |
> |
MoleculeIterator i; |
134 |
|
|
135 |
+ |
i = molecules_.find(mol->getGlobalIndex()); |
136 |
+ |
if (i == molecules_.end() ) { |
137 |
+ |
|
138 |
+ |
molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
139 |
+ |
|
140 |
|
nAtoms_ += mol->getNAtoms(); |
141 |
|
nBonds_ += mol->getNBonds(); |
142 |
|
nBends_ += mol->getNBends(); |
146 |
|
nCutoffGroups_ += mol->getNCutoffGroups(); |
147 |
|
nConstraints_ += mol->getNConstraints(); |
148 |
|
|
149 |
+ |
addExcludePairs(mol); |
150 |
+ |
|
151 |
|
return true; |
152 |
|
} else { |
153 |
|
return false; |
155 |
|
} |
156 |
|
|
157 |
|
bool SimInfo::removeMolecule(Molecule* mol) { |
158 |
< |
std::vector<Molecule*>::iterator i; |
159 |
< |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
158 |
> |
MoleculeIterator i; |
159 |
> |
i = molecules_.find(mol->getGlobalIndex()); |
160 |
|
|
161 |
|
if (i != molecules_.end() ) { |
162 |
< |
molecules_.push_back(mol); |
162 |
> |
|
163 |
> |
assert(mol == i->second); |
164 |
> |
|
165 |
|
nAtoms_ -= mol->getNAtoms(); |
166 |
|
nBonds_ -= mol->getNBonds(); |
167 |
|
nBends_ -= mol->getNBends(); |
171 |
|
nCutoffGroups_ -= mol->getNCutoffGroups(); |
172 |
|
nConstraints_ -= mol->getNConstraints(); |
173 |
|
|
174 |
+ |
removeExcludePairs(mol); |
175 |
+ |
molecules_.erase(mol->getGlobalIndex()); |
176 |
+ |
|
177 |
+ |
delete mol; |
178 |
+ |
|
179 |
|
return true; |
180 |
|
} else { |
181 |
|
return false; |
185 |
|
} |
186 |
|
|
187 |
|
|
188 |
< |
Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) { |
188 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
189 |
|
i = molecules_.begin(); |
190 |
< |
return i == molecules_.end() ? NULL : *i; |
190 |
> |
return i == molecules_.end() ? NULL : i->second; |
191 |
|
} |
192 |
|
|
193 |
< |
Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) { |
193 |
> |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
194 |
|
++i; |
195 |
< |
return i == molecules_.end() ? NULL : *i; |
195 |
> |
return i == molecules_.end() ? NULL : i->second; |
196 |
|
} |
197 |
|
|
198 |
|
|
199 |
< |
void SimInfo::calcNDF() { |
199 |
> |
void SimInfo::calcNdf() { |
200 |
|
int ndf_local; |
201 |
< |
std::vector<Molecule*>::iterator i; |
201 |
> |
MoleculeIterator i; |
202 |
|
std::vector<StuntDouble*>::iterator j; |
203 |
|
Molecule* mol; |
204 |
|
StuntDouble* integrableObject; |
231 |
|
ndf_ = ndf_local; |
232 |
|
#endif |
233 |
|
|
234 |
< |
// nZconstraints is global, as are the 3 COM translations for the |
234 |
> |
// nZconstraints_ is global, as are the 3 COM translations for the |
235 |
|
// entire system: |
236 |
< |
ndf_ = ndf_ - 3 - nZconstraints; |
236 |
> |
ndf_ = ndf_ - 3 - nZconstraint_; |
237 |
|
|
238 |
|
} |
239 |
|
|
240 |
< |
void SimInfo::calcNDFRaw() { |
240 |
> |
void SimInfo::calcNdfRaw() { |
241 |
|
int ndfRaw_local; |
242 |
|
|
243 |
< |
std::vector<Molecule*>::iterator i; |
243 |
> |
MoleculeIterator i; |
244 |
|
std::vector<StuntDouble*>::iterator j; |
245 |
|
Molecule* mol; |
246 |
|
StuntDouble* integrableObject; |
272 |
|
#endif |
273 |
|
} |
274 |
|
|
275 |
< |
void SimInfo::calcNDFTrans() { |
275 |
> |
void SimInfo::calcNdfTrans() { |
276 |
|
int ndfTrans_local; |
277 |
|
|
278 |
|
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
284 |
|
ndfTrans_ = ndfTrans_local; |
285 |
|
#endif |
286 |
|
|
287 |
< |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
287 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
288 |
|
|
289 |
|
} |
