33 |
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#include <algorithm> |
34 |
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|
35 |
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#include "brains/SimInfo.hpp" |
36 |
+ |
#include "primitives/Molecule.hpp" |
37 |
+ |
#include "UseTheForce/notifyCutoffs_interface.h" |
38 |
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#include "utils/MemoryUtils.hpp" |
39 |
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#include "utils/simError.h" |
40 |
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|
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namespace oopse { |
42 |
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|
43 |
< |
SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
44 |
< |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){ |
43 |
> |
SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
44 |
> |
ForceField* ff, Globals* globals) : |
45 |
> |
forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
46 |
> |
nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
47 |
> |
nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL), |
48 |
> |
fortranInitialized_(false) { |
49 |
> |
|
50 |
> |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
51 |
> |
MoleculeStamp* molStamp; |
52 |
> |
int nMolWithSameStamp; |
53 |
> |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
54 |
> |
int nGroups; //total cutoff groups defined in meta-data file |
55 |
> |
CutoffGroupStamp* cgStamp; |
56 |
> |
int nAtomsInGroups; |
57 |
> |
int nCutoffGroupsInStamp; |
58 |
> |
|
59 |
> |
RigidBodyStamp* rbStamp; |
60 |
> |
int nAtomsInRigidBodies; |
61 |
> |
int nRigidBodiesInStamp; |
62 |
> |
int nRigidAtoms; |
63 |
> |
int nRigidBodies; |
64 |
> |
|
65 |
> |
nGlobalAtoms_ = 0; |
66 |
> |
|
67 |
> |
nGroups = 0; |
68 |
> |
nCutoffAtoms = 0; |
69 |
> |
nRigidBodies = 0; |
70 |
> |
|
71 |
> |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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> |
molStamp = i->first; |
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> |
nMolWithSameStamp = i->second; |
74 |
> |
|
75 |
> |
addMoleculeStamp(molStamp, nMolWithSameStamp); |
76 |
> |
|
77 |
> |
//calculate atoms in molecules |
78 |
> |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
79 |
> |
|
80 |
> |
|
81 |
> |
//calculate atoms in cutoff groups |
82 |
> |
nAtomsInGroups = 0; |
83 |
> |
nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
84 |
> |
|
85 |
> |
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
86 |
> |
cgStamp = molStamp->getCutoffGroup(j); |
87 |
> |
nAtomsInGroups += cgStamp->getNMembers(); |
88 |
> |
} |
89 |
> |
|
90 |
> |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
91 |
> |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
92 |
> |
|
93 |
> |
//calculate atoms in rigid bodies |
94 |
> |
nAtomsInRigidBodies = 0; |
95 |
> |
nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
96 |
> |
|
97 |
> |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
98 |
> |
rbStamp = molStamp->getRigidBody(j); |
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> |
nRigidBodiesInStamp += rbStamp->getNMembers(); |
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> |
} |
101 |
> |
|
102 |
> |
nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
103 |
> |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
104 |
> |
|
105 |
> |
} |
106 |
> |
|
107 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
108 |
> |
//therefore the total number of cutoff groups in the system is equal to |
109 |
> |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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//file plus the number of cutoff groups defined in meta-data file |
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> |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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> |
|
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> |
//every free atom (atom does not belong to rigid bodies) is a rigid body |
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> |
//therefore the total number of cutoff groups in the system is equal to |
115 |
> |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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> |
//file plus the number of rigid bodies defined in meta-data file |
117 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies; |
