31 |
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*/ |
32 |
|
|
33 |
|
#include <algorithm> |
34 |
< |
|
34 |
> |
#include <set> |
35 |
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#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(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
45 |
< |
ForceField* ff, Globals* globals) : |
46 |
< |
forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
47 |
< |
nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
48 |
< |
nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL), |
49 |
< |
fortranInitialized_(false) { |
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; // number of atoms belong to cutoff groups |
59 |
< |
int nGroups; //total cutoff groups defined in meta-data file |
60 |
< |
CutoffGroupStamp* cgStamp; |
53 |
< |
int nAtomsInGroups; |
54 |
< |
int nCutoffGroupsInStamp; |
55 |
< |
|
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 nAtomsInRigidBodies; |
58 |
< |
int nRigidBodiesInStamp; |
59 |
< |
int nRigidAtoms; |
60 |
< |
int nRigidBodies; |
61 |
< |
|
62 |
< |
nGlobalAtoms_ = 0; |
62 |
> |
int nRigidAtoms = 0; |
63 |
|
|
64 |
– |
nGroups = 0; |
65 |
– |
nCutoffAtoms = 0; |
66 |
– |
|
67 |
– |
nRigidBodies |
68 |
– |
nRigidBodies = 0; |
69 |
– |
|
64 |
|
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
65 |
|
molStamp = i->first; |
66 |
|
nMolWithSameStamp = i->second; |
72 |
|
|
73 |
|
|
74 |
|
//calculate atoms in cutoff groups |
75 |
< |
nAtomsInGroups = 0; |
76 |
< |
nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
75 |
> |
int nAtomsInGroups = 0; |
76 |
> |
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
77 |
|
|
78 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
79 |
|
cgStamp = molStamp->getCutoffGroup(j); |
84 |
|
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
85 |
|
|
86 |
|
//calculate atoms in rigid bodies |
87 |
< |
nAtomsInRigidBodies = 0; |
88 |
< |
nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
87 |
> |
int nAtomsInRigidBodies = 0; |
88 |
> |
int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
89 |
|
|
90 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
91 |
|
rbStamp = molStamp->getRigidBody(j); |
92 |
< |
nRigidBodiesInStamp += rbStamp->getNMembers(); |
92 |
> |
nAtomsInRigidBodies += rbStamp->getNMembers(); |
93 |
|
} |
94 |
|
|
95 |
< |
nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
95 |
> |
nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
96 |
|
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
97 |
|
|
98 |
|
} |
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 a rigid body |
107 |
< |
//therefore the total number of cutoff groups in the system is equal to |
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 + nRigidBodies; |
110 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
111 |
|
|
118 |
– |
//initialize globalGroupMembership_, every element of this array will be 0 |
119 |
– |
globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
120 |
– |
|
112 |
|
nGlobalMols_ = molStampIds_.size(); |
113 |
|
|
114 |
|
#ifdef IS_MPI |
123 |
|
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
124 |
|
|
125 |
|
delete sman_; |
126 |
< |
delete globals_; |
126 |
> |
delete simParams_; |
127 |
|
delete forceField_; |
128 |
|
|
129 |
|
} |
133 |
|
MoleculeIterator i; |
134 |
|
|
135 |
|
i = molecules_.find(mol->getGlobalIndex()); |
136 |
< |
if (i != molecules_.end() ) { |
136 |
> |
if (i == molecules_.end() ) { |
137 |
|
|
138 |
< |
molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
138 |
> |
molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
139 |
|
|
140 |
|
nAtoms_ += mol->getNAtoms(); |
141 |
|
nBonds_ += mol->getNBonds(); |
230 |
|
|
231 |
|