290 |
|
|
316 |
|
exclude_.addPair(b, c); |
317 |
|
} |
318 |
|
|
319 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
319 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
320 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
321 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
322 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
361 |
|
exclude_.removePair(b, c); |
362 |
|
} |
363 |
|
|
364 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
364 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
365 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
366 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
367 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
378 |
|
} |
379 |
|
|
380 |
|
|
381 |
+ |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
382 |
+ |
int curStampId; |
383 |
+ |
|
384 |
+ |
//index from 0 |
385 |
+ |
curStampId = molStampIds_.size(); |
386 |
+ |
|
387 |
+ |
moleculeStamps_.push_back(molStamp); |
388 |
+ |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
389 |
+ |
} |
390 |
+ |
|
391 |
+ |
void SimInfo::update() { |
392 |
+ |
|
393 |
+ |
setupSimType(); |
394 |
+ |
|
395 |
+ |
#ifdef IS_MPI |
396 |
+ |
setupFortranParallel(); |
397 |
+ |
#endif |
398 |
+ |
|
399 |
+ |
setupFortranSim(); |
400 |
+ |
|
401 |
+ |
//setup fortran force field |
402 |
+ |
/** @deprecate */ |
403 |
+ |
int isError = 0; |
404 |
+ |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
405 |
+ |
if(isError){ |
406 |
+ |
sprintf( painCave.errMsg, |
407 |
+ |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
408 |
+ |
painCave.isFatal = 1; |
409 |
+ |
simError(); |
410 |
+ |
} |
411 |
+ |
|
412 |
+ |
|
413 |
+ |
setupCutoff(); |
414 |
+ |
|
415 |
+ |
calcNdf(); |
416 |
+ |
calcNdfRaw(); |
417 |
+ |
calcNdfTrans(); |
418 |
+ |
|
419 |
+ |
fortranInitialized_ = true; |
420 |
+ |
} |
421 |
+ |
|
422 |
+ |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
423 |
+ |
SimInfo::MoleculeIterator mi; |
424 |
+ |
Molecule* mol; |
425 |
+ |
Molecule::AtomIterator ai; |
426 |
+ |
Atom* atom; |
427 |
+ |
std::set<AtomType*> atomTypes; |
428 |
+ |
|
429 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
430 |
+ |
|
431 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
432 |
+ |
atomTypes.insert(atom->getAtomType()); |
433 |
+ |
} |
434 |
+ |
|
435 |
+ |
} |
436 |
+ |
|
437 |
+ |
return atomTypes; |
438 |
+ |
} |
439 |
+ |
|
440 |
+ |
void SimInfo::setupSimType() { |
441 |
+ |
std::set<AtomType*>::iterator i; |
442 |
+ |
std::set<AtomType*> atomTypes; |
443 |
+ |
atomTypes = getUniqueAtomTypes(); |
444 |
+ |
|
445 |
+ |
int useLennardJones = 0; |
446 |
+ |
int useElectrostatic = 0; |
447 |
+ |
int useEAM = 0; |
448 |
+ |
int useCharge = 0; |
449 |
+ |
int useDirectional = 0; |
450 |
+ |
int useDipole = 0; |
451 |
+ |
int useGayBerne = 0; |
452 |
+ |
int useSticky = 0; |
453 |
+ |
int useShape = 0; |
454 |
+ |
int useFLARB = 0; //it is not in AtomType yet |
455 |
+ |
int useDirectionalAtom = 0; |
456 |
+ |
int useElectrostatics = 0; |
457 |
+ |
//usePBC and useRF are from simParams |
458 |
+ |
bool usePBC = simParams_->getPBC(); |
459 |
+ |
bool useRF = simParams_->getUseRF(); |
460 |
+ |
|
461 |
+ |
//loop over all of the atom types |
462 |
+ |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
463 |
+ |
useLennardJones |= (*i)->isLennardJones(); |
464 |
+ |
useElectrostatic |= (*i)->isElectrostatic(); |
465 |
+ |
useEAM |= (*i)->isEAM(); |
466 |
+ |