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|
119 |
+ |
//initialize globalGroupMembership_, every element of this array will be 0 |
120 |
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globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
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|
122 |
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nGlobalMols_ = molStampIds_.size(); |
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|
124 |
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#ifdef IS_MPI |
125 |
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molToProcMap_.resize(nGlobalMols_); |
126 |
+ |
#endif |
127 |
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|
128 |
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} |
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|
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SimInfo::~SimInfo() { |
131 |
< |
MemoryUtils::deleteVectorOfPointer(molecules_); |
131 |
> |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
132 |
> |
|
133 |
> |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
134 |
> |
|
135 |
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delete sman_; |
136 |
+ |
delete globals_; |
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+ |
delete forceField_; |
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|
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} |
140 |
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|
141 |
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|
142 |
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bool SimInfo::addMolecule(Molecule* mol) { |
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< |
std::vector<Molecule*>::iterator i; |
144 |
< |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
143 |
> |
MoleculeIterator i; |
144 |
> |
|
145 |
> |
i = molecules_.find(mol->getGlobalIndex()); |
146 |
|
if (i != molecules_.end() ) { |
56 |
– |
molecules_.push_back(mol); |
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|
148 |
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molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
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|
150 |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraints(); |
158 |
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|
67 |
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globalIndexToMol_.insert(make_pair(mol->getGlobalIndex(), mol)); |
159 |
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return true; |
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} else { |
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return false; |
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} |
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|
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bool SimInfo::removeMolecule(Molecule* mol) { |
166 |
< |
std::vector<Molecule*>::iterator i; |
167 |
< |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
166 |
> |
MoleculeIterator i; |
167 |
> |
i = molecules_.find(mol->getGlobalIndex()); |
168 |
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|
169 |
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if (i != molecules_.end() ) { |
170 |
< |
molecules_.push_back(mol); |
170 |
> |
|
171 |
> |
assert(mol == i->second); |
172 |
> |
|
173 |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraints(); |
181 |
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|
182 |
< |
globalIndexToMol_.erase(mol->getGlobalIndex()); |
182 |
> |
molecules_.erase(mol->getGlobalIndex()); |
183 |
> |
|
184 |
> |
delete mol; |
185 |
> |
|
186 |
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return true; |
187 |
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} else { |
188 |
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return false; |
192 |
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} |
193 |
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|
194 |
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|
195 |
< |
Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) { |
195 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
196 |
|
i = molecules_.begin(); |
197 |
< |
return i == molecules_.end() ? NULL : *i; |
197 |
> |
return i == molecules_.end() ? NULL : i->second; |
198 |
|
} |
199 |
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|
200 |
< |
Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) { |
200 |
> |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
201 |
|
++i; |
202 |
< |
return i == molecules_.end() ? NULL : *i; |
202 |
> |
return i == molecules_.end() ? NULL : i->second; |
203 |
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} |
204 |
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|
205 |
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|
206 |
|
void SimInfo::calcNdf() { |
207 |
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int ndf_local; |
208 |
< |
std::vector<Molecule*>::iterator i; |
208 |
> |
MoleculeIterator i; |
209 |
|
std::vector<StuntDouble*>::iterator j; |
210 |
|
Molecule* mol; |
211 |
|
StuntDouble* integrableObject; |
238 |
|
ndf_ = ndf_local; |
239 |
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#endif |
240 |
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|
241 |
< |
// nZconstraints is global, as are the 3 COM translations for the |
241 |
> |
// nZconstraints_ is global, as are the 3 COM translations for the |
242 |
|
// entire system: |
243 |
< |
ndf_ = ndf_ - 3 - nZconstraints; |
243 |
> |
ndf_ = ndf_ - 3 - nZconstraint_; |
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|
245 |
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} |
246 |
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|
247 |
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void SimInfo::calcNdfRaw() { |
248 |
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int ndfRaw_local; |
249 |
|
|
250 |
< |
std::vector<Molecule*>::iterator i; |
250 |
> |
MoleculeIterator i; |
251 |
|
std::vector<StuntDouble*>::iterator j; |
252 |
|
Molecule* mol; |
253 |
|
StuntDouble* integrableObject; |
291 |
|
ndfTrans_ = ndfTrans_local; |
292 |
|
#endif |
293 |
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|
294 |
< |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
294 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
295 |
|
|
296 |
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} |
297 |
|
|
323 |
|
exclude_.addPair(b, c); |
324 |
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} |
325 |
|
|
326 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
326 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
327 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
328 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
329 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
368 |
|
exclude_.removePair(b, c); |
369 |
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} |
370 |
|
|
371 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
371 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
372 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
373 |
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b = torsion->getAtomB()->getGlobalIndex(); |
374 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
392 |
|
curStampId = molStampIds_.size(); |
393 |
|
|
394 |
|
moleculeStamps_.push_back(molStamp); |
395 |
< |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
395 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
396 |
|
} |
397 |
|
|
398 |
+ |
void SimInfo::update() { |
399 |
+ |
|
400 |
+ |
setupSimType(); |
401 |
+ |
|
402 |
+ |
#ifdef IS_MPI |
403 |
+ |
setupFortranParallel(); |
404 |
+ |
#endif |
405 |
+ |
|
406 |
+ |
setupFortranSim(); |
407 |
+ |
|
408 |
+ |
setupCutoff(); |
409 |
+ |
|
410 |
+ |
//notify fortran whether reaction field is used or not. It is deprecated now |
411 |
+ |
//int isError = 0; |
412 |
+ |
//initFortranFF( &useReactionField, &isError ); |
413 |
+ |
|
414 |
+ |
//if(isError){ |
415 |
+ |
// sprintf( painCave.errMsg, |
416 |
+ |
// "SimCreator::initFortran() error: There was an error initializing the forceField in fortran.\n" ); |
417 |
+ |
// painCave.isFatal = 1; |
418 |
+ |
// simError(); |
419 |
+ |
//} |
420 |
+ |
|
421 |
+ |
calcNdf(); |
422 |
+ |
calcNdfRaw(); |
423 |
+ |
calcNdfTrans(); |
424 |
+ |
|
425 |
+ |
fortranInitialized_ = true; |
426 |
+ |
} |
427 |
+ |
|
428 |
+ |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
429 |
+ |
SimInfo::MoleculeIterator mi; |
430 |
+ |
Molecule* mol; |
431 |
+ |
Molecule::AtomIterator ai; |
432 |
+ |
Atom* atom; |
433 |
+ |
std::set<AtomType*> atomTypes; |
434 |
+ |
|
435 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
436 |
+ |
|
437 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
438 |
+ |
atomTypes.insert(atom->getAtomType()); |