// nZconstraints_ is global, as are the 3 COM translations for the |
232 |
|
// entire system: |
233 |
< |
ndf_ = ndf_ - 3 - nZconstraints_; |
233 |
> |
ndf_ = ndf_ - 3 - nZconstraint_; |
234 |
|
|
235 |
|
} |
236 |
|
|
281 |
|
ndfTrans_ = ndfTrans_local; |
282 |
|
#endif |
283 |
|
|
284 |
< |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints_; |
284 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
285 |
|
|
286 |
|
} |
287 |
|
|
313 |
|
exclude_.addPair(b, c); |
314 |
|
} |
315 |
|
|
316 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
316 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
317 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
318 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
319 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
358 |
|
exclude_.removePair(b, c); |
359 |
|
} |
360 |
|
|
361 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
361 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
362 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
363 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
364 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
382 |
|
curStampId = molStampIds_.size(); |
383 |
|
|
384 |
|
moleculeStamps_.push_back(molStamp); |
385 |
< |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
385 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
386 |
|
} |
387 |
|
|
388 |
|
void SimInfo::update() { |
395 |
|
|
396 |
|
setupFortranSim(); |
397 |
|
|
398 |
+ |
//setup fortran force field |
399 |
+ |
/** @deprecate */ |
400 |
+ |
int isError = 0; |
401 |
+ |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
402 |
+ |
if(isError){ |
403 |
+ |
sprintf( painCave.errMsg, |
404 |
+ |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
405 |
+ |
painCave.isFatal = 1; |
406 |
+ |
simError(); |
407 |
+ |
} |
408 |
+ |
|
409 |
+ |
|
410 |
|
setupCutoff(); |
411 |
|
|
409 |
– |
//notify fortran whether reaction field is used or not. It is deprecated now |
410 |
– |
//int isError = 0; |
411 |
– |
//initFortranFF( &useReactionField, &isError ); |
412 |
– |
|
413 |
– |
//if(isError){ |
414 |
– |
// sprintf( painCave.errMsg, |
415 |
– |
// "SimCreator::initFortran() error: There was an error initializing the forceField in fortran.\n" ); |
416 |
– |
// painCave.isFatal = 1; |
417 |
– |
// simError(); |
418 |
– |
//} |
419 |
– |
|
412 |
|
calcNdf(); |
413 |
|
calcNdfRaw(); |
414 |
|
calcNdfTrans(); |
417 |
|
} |
418 |
|
|
419 |
|
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
420 |
< |
typename SimInfo::MoleculeIterator mi; |
420 |
> |
SimInfo::MoleculeIterator mi; |
421 |
|
Molecule* mol; |
422 |
< |
typename Molecule::AtomIterator ai; |
422 |
> |
Molecule::AtomIterator ai; |
423 |
|
Atom* atom; |
424 |
|
std::set<AtomType*> atomTypes; |
425 |
|
|
451 |
|
int useFLARB = 0; //it is not in AtomType yet |
452 |
|
int useDirectionalAtom = 0; |
453 |
|
int useElectrostatics = 0; |
454 |
< |
//usePBC and useRF are from globals |
455 |
< |
bool usePBC = globals_->getPBC(); |
456 |
< |
bool useRF = globals_->getUseRF(); |
454 |
> |
//usePBC and useRF are from simParams |
455 |
> |
bool usePBC = simParams_->getPBC(); |
456 |
> |
bool useRF = simParams_->getUseRF(); |
457 |
|
|
458 |
|
//loop over all of the atom types |
459 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
460 |
< |
useLennardJones |= i->isLennardJones(); |
461 |
< |
useElectrostatic |= i->isElectrostatic(); |
462 |
< |
useEAM |= i->isEAM(); |
463 |
< |
useCharge |= i->isCharge(); |
464 |
< |
useDirectional |= i->isDirectional(); |
465 |
< |
useDipole |= i->isDipole(); |
466 |
< |
useGayBerne |= i->isGayBerne(); |
467 |
< |
useSticky |= i->isSticky(); |
468 |
< |
useShape |= i->isShape(); |
460 |
> |
