48 |
|
|
49 |
|
#include <algorithm> |
50 |
|
#include <set> |
51 |
+ |
#include <map> |
52 |
|
|
53 |
|
#include "brains/SimInfo.hpp" |
54 |
|
#include "math/Vector3.hpp" |
55 |
|
#include "primitives/Molecule.hpp" |
56 |
|
#include "UseTheForce/fCutoffPolicy.h" |
57 |
|
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
58 |
+ |
#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
59 |
+ |
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
60 |
|
#include "UseTheForce/doForces_interface.h" |
61 |
|
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
62 |
|
#include "UseTheForce/notifyCutoffs_interface.h" |
63 |
+ |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
64 |
|
#include "utils/MemoryUtils.hpp" |
65 |
|
#include "utils/simError.h" |
66 |
|
#include "selection/SelectionManager.hpp" |
71 |
|
#endif |
72 |
|
|
73 |
|
namespace oopse { |
74 |
+ |
std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
75 |
+ |
std::map<int, std::set<int> >::iterator i = container.find(index); |
76 |
+ |
std::set<int> result; |
77 |
+ |
if (i != container.end()) { |
78 |
+ |
result = i->second; |
79 |
+ |
} |
80 |
|
|
81 |
+ |
return result; |
82 |
+ |
} |
83 |
+ |
|
84 |
|
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
85 |
|
ForceField* ff, Globals* simParams) : |
86 |
|
stamps_(stamps), forceField_(ff), simParams_(simParams), |
96 |
|
MoleculeStamp* molStamp; |
97 |
|
int nMolWithSameStamp; |
98 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
99 |
< |
int nGroups = 0; //total cutoff groups defined in meta-data file |
99 |
> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
100 |
|
CutoffGroupStamp* cgStamp; |
101 |
|
RigidBodyStamp* rbStamp; |
102 |
|
int nRigidAtoms = 0; |
121 |
|
} |
122 |
|
|
123 |
|
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
124 |
+ |
|
125 |
|
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
126 |
|
|
127 |
|
//calculate atoms in rigid bodies |
138 |
|
|
139 |
|
} |
140 |
|
|
141 |
< |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
142 |
< |
//therefore the total number of cutoff groups in the system is equal to |
143 |
< |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
144 |
< |
//file plus the number of cutoff groups defined in meta-data file |
141 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff |
142 |
> |
//group therefore the total number of cutoff groups in the system is |
143 |
> |
//equal to the total number of atoms minus number of atoms belong to |
144 |
> |
//cutoff group defined in meta-data file plus the number of cutoff |
145 |
> |
//groups defined in meta-data file |
146 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
147 |
|
|
148 |
< |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
149 |
< |
//therefore the total number of integrable objects in the system is equal to |
150 |
< |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
151 |
< |
//file plus the number of rigid bodies defined in meta-data file |
152 |
< |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
153 |
< |
|
148 |
> |
//every free atom (atom does not belong to rigid bodies) is an |
149 |
> |
//integrable object therefore the total number of integrable objects |
150 |
> |
//in the system is equal to the total number of atoms minus number of |
151 |
> |
//atoms belong to rigid body defined in meta-data file plus the number |
152 |
> |
//of rigid bodies defined in meta-data file |
153 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
154 |
> |
+ nGlobalRigidBodies_; |
155 |
> |
|
156 |
|
nGlobalMols_ = molStampIds_.size(); |
157 |
|
|
158 |
|
#ifdef IS_MPI |
355 |
|
int b; |
356 |
|
int c; |
357 |
|
int d; |
358 |
+ |
|
359 |
+ |
std::map<int, std::set<int> > atomGroups; |
360 |
+ |
|
361 |
+ |
Molecule::RigidBodyIterator rbIter; |
362 |
+ |
RigidBody* rb; |
363 |
+ |
Molecule::IntegrableObjectIterator ii; |
364 |
+ |
StuntDouble* integrableObject; |
365 |
|
|
366 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
367 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
368 |
+ |
|
369 |
+ |
if (integrableObject->isRigidBody()) { |
370 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
371 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
372 |
+ |
std::set<int> rigidAtoms; |
373 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
374 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
375 |
+ |
} |
376 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
377 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
378 |
+ |
} |
379 |
+ |
} else { |
380 |
+ |
std::set<int> oneAtomSet; |
381 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
382 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
383 |
+ |
} |
384 |
+ |
} |
385 |
+ |
|
386 |
+ |
|
387 |
+ |
|
388 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
389 |
|
a = bond->getAtomA()->getGlobalIndex(); |
390 |
|
b = bond->getAtomB()->getGlobalIndex(); |