439 |
+ |
} |
440 |
+ |
|
441 |
+ |
} |
442 |
+ |
|
443 |
+ |
return atomTypes; |
444 |
+ |
} |
445 |
+ |
|
446 |
+ |
void SimInfo::setupSimType() { |
447 |
+ |
std::set<AtomType*>::iterator i; |
448 |
+ |
std::set<AtomType*> atomTypes; |
449 |
+ |
atomTypes = getUniqueAtomTypes(); |
450 |
+ |
|
451 |
+ |
int useLennardJones = 0; |
452 |
+ |
int useElectrostatic = 0; |
453 |
+ |
int useEAM = 0; |
454 |
+ |
int useCharge = 0; |
455 |
+ |
int useDirectional = 0; |
456 |
+ |
int useDipole = 0; |
457 |
+ |
int useGayBerne = 0; |
458 |
+ |
int useSticky = 0; |
459 |
+ |
int useShape = 0; |
460 |
+ |
int useFLARB = 0; //it is not in AtomType yet |
461 |
+ |
int useDirectionalAtom = 0; |
462 |
+ |
int useElectrostatics = 0; |
463 |
+ |
//usePBC and useRF are from globals |
464 |
+ |
bool usePBC = globals_->getPBC(); |
465 |
+ |
bool useRF = globals_->getUseRF(); |
466 |
+ |
|
467 |
+ |
//loop over all of the atom types |
468 |
+ |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
469 |
+ |
useLennardJones |= (*i)->isLennardJones(); |
470 |
+ |
useElectrostatic |= (*i)->isElectrostatic(); |
471 |
+ |
useEAM |= (*i)->isEAM(); |
472 |
+ |
useCharge |= (*i)->isCharge(); |
473 |
+ |
useDirectional |= (*i)->isDirectional(); |
474 |
+ |
useDipole |= (*i)->isDipole(); |
475 |
+ |
useGayBerne |= (*i)->isGayBerne(); |
476 |
+ |
useSticky |= (*i)->isSticky(); |
477 |
+ |
useShape |= (*i)->isShape(); |
478 |
+ |
} |
479 |
+ |
|
480 |
+ |
if (useSticky || useDipole || useGayBerne || useShape) { |
481 |
+ |
useDirectionalAtom = 1; |
482 |
+ |
} |
483 |
+ |
|
484 |
+ |
if (useCharge || useDipole) { |
485 |
+ |
useElectrostatics = 1; |
486 |
+ |
} |
487 |
+ |
|
488 |
+ |
#ifdef IS_MPI |
489 |
+ |
int temp; |
490 |
+ |
|
491 |
+ |
temp = usePBC; |
492 |
+ |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
493 |
+ |
|
494 |
+ |
temp = useDirectionalAtom; |
495 |
+ |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
496 |
+ |
|
497 |
+ |
temp = useLennardJones; |
498 |
+ |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
499 |
+ |
|
500 |
+ |
temp = useElectrostatics; |
501 |
+ |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
502 |
+ |
|
503 |
+ |
temp = useCharge; |
504 |
+ |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
505 |
+ |
|
506 |
+ |
temp = useDipole; |
507 |
+ |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
508 |
+ |
|
509 |
+ |
temp = useSticky; |
510 |
+ |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
511 |
+ |
|
512 |
+ |
temp = useGayBerne; |
513 |
+ |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
514 |
+ |
|
515 |
+ |
temp = useEAM; |
516 |
+ |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
517 |
+ |
|
518 |
+ |
temp = useShape; |
519 |
+ |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
520 |
+ |
|
521 |
+ |
temp = useFLARB; |
522 |
+ |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
523 |
+ |
|
524 |
+ |
temp = useRF; |
525 |
+ |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
526 |
+ |
|
527 |
+ |
#endif |
528 |
+ |
|
529 |
+ |
fInfo_.SIM_uses_PBC = usePBC; |
530 |
+ |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
531 |
+ |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
532 |
+ |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
533 |
+ |
fInfo_.SIM_uses_Charges = useCharge; |
534 |
+ |
fInfo_.SIM_uses_Dipoles = useDipole; |
535 |
+ |
fInfo_.SIM_uses_Sticky = useSticky; |
536 |
+ |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
537 |
+ |
fInfo_.SIM_uses_EAM = useEAM; |
538 |
+ |
fInfo_.SIM_uses_Shapes = useShape; |
539 |
+ |
fInfo_.SIM_uses_FLARB = useFLARB; |
540 |
+ |
fInfo_.SIM_uses_RF = useRF; |
541 |
+ |
|
542 |
+ |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
543 |
+ |
|
544 |
+ |
if (globals_->haveDielectric()) { |
545 |
+ |
fInfo_.dielect = globals_->getDielectric(); |
546 |
+ |
} else { |
547 |
+ |
sprintf(painCave.errMsg, |
548 |
+ |
"SimSetup Error: No Dielectric constant was set.\n" |
549 |
+ |
"\tYou are trying to use Reaction Field without" |
550 |
+ |
"\tsetting a dielectric constant!\n"); |
551 |
+ |
painCave.isFatal = 1; |
552 |
+ |
simError(); |
553 |
+ |
} |
554 |
+ |
|
555 |
+ |
} else { |
556 |
+ |
fInfo_.dielect = 0.0; |
557 |
+ |
} |
558 |
+ |
|
559 |
+ |
} |
560 |
+ |
|
561 |
+ |
void SimInfo::setupFortranSim() { |
562 |
+ |
int isError; |
563 |
+ |
int nExclude; |
564 |
+ |
std::vector<int> fortranGlobalGroupMembership; |
