33 |
|
#include <algorithm> |
34 |
|
|
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(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
44 |
> |
SimInfo::SimInfo(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), |
48 |
> |
nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL), |
49 |
|
fortranInitialized_(false) { |
50 |
|
|
51 |
|
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
67 |
|
|
68 |
|
nGroups = 0; |
69 |
|
nCutoffAtoms = 0; |
66 |
– |
|
67 |
– |
nRigidBodies |
70 |
|
nRigidBodies = 0; |
71 |
|
|
72 |
|
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
241 |
|
|
242 |
|
// nZconstraints_ is global, as are the 3 COM translations for the |
243 |
|
// entire system: |
244 |
< |
ndf_ = ndf_ - 3 - nZconstraints_; |
244 |
> |
ndf_ = ndf_ - 3 - nZconstraint_; |
245 |
|
|
246 |
|
} |
247 |
|
|
292 |
|
ndfTrans_ = ndfTrans_local; |
293 |
|
#endif |
294 |
|
|
295 |
< |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints_; |
295 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
296 |
|
|
297 |
|
} |
298 |
|
|
324 |
|
exclude_.addPair(b, c); |
325 |
|
} |
326 |
|
|
327 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
327 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
328 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
329 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
330 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
369 |
|
exclude_.removePair(b, c); |
370 |
|
} |
371 |
|
|
372 |
< |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
372 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
373 |
|
a = torsion->getAtomA()->getGlobalIndex(); |
374 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
375 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
393 |
|
curStampId = molStampIds_.size(); |
394 |
|
|
395 |
|
moleculeStamps_.push_back(molStamp); |
396 |
< |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
396 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
397 |
|
} |
398 |
|
|
399 |
|
void SimInfo::update() { |
406 |
|
|
407 |
|
setupFortranSim(); |
408 |
|
|
409 |
+ |
//setup fortran force field |
410 |
+ |
/** @deprecate */ |
411 |
+ |
int isError = 0; |
412 |
+ |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
413 |
+ |
if(isError){ |
414 |
+ |
sprintf( painCave.errMsg, |
415 |
+ |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
416 |
+ |
painCave.isFatal = 1; |
417 |
+ |
simError(); |
418 |
+ |
} |
419 |
+ |
|
420 |
+ |
|
421 |
|
setupCutoff(); |
408 |
– |
|
409 |
– |
//notify fortran whether reaction field is used or not. It is deprecated now |
410 |
– |
//int isError = 0; |
411 |
– |
//initFortranFF( &useReactionField, &isError ); |
422 |
|
|
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 |
– |
|
423 |
|
calcNdf(); |
424 |
|
calcNdfRaw(); |
425 |
|
calcNdfTrans(); |
428 |
|
} |
429 |
|
|
430 |
|
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
431 |
< |
typename SimInfo::MoleculeIterator mi; |
431 |
> |
SimInfo::MoleculeIterator mi; |
432 |
|
Molecule* mol; |
433 |
< |
typename Molecule::AtomIterator ai; |
433 |
> |
Molecule::AtomIterator ai; |
434 |
|
Atom* atom; |
435 |
|
std::set<AtomType*> atomTypes; |
436 |
|
|
468 |
|
|
469 |
|
//loop over all of the atom types |
470 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
471 |
< |
useLennardJones |= i->isLennardJones(); |
472 |
< |
useElectrostatic |= i->isElectrostatic(); |
473 |
< |
useEAM |= i->isEAM(); |
474 |
< |
useCharge |= i->isCharge(); |
475 |
< |
useDirectional |= i->isDirectional(); |
476 |
< |
useDipole |= i->isDipole(); |
477 |
< |
useGayBerne |= i->isGayBerne(); |
478 |
< |
useSticky |= i->isSticky(); |
479 |
< |
useShape |= i->isShape(); |
471 |
> |
useLennardJones |= (*i)->isLennardJones(); |
472 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
473 |
> |
useEAM |= (*i)->isEAM(); |
474 |
> |
useCharge |= (*i)->isCharge(); |
475 |
> |
useDirectional |= (*i)->isDirectional(); |
476 |
> |
useDipole |= (*i)->isDipole(); |
477 |
> |
useGayBerne |= (*i)->isGayBerne(); |
478 |
> |
useSticky |= (*i)->isSticky(); |
479 |
> |
useShape |= (*i)->isShape(); |
480 |
|
} |
481 |
|
|
482 |
|