useCharge |= (*i)->isCharge(); |
467 |
+ |
useDirectional |= (*i)->isDirectional(); |
468 |
+ |
useDipole |= (*i)->isDipole(); |
469 |
+ |
useGayBerne |= (*i)->isGayBerne(); |
470 |
+ |
useSticky |= (*i)->isSticky(); |
471 |
+ |
useShape |= (*i)->isShape(); |
472 |
+ |
} |
473 |
+ |
|
474 |
+ |
if (useSticky || useDipole || useGayBerne || useShape) { |
475 |
+ |
useDirectionalAtom = 1; |
476 |
+ |
} |
477 |
+ |
|
478 |
+ |
if (useCharge || useDipole) { |
479 |
+ |
useElectrostatics = 1; |
480 |
+ |
} |
481 |
+ |
|
482 |
+ |
#ifdef IS_MPI |
483 |
+ |
int temp; |
484 |
+ |
|
485 |
+ |
temp = usePBC; |
486 |
+ |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
487 |
+ |
|
488 |
+ |
temp = useDirectionalAtom; |
489 |
+ |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
490 |
+ |
|
491 |
+ |
temp = useLennardJones; |
492 |
+ |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
493 |
+ |
|
494 |
+ |
temp = useElectrostatics; |
495 |
+ |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
496 |
+ |
|
497 |
+ |
temp = useCharge; |
498 |
+ |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
499 |
+ |
|
500 |
+ |
temp = useDipole; |
501 |
+ |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
502 |
+ |
|
503 |
+ |
temp = useSticky; |
504 |
+ |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
505 |
+ |
|
506 |
+ |
temp = useGayBerne; |
507 |
+ |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
508 |
+ |
|
509 |
+ |
temp = useEAM; |
510 |
+ |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
511 |
+ |
|
512 |
+ |
temp = useShape; |
513 |
+ |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
514 |
+ |
|
515 |
+ |
temp = useFLARB; |
516 |
+ |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
517 |
+ |
|
518 |
+ |
temp = useRF; |
519 |
+ |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
520 |
+ |
|
521 |
+ |
#endif |
522 |
+ |
|
523 |
+ |
fInfo_.SIM_uses_PBC = usePBC; |
524 |
+ |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
525 |
+ |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
526 |
+ |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
527 |
+ |
fInfo_.SIM_uses_Charges = useCharge; |
528 |
+ |
fInfo_.SIM_uses_Dipoles = useDipole; |
529 |
+ |
fInfo_.SIM_uses_Sticky = useSticky; |
530 |
+ |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
531 |
+ |
fInfo_.SIM_uses_EAM = useEAM; |
532 |
+ |
fInfo_.SIM_uses_Shapes = useShape; |
533 |
+ |
fInfo_.SIM_uses_FLARB = useFLARB; |
534 |
+ |
fInfo_.SIM_uses_RF = useRF; |
535 |
+ |
|
536 |
+ |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
537 |
+ |
|
538 |
+ |
if (simParams_->haveDielectric()) { |
539 |
+ |
fInfo_.dielect = simParams_->getDielectric(); |
540 |
+ |
} else { |
541 |
+ |
sprintf(painCave.errMsg, |
542 |
+ |
"SimSetup Error: No Dielectric constant was set.\n" |
543 |
+ |
"\tYou are trying to use Reaction Field without" |
544 |
+ |
"\tsetting a dielectric constant!\n"); |
545 |
+ |
painCave.isFatal = 1; |
546 |
+ |
simError(); |
547 |
+ |
} |
548 |
+ |
|
549 |
+ |
} else { |
550 |
+ |
fInfo_.dielect = 0.0; |
551 |
+ |
} |
552 |
+ |
|
553 |
+ |
} |
554 |
+ |
|
555 |
+ |
void SimInfo::setupFortranSim() { |
556 |
+ |
int isError; |
557 |
+ |
int nExclude; |
558 |
+ |
std::vector<int> fortranGlobalGroupMembership; |
559 |
+ |
|
560 |
+ |
nExclude = exclude_.getSize(); |
561 |
+ |
isError = 0; |
562 |
+ |
|
563 |
+ |
//globalGroupMembership_ is filled by SimCreator |
564 |
+ |
for (int i = 0; i < nGlobalAtoms_; i++) { |