395 |
|
a = bend->getAtomA()->getGlobalIndex(); |
396 |
|
b = bend->getAtomB()->getGlobalIndex(); |
397 |
|
c = bend->getAtomC()->getGlobalIndex(); |
398 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
399 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
400 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
401 |
|
|
402 |
< |
exclude_.addPair(a, b); |
403 |
< |
exclude_.addPair(a, c); |
404 |
< |
exclude_.addPair(b, c); |
402 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
403 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
404 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
405 |
> |
|
406 |
> |
//exclude_.addPair(a, b); |
407 |
> |
//exclude_.addPair(a, c); |
408 |
> |
//exclude_.addPair(b, c); |
409 |
|
} |
410 |
|
|
411 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
413 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
414 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
415 |
|
d = torsion->getAtomD()->getGlobalIndex(); |
416 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
417 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
418 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
419 |
+ |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
420 |
+ |
|
421 |
+ |
exclude_.addPairs(rigidSetA, rigidSetB); |
422 |
+ |
exclude_.addPairs(rigidSetA, rigidSetC); |
423 |
+ |
exclude_.addPairs(rigidSetA, rigidSetD); |
424 |
+ |
exclude_.addPairs(rigidSetB, rigidSetC); |
425 |
+ |
exclude_.addPairs(rigidSetB, rigidSetD); |
426 |
+ |
exclude_.addPairs(rigidSetC, rigidSetD); |
427 |
|
|
428 |
+ |
/* |
429 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
430 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
431 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
432 |
+ |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
433 |
+ |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
434 |
+ |
exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
435 |
+ |
|
436 |
+ |
|
437 |
|
exclude_.addPair(a, b); |
438 |
|
exclude_.addPair(a, c); |
439 |
|
exclude_.addPair(a, d); |
440 |
|
exclude_.addPair(b, c); |
441 |
|
exclude_.addPair(b, d); |
442 |
|
exclude_.addPair(c, d); |
443 |
+ |
*/ |
444 |
|
} |
445 |
|
|
372 |
– |
Molecule::RigidBodyIterator rbIter; |
373 |
– |
RigidBody* rb; |
446 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
447 |
|
std::vector<Atom*> atoms = rb->getAtoms(); |
448 |
|
for (int i = 0; i < atoms.size() -1 ; ++i) { |
467 |
|
int b; |
468 |
|
int c; |
469 |
|
int d; |
470 |
+ |
|
471 |
+ |
std::map<int, std::set<int> > atomGroups; |
472 |
+ |
|
473 |
+ |
Molecule::RigidBodyIterator rbIter; |
474 |
+ |
RigidBody* rb; |
475 |
+ |
Molecule::IntegrableObjectIterator ii; |
476 |
+ |
StuntDouble* integrableObject; |
477 |
|
|
478 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
479 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
480 |
+ |
|
481 |
+ |
if (integrableObject->isRigidBody()) { |
482 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
483 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
484 |
+ |
std::set<int> rigidAtoms; |
485 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
486 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
487 |
+ |
} |
488 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
489 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
490 |
+ |
} |
491 |
+ |
} else { |
492 |
+ |
std::set<int> oneAtomSet; |
493 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
494 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
495 |
+ |
} |
496 |
+ |
} |
497 |
+ |
|
498 |
+ |
|
499 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
500 |
|
a = bond->getAtomA()->getGlobalIndex(); |
501 |
|
b = bond->getAtomB()->getGlobalIndex(); |
507 |
|
b = bend->getAtomB()->getGlobalIndex(); |
508 |
|
c = bend->getAtomC()->getGlobalIndex(); |
509 |
|
|
510 |
< |
exclude_.removePair(a, b); |
511 |
< |
exclude_.removePair(a, c); |
512 |
< |
exclude_.removePair(b, c); |
510 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
511 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
512 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
513 |
> |
|
514 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
515 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
516 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
517 |
> |
|
518 |
> |
//exclude_.removePair(a, b); |
519 |
> |
//exclude_.removePair(a, c); |
520 |
> |
//exclude_.removePair(b, c); |
521 |
|
} |
522 |
|
|
523 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
526 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
527 |
|
d = torsion->getAtomD()->getGlobalIndex(); |
528 |
|
|
529 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
530 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
531 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
532 |
+ |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