if (useSticky || useDipole || useGayBerne || useShape) { |
542 |
|
fInfo_.SIM_uses_RF = useRF; |
543 |
|
|
544 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
545 |
< |
fInfo_.dielect = dielectric; |
545 |
> |
|
546 |
> |
if (globals_->haveDielectric()) { |
547 |
> |
fInfo_.dielect = globals_->getDielectric(); |
548 |
> |
} else { |
549 |
> |
sprintf(painCave.errMsg, |
550 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
551 |
> |
"\tYou are trying to use Reaction Field without" |
552 |
> |
"\tsetting a dielectric constant!\n"); |
553 |
> |
painCave.isFatal = 1; |
554 |
> |
simError(); |
555 |
> |
} |
556 |
> |
|
557 |
|
} else { |
558 |
|
fInfo_.dielect = 0.0; |
559 |
|
} |
575 |
|
|
576 |
|
//calculate mass ratio of cutoff group |
577 |
|
std::vector<double> mfact; |
578 |
< |
typename SimInfo::MoleculeIterator mi; |
578 |
> |
SimInfo::MoleculeIterator mi; |
579 |
|
Molecule* mol; |
580 |
< |
typename Molecule::CutoffGroupIterator ci; |
580 |
> |
Molecule::CutoffGroupIterator ci; |
581 |
|
CutoffGroup* cg; |
582 |
< |
typename Molecule::AtomIterator ai; |
582 |
> |
Molecule::AtomIterator ai; |
583 |
|
Atom* atom; |
584 |
|
double totalMass; |
585 |
|
|
620 |
|
//gloalExcludes and molMembershipArray should go away (They are never used) |
621 |
|
//why the hell fortran need to know molecule? |
622 |
|
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
623 |
< |
|
624 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, exclude_->getExcludeList(), |
625 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
623 |
> |
int nGlobalExcludes = 0; |
624 |
> |
int* globalExcludes = NULL; |
625 |
> |
int* excludeList = exclude_.getExcludeList(); |
626 |
> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
627 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
628 |
|
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
629 |
|
|
630 |
|
if( isError ){ |
650 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
651 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
652 |
|
std::vector<int> localToGlobalCutoffGroupIndex; |
653 |
< |
typename SimInfo::MoleculeIterator mi; |
654 |
< |
typename Molecule::AtomIterator ai; |
655 |
< |
typename Molecule::CutoffGroupIterator ci; |
653 |
> |
SimInfo::MoleculeIterator mi; |
654 |
> |
Molecule::AtomIterator ai; |
655 |
> |
Molecule::CutoffGroupIterator ci; |
656 |
|
Molecule* mol; |
657 |
|
Atom* atom; |
658 |
|
CutoffGroup* cg; |
706 |
|
double SimInfo::calcMaxCutoffRadius() { |
707 |
|
|
708 |
|
|
709 |
< |
std::vector<AtomType*> atomTypes; |
710 |
< |
std::vector<AtomType*>::iterator i; |
709 |
> |
std::set<AtomType*> atomTypes; |
710 |
> |
std::set<AtomType*>::iterator i; |
711 |
|
std::vector<double> cutoffRadius; |
712 |
|
|
713 |
|
//get the unique atom types |
718 |
|
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
719 |
|
} |
720 |
|
|
721 |
< |
double maxCutoffRadius = std::max_element(cutoffRadius.begin(), cutoffRadius.end()); |
721 |
> |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
722 |
|
#ifdef IS_MPI |
723 |
|
//pick the max cutoff radius among the processors |
724 |
|
#endif |
768 |
|
} |
769 |
|
|
770 |
|
if (globals_->haveRsw()) { |
771 |
< |
rsw_ = globals_->getRsw() |
771 |
> |
rsw_ = globals_->getRsw(); |
772 |
|
} else { |
773 |
|
rsw_ = rcut_; |
774 |
|
} |
805 |
|
return properties_.getPropertyByName(propName); |
806 |
|
} |
807 |
|
|
808 |
+ |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
809 |
+ |
sman_ = sman; |
810 |
|
|
811 |
+ |
Molecule* mol; |
812 |
+ |
RigidBody* rb; |
813 |
+ |
Atom* atom; |
814 |
+ |
SimInfo::MoleculeIterator mi; |
815 |
+ |
Molecule::RigidBodyIterator rbIter; |
816 |
+ |
Molecule::AtomIterator atomIter;; |
817 |
+ |
|
818 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
819 |
+ |
|
820 |
+ |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
821 |
+ |
atom->setSnapshotManager(sman_); |
822 |
+ |
} |
823 |
+ |
|
824 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
825 |
+ |
rb->setSnapshotManager(sman_); |
826 |
+ |
} |
827 |
+ |
} |
828 |
+ |
|
829 |
+ |
} |
830 |
+ |
|
831 |
|
std::ostream& operator <<(ostream& o, SimInfo& info) { |
832 |
|
|
833 |
|
return o; |