565 |
+ |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
566 |
+ |
} |
567 |
+ |
|
568 |
+ |
//calculate mass ratio of cutoff group |
569 |
+ |
std::vector<double> mfact; |
570 |
+ |
SimInfo::MoleculeIterator mi; |
571 |
+ |
Molecule* mol; |
572 |
+ |
Molecule::CutoffGroupIterator ci; |
573 |
+ |
CutoffGroup* cg; |
574 |
+ |
Molecule::AtomIterator ai; |
575 |
+ |
Atom* atom; |
576 |
+ |
double totalMass; |
577 |
+ |
|
578 |
+ |
//to avoid memory reallocation, reserve enough space for mfact |
579 |
+ |
mfact.reserve(getNCutoffGroups()); |
580 |
+ |
|
581 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
582 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
583 |
+ |
|
584 |
+ |
totalMass = cg->getMass(); |
585 |
+ |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
586 |
+ |
mfact.push_back(atom->getMass()/totalMass); |
587 |
+ |
} |
588 |
+ |
|
589 |
+ |
} |
590 |
+ |
} |
591 |
+ |
|
592 |
+ |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
593 |
+ |
std::vector<int> identArray; |
594 |
+ |
|
595 |
+ |
//to avoid memory reallocation, reserve enough space identArray |
596 |
+ |
identArray.reserve(getNAtoms()); |
597 |
+ |
|
598 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
599 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
600 |
+ |
identArray.push_back(atom->getIdent()); |
601 |
+ |
} |
602 |
+ |
} |
603 |
+ |
|
604 |
+ |
//fill molMembershipArray |
605 |
+ |
//molMembershipArray is filled by SimCreator |
606 |
+ |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
607 |
+ |
for (int i = 0; i < nGlobalAtoms_; i++) { |
608 |
+ |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
609 |
+ |
} |
610 |
+ |
|
611 |
+ |
//setup fortran simulation |
612 |
+ |
//gloalExcludes and molMembershipArray should go away (They are never used) |
613 |
+ |
//why the hell fortran need to know molecule? |
614 |
+ |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
615 |
+ |
int nGlobalExcludes = 0; |
616 |
+ |
int* globalExcludes = NULL; |
617 |
+ |
int* excludeList = exclude_.getExcludeList(); |
618 |
+ |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
619 |
+ |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
620 |
+ |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
621 |
+ |
|
622 |
+ |
if( isError ){ |
623 |
+ |
|
624 |
+ |
sprintf( painCave.errMsg, |
625 |
+ |
"There was an error setting the simulation information in fortran.\n" ); |
626 |
+ |
painCave.isFatal = 1; |
627 |
+ |
painCave.severity = OOPSE_ERROR; |
628 |
+ |
simError(); |
629 |
+ |
} |
630 |
+ |
|
631 |
+ |
#ifdef IS_MPI |
632 |
+ |
sprintf( checkPointMsg, |
633 |
+ |
"succesfully sent the simulation information to fortran.\n"); |
634 |
+ |
MPIcheckPoint(); |
635 |
+ |
#endif // is_mpi |
636 |
+ |
} |
637 |
+ |
|
638 |
+ |
|
639 |
+ |
#ifdef IS_MPI |
640 |
+ |
void SimInfo::setupFortranParallel() { |
641 |
+ |
|
642 |
+ |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
643 |
+ |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
644 |
+ |
std::vector<int> localToGlobalCutoffGroupIndex; |
645 |
+ |
SimInfo::MoleculeIterator mi; |
646 |
+ |
Molecule::AtomIterator ai; |
647 |
+ |
Molecule::CutoffGroupIterator ci; |
648 |
+ |
Molecule* mol; |
649 |
+ |
Atom* atom; |
650 |
+ |
CutoffGroup* cg; |
651 |
+ |
mpiSimData parallelData; |
652 |
+ |
int isError; |
653 |
+ |
|
654 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
655 |
+ |
|
656 |
+ |
//local index(index in DataStorge) of atom is important |