565 |
+ |
|
566 |
+ |
nExclude = exclude_.getSize(); |
567 |
+ |
isError = 0; |
568 |
+ |
|
569 |
+ |
//globalGroupMembership_ is filled by SimCreator |
570 |
+ |
for (int i = 0; i < nGlobalAtoms_; i++) { |
571 |
+ |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
572 |
+ |
} |
573 |
+ |
|
574 |
+ |
//calculate mass ratio of cutoff group |
575 |
+ |
std::vector<double> mfact; |
576 |
+ |
SimInfo::MoleculeIterator mi; |
577 |
+ |
Molecule* mol; |
578 |
+ |
Molecule::CutoffGroupIterator ci; |
579 |
+ |
CutoffGroup* cg; |
580 |
+ |
Molecule::AtomIterator ai; |
581 |
+ |
Atom* atom; |
582 |
+ |
double totalMass; |
583 |
+ |
|
584 |
+ |
//to avoid memory reallocation, reserve enough space for mfact |
585 |
+ |
mfact.reserve(getNCutoffGroups()); |
586 |
+ |
|
587 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
588 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
589 |
+ |
|
590 |
+ |
totalMass = cg->getMass(); |
591 |
+ |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
592 |
+ |
mfact.push_back(atom->getMass()/totalMass); |
593 |
+ |
} |
594 |
+ |
|
595 |
+ |
} |
596 |
+ |
} |
597 |
+ |
|
598 |
+ |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
599 |
+ |
std::vector<int> identArray; |
600 |
+ |
|
601 |
+ |
//to avoid memory reallocation, reserve enough space identArray |
602 |
+ |
identArray.reserve(getNAtoms()); |
603 |
+ |
|
604 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
605 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
606 |
+ |
identArray.push_back(atom->getIdent()); |
607 |
+ |
} |
608 |
+ |
} |
609 |
+ |
|
610 |
+ |
//fill molMembershipArray |
611 |
+ |
//molMembershipArray is filled by SimCreator |
612 |
+ |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
613 |
+ |
for (int i = 0; i < nGlobalAtoms_; i++) { |
614 |
+ |
molMembershipArray.push_back(globalMolMembership_[i] + 1); |
615 |
+ |
} |
616 |
+ |
|
617 |
+ |
//setup fortran simulation |
618 |
+ |
//gloalExcludes and molMembershipArray should go away (They are never used) |
619 |
+ |
//why the hell fortran need to know molecule? |
620 |
+ |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
621 |
+ |
int nGlobalExcludes = 0; |
622 |
+ |
int* globalExcludes = NULL; |
623 |
+ |
int* excludeList = exclude_.getExcludeList(); |
624 |
+ |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
625 |
+ |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
626 |
+ |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
627 |
+ |
|
628 |
+ |
if( isError ){ |
629 |
+ |
|
630 |
+ |
sprintf( painCave.errMsg, |
631 |
+ |
"There was an error setting the simulation information in fortran.\n" ); |
632 |
+ |
painCave.isFatal = 1; |
633 |
+ |
painCave.severity = OOPSE_ERROR; |
634 |
+ |
simError(); |
635 |
+ |
} |
636 |
+ |
|
637 |
+ |
#ifdef IS_MPI |
638 |
+ |
sprintf( checkPointMsg, |
639 |
+ |
"succesfully sent the simulation information to fortran.\n"); |
640 |
+ |
MPIcheckPoint(); |
641 |
+ |
#endif // is_mpi |
642 |
+ |
} |
643 |
+ |
|
644 |
+ |
|
645 |
+ |
#ifdef IS_MPI |
646 |
+ |
void SimInfo::setupFortranParallel() { |
647 |
+ |
|
648 |
+ |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
649 |
+ |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
650 |
+ |
std::vector<int> localToGlobalCutoffGroupIndex; |
651 |
+ |
SimInfo::MoleculeIterator mi; |
652 |
+ |
Molecule::AtomIterator ai; |
653 |
+ |
Molecule::CutoffGroupIterator ci; |
654 |
+ |
Molecule* mol; |
655 |
+ |
Atom* atom; |
656 |
+ |
CutoffGroup* cg; |
657 |
+ |
mpiSimData parallelData; |
658 |
+ |
int isError; |
659 |
+ |
|
660 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
661 |
+ |
|
662 |
+ |
//local index(index in DataStorge) of atom is important |
663 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
664 |
+ |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
665 |
+ |
} |
666 |
+ |
|
667 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
668 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
669 |
+ |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
670 |
+ |
} |
671 |
+ |
|
672 |
+ |
} |
673 |
+ |
|
674 |
+ |
//fill up mpiSimData struct |
675 |
+ |
parallelData.nMolGlobal = getNGlobalMolecules(); |
676 |
+ |
parallelData.nMolLocal = getNMolecules(); |
677 |
+ |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
678 |
+ |
parallelData.nAtomsLocal = getNAtoms(); |
679 |
+ |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