useLennardJones |= (*i)->isLennardJones(); |
461 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
462 |
> |
useEAM |= (*i)->isEAM(); |
463 |
> |
useCharge |= (*i)->isCharge(); |
464 |
> |
useDirectional |= (*i)->isDirectional(); |
465 |
> |
useDipole |= (*i)->isDipole(); |
466 |
> |
useGayBerne |= (*i)->isGayBerne(); |
467 |
> |
useSticky |= (*i)->isSticky(); |
468 |
> |
useShape |= (*i)->isShape(); |
469 |
|
} |
470 |
|
|
471 |
|
if (useSticky || useDipole || useGayBerne || useShape) { |
531 |
|
fInfo_.SIM_uses_RF = useRF; |
532 |
|
|
533 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
534 |
< |
fInfo_.dielect = dielectric; |
534 |
> |
|
535 |
> |
if (simParams_->haveDielectric()) { |
536 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
537 |
> |
} else { |
538 |
> |
sprintf(painCave.errMsg, |
539 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
540 |
> |
"\tYou are trying to use Reaction Field without" |
541 |
> |
"\tsetting a dielectric constant!\n"); |
542 |
> |
painCave.isFatal = 1; |
543 |
> |
simError(); |
544 |
> |
} |
545 |
> |
|
546 |
|
} else { |
547 |
|
fInfo_.dielect = 0.0; |
548 |
|
} |
564 |
|
|
565 |
|
//calculate mass ratio of cutoff group |
566 |
|
std::vector<double> mfact; |
567 |
< |
typename SimInfo::MoleculeIterator mi; |
567 |
> |
SimInfo::MoleculeIterator mi; |
568 |
|
Molecule* mol; |
569 |
< |
typename Molecule::CutoffGroupIterator ci; |
569 |
> |
Molecule::CutoffGroupIterator ci; |
570 |
|
CutoffGroup* cg; |
571 |
< |
typename Molecule::AtomIterator ai; |
571 |
> |
Molecule::AtomIterator ai; |
572 |
|
Atom* atom; |
573 |
|
double totalMass; |
574 |
|
|
602 |
|
//molMembershipArray is filled by SimCreator |
603 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
604 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
605 |
< |
molMembershipArray.push_back(globalMolMembership_[i] + 1); |
605 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
606 |
|
} |
607 |
|
|
608 |
|
//setup fortran simulation |
609 |
|
//gloalExcludes and molMembershipArray should go away (They are never used) |
610 |
|
//why the hell fortran need to know molecule? |
611 |
|
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
612 |
< |
|
613 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, exclude_->getExcludeList(), |
614 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
612 |
> |
int nGlobalExcludes = 0; |
613 |
> |
int* globalExcludes = NULL; |
614 |
> |
int* excludeList = exclude_.getExcludeList(); |
615 |
> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
616 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
617 |
|
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
618 |
|
|
619 |
|
if( isError ){ |
639 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
640 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
641 |
|
std::vector<int> localToGlobalCutoffGroupIndex; |
642 |
< |
typename SimInfo::MoleculeIterator mi; |
643 |
< |
typename Molecule::AtomIterator ai; |
644 |
< |
typename Molecule::CutoffGroupIterator ci; |
642 |
> |
SimInfo::MoleculeIterator mi; |
643 |
> |
Molecule::AtomIterator ai; |
644 |
> |
Molecule::CutoffGroupIterator ci; |
645 |
|
Molecule* mol; |
646 |
|
Atom* atom; |
647 |
|
CutoffGroup* cg; |
695 |
|
double SimInfo::calcMaxCutoffRadius() { |
696 |
|
|
697 |
|
|
698 |
< |
std::vector<AtomType*> atomTypes; |
699 |
< |
std::vector<AtomType*>::iterator i; |
698 |
> |
std::set<AtomType*> atomTypes; |
699 |
> |
std::set<AtomType*>::iterator i; |
700 |
|
std::vector<double> cutoffRadius; |
701 |
|
|
702 |
|
//get the unique atom types |
707 |
|
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
708 |
|
} |
709 |
|
|
710 |
< |
double maxCutoffRadius = std::max_element(cutoffRadius.begin(), cutoffRadius.end()); |