657 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
658 |
+ |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
659 |
+ |
} |
660 |
+ |
|
661 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
662 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
663 |
+ |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
664 |
+ |
} |
665 |
+ |
|
666 |
+ |
} |
667 |
+ |
|
668 |
+ |
//fill up mpiSimData struct |
669 |
+ |
parallelData.nMolGlobal = getNGlobalMolecules(); |
670 |
+ |
parallelData.nMolLocal = getNMolecules(); |
671 |
+ |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
672 |
+ |
parallelData.nAtomsLocal = getNAtoms(); |
673 |
+ |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
674 |
+ |
parallelData.nGroupsLocal = getNCutoffGroups(); |
675 |
+ |
parallelData.myNode = worldRank; |
676 |
+ |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
677 |
+ |
|
678 |
+ |
//pass mpiSimData struct and index arrays to fortran |
679 |
+ |
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
680 |
+ |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
681 |
+ |
&localToGlobalCutoffGroupIndex[0], &isError); |
682 |
+ |
|
683 |
+ |
if (isError) { |
684 |
+ |
sprintf(painCave.errMsg, |
685 |
+ |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
686 |
+ |
painCave.isFatal = 1; |
687 |
+ |
simError(); |
688 |
+ |
} |
689 |
+ |
|
690 |
+ |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
691 |
+ |
MPIcheckPoint(); |
692 |
+ |
|
693 |
+ |
|
694 |
+ |
} |
695 |
+ |
|
696 |
+ |
#endif |
697 |
+ |
|
698 |
+ |
double SimInfo::calcMaxCutoffRadius() { |
699 |
+ |
|
700 |
+ |
|
701 |
+ |
std::set<AtomType*> atomTypes; |
702 |
+ |
std::set<AtomType*>::iterator i; |
703 |
+ |
std::vector<double> cutoffRadius; |
704 |
+ |
|
705 |
+ |
//get the unique atom types |
706 |
+ |
atomTypes = getUniqueAtomTypes(); |
707 |
+ |
|
708 |
+ |
//query the max cutoff radius among these atom types |
709 |
+ |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
710 |
+ |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
711 |
+ |
} |
712 |
+ |
|
713 |
+ |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
714 |
+ |
#ifdef IS_MPI |
715 |
+ |
//pick the max cutoff radius among the processors |
716 |
+ |
#endif |
717 |
+ |
|
718 |
+ |
return maxCutoffRadius; |
719 |
+ |
} |
720 |
+ |
|
721 |
+ |
void SimInfo::setupCutoff() { |
722 |
+ |
double rcut_; //cutoff radius |
723 |
+ |
double rsw_; //switching radius |
724 |
+ |
|
725 |
+ |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
726 |
+ |
|
727 |
+ |
if (!simParams_->haveRcut()){ |
728 |
+ |
sprintf(painCave.errMsg, |
729 |
+ |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
730 |
+ |
"\tOOPSE will use a default value of 15.0 angstroms" |
731 |
+ |
"\tfor the cutoffRadius.\n"); |
732 |
+ |
painCave.isFatal = 0; |
733 |
+ |
simError(); |
734 |
+ |
rcut_ = 15.0; |
735 |
+ |
} else{ |
736 |
+ |
rcut_ = simParams_->getRcut(); |
737 |
+ |
} |
738 |
+ |
|
739 |
+ |
if (!simParams_->haveRsw()){ |
740 |
+ |
sprintf(painCave.errMsg, |
741 |
+ |
"SimCreator Warning: No value was set for switchingRadius.\n" |
742 |
+ |
"\tOOPSE will use a default value of\n" |
743 |
+ |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
744 |
+ |
painCave.isFatal = 0; |
745 |
+ |
simError(); |
746 |
+ |
rsw_ = 0.95 * rcut_; |
747 |
+ |
} else{ |
748 |
+ |
rsw_ = simParams_->getRsw(); |
749 |
+ |
} |
750 |
+ |
|
751 |
+ |
} else { |
752 |
+ |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