680 |
+ |
parallelData.nGroupsLocal = getNCutoffGroups(); |
681 |
+ |
parallelData.myNode = worldRank; |
682 |
+ |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
683 |
+ |
|
684 |
+ |
//pass mpiSimData struct and index arrays to fortran |
685 |
+ |
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
686 |
+ |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
687 |
+ |
&localToGlobalCutoffGroupIndex[0], &isError); |
688 |
+ |
|
689 |
+ |
if (isError) { |
690 |
+ |
sprintf(painCave.errMsg, |
691 |
+ |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
692 |
+ |
painCave.isFatal = 1; |
693 |
+ |
simError(); |
694 |
+ |
} |
695 |
+ |
|
696 |
+ |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
697 |
+ |
MPIcheckPoint(); |
698 |
+ |
|
699 |
+ |
|
700 |
+ |
} |
701 |
+ |
|
702 |
+ |
#endif |
703 |
+ |
|
704 |
+ |
double SimInfo::calcMaxCutoffRadius() { |
705 |
+ |
|
706 |
+ |
|
707 |
+ |
std::set<AtomType*> atomTypes; |
708 |
+ |
std::set<AtomType*>::iterator i; |
709 |
+ |
std::vector<double> cutoffRadius; |
710 |
+ |
|
711 |
+ |
//get the unique atom types |
712 |
+ |
atomTypes = getUniqueAtomTypes(); |
713 |
+ |
|
714 |
+ |
//query the max cutoff radius among these atom types |
715 |
+ |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
716 |
+ |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
717 |
+ |
} |
718 |
+ |
|
719 |
+ |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
720 |
+ |
#ifdef IS_MPI |
721 |
+ |
//pick the max cutoff radius among the processors |
722 |
+ |
#endif |
723 |
+ |
|
724 |
+ |
return maxCutoffRadius; |
725 |
+ |
} |
726 |
+ |
|
727 |
+ |
void SimInfo::setupCutoff() { |
728 |
+ |
double rcut_; //cutoff radius |
729 |
+ |
double rsw_; //switching radius |
730 |
+ |
|
731 |
+ |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
732 |
+ |
|
733 |
+ |
if (!globals_->haveRcut()){ |
734 |
+ |
sprintf(painCave.errMsg, |
735 |
+ |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
736 |
+ |
"\tOOPSE will use a default value of 15.0 angstroms" |
737 |
+ |
"\tfor the cutoffRadius.\n"); |
738 |
+ |
painCave.isFatal = 0; |
739 |
+ |
simError(); |
740 |
+ |
rcut_ = 15.0; |
741 |
+ |
} else{ |
742 |
+ |
rcut_ = globals_->getRcut(); |
743 |
+ |
} |
744 |
+ |
|
745 |
+ |
if (!globals_->haveRsw()){ |
746 |
+ |
sprintf(painCave.errMsg, |
747 |
+ |
"SimCreator Warning: No value was set for switchingRadius.\n" |
748 |
+ |
"\tOOPSE will use a default value of\n" |
749 |
+ |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
750 |
+ |
painCave.isFatal = 0; |
751 |
+ |
simError(); |
752 |
+ |
rsw_ = 0.95 * rcut_; |
753 |
+ |
} else{ |
754 |
+ |
rsw_ = globals_->getRsw(); |
755 |
+ |
} |
756 |
+ |
|
757 |
+ |
} else { |
758 |
+ |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
759 |
+ |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
760 |
+ |
|
761 |
+ |
if (globals_->haveRcut()) { |
762 |
+ |
rcut_ = globals_->getRcut(); |
763 |
+ |
} else { |
764 |
+ |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
765 |
+ |
rcut_ = calcMaxCutoffRadius(); |
766 |
+ |
} |
767 |
+ |
|
768 |
+ |
if (globals_->haveRsw()) { |
769 |
+ |
rsw_ = globals_->getRsw(); |
770 |
+ |
} else { |
771 |
+ |
rsw_ = rcut_; |
772 |
+ |
} |
773 |
+ |
|
774 |
+ |
} |
775 |
+ |
|
776 |
+ |
double rnblist = rcut_ + 1; // skin of neighbor list |
777 |
+ |
|
778 |
+ |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
779 |
+ |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
780 |
+ |
} |
781 |
+ |
|
782 |
+ |
void SimInfo::addProperty(GenericData* genData) { |
783 |
+ |
properties_.addProperty(genData); |
784 |
+ |
} |
785 |
+ |
|
786 |
+ |
void SimInfo::removeProperty(const std::string& propName) { |
787 |
+ |
properties_.removeProperty(propName); |
788 |
+ |
} |
789 |
+ |
|
790 |
+ |
void SimInfo::clearProperties() { |
791 |
+ |
properties_.clearProperties(); |
792 |
+ |
} |
793 |
+ |
|
794 |
+ |
std::vector<std::string> SimInfo::getPropertyNames() { |
795 |
+ |
return properties_.getPropertyNames(); |
796 |
+ |
} |
797 |
+ |
|
798 |
+ |
std::vector<GenericData*> SimInfo::getProperties() { |
799 |
+ |
return properties_.getProperties(); |
800 |
+ |
} |
801 |
+ |
|
802 |
+ |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
803 |
+ |
return properties_.getPropertyByName(propName); |
804 |
+ |
} |
805 |
+ |
|
806 |
+ |
|
807 |
|
std::ostream& operator <<(ostream& o, SimInfo& info) { |
808 |
|
|
809 |
|
return o; |