710 |
> |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
711 |
|
#ifdef IS_MPI |
712 |
|
//pick the max cutoff radius among the processors |
713 |
|
#endif |
721 |
|
|
722 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
723 |
|
|
724 |
< |
if (!globals_->haveRcut()){ |
724 |
> |
if (!simParams_->haveRcut()){ |
725 |
|
sprintf(painCave.errMsg, |
726 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
727 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
730 |
|
simError(); |
731 |
|
rcut_ = 15.0; |
732 |
|
} else{ |
733 |
< |
rcut_ = globals_->getRcut(); |
733 |
> |
rcut_ = simParams_->getRcut(); |
734 |
|
} |
735 |
|
|
736 |
< |
if (!globals_->haveRsw()){ |
736 |
> |
if (!simParams_->haveRsw()){ |
737 |
|
sprintf(painCave.errMsg, |
738 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
739 |
|
"\tOOPSE will use a default value of\n" |
742 |
|
simError(); |
743 |
|
rsw_ = 0.95 * rcut_; |
744 |
|
} else{ |
745 |
< |
rsw_ = globals_->getRsw(); |
745 |
> |
rsw_ = simParams_->getRsw(); |
746 |
|
} |
747 |
|
|
748 |
|
} else { |
749 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
750 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
751 |
|
|
752 |
< |
if (globals_->haveRcut()) { |
753 |
< |
rcut_ = globals_->getRcut(); |
752 |
> |
if (simParams_->haveRcut()) { |
753 |
> |
rcut_ = simParams_->getRcut(); |
754 |
|
} else { |
755 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
756 |
|
rcut_ = calcMaxCutoffRadius(); |
757 |
|
} |
758 |
|
|
759 |
< |
if (globals_->haveRsw()) { |
760 |
< |
rsw_ = globals_->getRsw() |
759 |
> |
if (simParams_->haveRsw()) { |
760 |
> |
rsw_ = simParams_->getRsw(); |
761 |
|
} else { |
762 |
|
rsw_ = rcut_; |
763 |
|
} |
794 |
|
return properties_.getPropertyByName(propName); |
795 |
|
} |
796 |
|
|
797 |
+ |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
798 |
+ |
sman_ = sman; |
799 |
|
|
800 |
< |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
800 |
> |
Molecule* mol; |
801 |
> |
RigidBody* rb; |
802 |
> |
Atom* atom; |
803 |
> |
SimInfo::MoleculeIterator mi; |
804 |
> |
Molecule::RigidBodyIterator rbIter; |
805 |
> |
Molecule::AtomIterator atomIter;; |
806 |
> |
|
807 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
808 |
> |
|
809 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
810 |
> |
atom->setSnapshotManager(sman_); |
811 |
> |
} |
812 |
> |
|
813 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
814 |
> |
rb->setSnapshotManager(sman_); |
815 |
> |
} |
816 |
> |
} |
817 |
> |
|
818 |
> |
} |
819 |
|
|
820 |
+ |
Vector3d SimInfo::getComVel(){ |
821 |
+ |
SimInfo::MoleculeIterator i; |
822 |
+ |
Molecule* mol; |
823 |
+ |
|
824 |
+ |
Vector3d comVel(0.0); |
825 |
+ |
double totalMass = 0.0; |
826 |
+ |
|
827 |
+ |
|
828 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
829 |
+ |
double mass = mol->getMass(); |
830 |
+ |
totalMass += mass; |
831 |
+ |
comVel += mass * mol->getComVel(); |
832 |
+ |
} |
833 |
+ |
|
834 |
+ |
comVel /= totalMass; |
835 |
+ |
|
836 |
+ |
return comVel; |
837 |
+ |
} |
838 |
+ |
|
839 |
+ |
Vector3d SimInfo::getCom(){ |
840 |
+ |
SimInfo::MoleculeIterator i; |
841 |
+ |
Molecule* mol; |
842 |
+ |
|
843 |
+ |
Vector3d com(0.0); |
844 |
+ |
double totalMass = 0.0; |
845 |
+ |
|
846 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
847 |
+ |
double mass = mol->getMass(); |
848 |
+ |
totalMass += mass; |
849 |
+ |
com += mass * mol->getCom(); |
850 |
+ |
} |
851 |
+ |
|
852 |
+ |
com /= totalMass; |
853 |
+ |
|
854 |
+ |
return com; |
855 |
+ |
|
856 |
+ |
} |
857 |
+ |
|
858 |
+ |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
859 |
+ |
|
860 |
|
return o; |
861 |
|
} |
862 |
|
|
863 |
|
}//end namespace oopse |
864 |
+ |
|