753 |
+ |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
754 |
+ |
|
755 |
+ |
if (simParams_->haveRcut()) { |
756 |
+ |
rcut_ = simParams_->getRcut(); |
757 |
+ |
} else { |
758 |
+ |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
759 |
+ |
rcut_ = calcMaxCutoffRadius(); |
760 |
+ |
} |
761 |
+ |
|
762 |
+ |
if (simParams_->haveRsw()) { |
763 |
+ |
rsw_ = simParams_->getRsw(); |
764 |
+ |
} else { |
765 |
+ |
rsw_ = rcut_; |
766 |
+ |
} |
767 |
+ |
|
768 |
+ |
} |
769 |
+ |
|
770 |
+ |
double rnblist = rcut_ + 1; // skin of neighbor list |
771 |
+ |
|
772 |
+ |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
773 |
+ |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
774 |
+ |
} |
775 |
+ |
|
776 |
+ |
void SimInfo::addProperty(GenericData* genData) { |
777 |
+ |
properties_.addProperty(genData); |
778 |
+ |
} |
779 |
+ |
|
780 |
+ |
void SimInfo::removeProperty(const std::string& propName) { |
781 |
+ |
properties_.removeProperty(propName); |
782 |
+ |
} |
783 |
+ |
|
784 |
+ |
void SimInfo::clearProperties() { |
785 |
+ |
properties_.clearProperties(); |
786 |
+ |
} |
787 |
+ |
|
788 |
+ |
std::vector<std::string> SimInfo::getPropertyNames() { |
789 |
+ |
return properties_.getPropertyNames(); |
790 |
+ |
} |
791 |
+ |
|
792 |
+ |
std::vector<GenericData*> SimInfo::getProperties() { |
793 |
+ |
return properties_.getProperties(); |
794 |
+ |
} |
795 |
+ |
|
796 |
+ |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
797 |
+ |
return properties_.getPropertyByName(propName); |
798 |
+ |
} |
799 |
+ |
|
800 |
+ |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
801 |
+ |
sman_ = sman; |
802 |
+ |
|
803 |
+ |
Molecule* mol; |
804 |
+ |
RigidBody* rb; |
805 |
+ |
Atom* atom; |
806 |
+ |
SimInfo::MoleculeIterator mi; |
807 |
+ |
Molecule::RigidBodyIterator rbIter; |
808 |
+ |
Molecule::AtomIterator atomIter;; |
809 |
+ |
|
810 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
811 |
+ |
|
812 |
+ |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
813 |
+ |
atom->setSnapshotManager(sman_); |
814 |
+ |
} |
815 |
+ |
|
816 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
817 |
+ |
rb->setSnapshotManager(sman_); |
818 |
+ |
} |
819 |
+ |
} |
820 |
+ |
|
821 |
+ |
} |
822 |
+ |
|
823 |
+ |
Vector3d SimInfo::getComVel(){ |
824 |
+ |
SimInfo::MoleculeIterator i; |
825 |
+ |
Molecule* mol; |
826 |
+ |
|
827 |
+ |
Vector3d comVel(0.0); |
828 |
+ |
double totalMass = 0.0; |
829 |
+ |
|
830 |
+ |
|
831 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
832 |
+ |
double mass = mol->getMass(); |
833 |
+ |
totalMass += mass; |
834 |
+ |
comVel += mass * mol->getComVel(); |
835 |
+ |
} |
836 |
+ |
|
837 |
+ |
comVel /= totalMass; |
838 |
+ |
|
839 |
+ |
return comVel; |
840 |
+ |
} |
841 |
+ |
|
842 |
+ |
Vector3d SimInfo::getCom(){ |
843 |
+ |
SimInfo::MoleculeIterator i; |
844 |
+ |
Molecule* mol; |
845 |
+ |
|
846 |
+ |
Vector3d com(0.0); |
847 |
+ |
double totalMass = 0.0; |
848 |
+ |
|
849 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
850 |
+ |
double mass = mol->getMass(); |
851 |
+ |
totalMass += mass; |
852 |
+ |
com += mass * mol->getCom(); |
853 |
+ |
} |
854 |
+ |
|
855 |
+ |
com /= totalMass; |
856 |
+ |
|
857 |
+ |
return com; |
858 |
+ |
|
859 |
+ |
} |
860 |
+ |
|
861 |
+ |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
862 |
+ |
|
863 |
+ |
return o; |
864 |
+ |
} |
865 |
+ |
|
866 |
|
}//end namespace oopse |
867 |
+ |
|