533 |
+ |
|
534 |
+ |
exclude_.removePairs(rigidSetA, rigidSetB); |
535 |
+ |
exclude_.removePairs(rigidSetA, rigidSetC); |
536 |
+ |
exclude_.removePairs(rigidSetA, rigidSetD); |
537 |
+ |
exclude_.removePairs(rigidSetB, rigidSetC); |
538 |
+ |
exclude_.removePairs(rigidSetB, rigidSetD); |
539 |
+ |
exclude_.removePairs(rigidSetC, rigidSetD); |
540 |
+ |
|
541 |
+ |
/* |
542 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
543 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
544 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
545 |
+ |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
546 |
+ |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
547 |
+ |
exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
548 |
+ |
|
549 |
+ |
|
550 |
|
exclude_.removePair(a, b); |
551 |
|
exclude_.removePair(a, c); |
552 |
|
exclude_.removePair(a, d); |
553 |
|
exclude_.removePair(b, c); |
554 |
|
exclude_.removePair(b, d); |
555 |
|
exclude_.removePair(c, d); |
556 |
+ |
*/ |
557 |
|
} |
558 |
|
|
429 |
– |
Molecule::RigidBodyIterator rbIter; |
430 |
– |
RigidBody* rb; |
559 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
560 |
|
std::vector<Atom*> atoms = rb->getAtoms(); |
561 |
|
for (int i = 0; i < atoms.size() -1 ; ++i) { |
595 |
|
int isError = 0; |
596 |
|
|
597 |
|
setupElectrostaticSummationMethod( isError ); |
598 |
+ |
setupSwitchingFunction(); |
599 |
|
|
600 |
|
if(isError){ |
601 |
|
sprintf( painCave.errMsg, |
640 |
|
int useLennardJones = 0; |
641 |
|
int useElectrostatic = 0; |
642 |
|
int useEAM = 0; |
643 |
+ |
int useSC = 0; |
644 |
|
int useCharge = 0; |
645 |
|
int useDirectional = 0; |
646 |
|
int useDipole = 0; |
652 |
|
int useDirectionalAtom = 0; |
653 |
|
int useElectrostatics = 0; |
654 |
|
//usePBC and useRF are from simParams |
655 |
< |
int usePBC = simParams_->getPBC(); |
655 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
656 |
|
int useRF; |
657 |
+ |
int useSF; |
658 |
+ |
std::string myMethod; |
659 |
|
|
660 |
|
// set the useRF logical |
661 |
< |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
662 |
< |
if (myMethod == "REACTION_FIELD") |
531 |
< |
useRF = 1; |
532 |
< |
else |
533 |
< |
useRF = 0; |
661 |
> |
useRF = 0; |
662 |
> |
useSF = 0; |
663 |
|
|
664 |
+ |
|
665 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
666 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
667 |
+ |
toUpper(myMethod); |
668 |
+ |
if (myMethod == "REACTION_FIELD") { |
669 |
+ |
useRF=1; |
670 |
+ |
} else { |
671 |
+ |
if (myMethod == "SHIFTED_FORCE") { |
672 |
+ |
useSF = 1; |
673 |
+ |
} |
674 |
+ |
} |
675 |
+ |
} |
676 |
+ |
|
677 |
|
//loop over all of the atom types |
678 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
679 |
|
useLennardJones |= (*i)->isLennardJones(); |
680 |
|
useElectrostatic |= (*i)->isElectrostatic(); |
681 |
|
useEAM |= (*i)->isEAM(); |
682 |
+ |
useSC |= (*i)->isSC(); |
683 |
|
useCharge |= (*i)->isCharge(); |
684 |
|
useDirectional |= (*i)->isDirectional(); |
685 |
|
useDipole |= (*i)->isDipole(); |
730 |
|
temp = useEAM; |
731 |
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
732 |
|
|
733 |
+ |
temp = useSC; |
734 |
+ |
MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
735 |
+ |
|
736 |
|
temp = useShape; |
737 |
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
738 |
|
|
742 |
|
temp = useRF; |
743 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
744 |
|
|
745 |
+ |
temp = useSF; |
746 |
+ |
MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
747 |
+ |
|
748 |
|
#endif |
749 |
|
|
750 |
|
fInfo_.SIM_uses_PBC = usePBC; |
757 |
|
fInfo_.SIM_uses_StickyPower = useStickyPower; |
758 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
759 |
|
fInfo_.SIM_uses_EAM = useEAM; |
760 |
+ |
fInfo_.SIM_uses_SC = useSC; |
761 |
|
fInfo_.SIM_uses_Shapes = useShape; |
762 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
763 |
|
fInfo_.SIM_uses_RF = useRF; |
764 |
+ |
fInfo_.SIM_uses_SF = useSF; |
765 |
|
|
766 |
< |
if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") { |
767 |
< |
|
766 |
> |
if( myMethod == "REACTION_FIELD") { |
767 |
> |
|
768 |
|
if (simParams_->haveDielectric()) { |
769 |
|
fInfo_.dielect = simParams_->getDielectric(); |
770 |
|
} else { |
774 |
|
"\tsetting a dielectric constant!\n"); |
775 |
|
painCave.isFatal = 1; |
776 |
|
simError(); |
777 |
< |
} |
627 |
< |
|
628 |
< |
} else { |
629 |
< |
fInfo_.dielect = 0.0; |
777 |
> |
} |
778 |
|
} |
779 |
|
|
780 |
|
} |
810 |
|
|
811 |
|
totalMass = cg->getMass(); |
812 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
813 |
< |
mfact.push_back(atom->getMass()/totalMass); |
813 |
> |
// Check for massless groups - set mfact to 1 if true |
814 |
> |
if (totalMass != 0) |
815 |
> |
mfact.push_back(atom->getMass()/totalMass); |
816 |
> |
else |
817 |
> |
mfact.push_back( 1.0 ); |
818 |
|
} |
819 |
|
|
820 |
|
} |
950 |
|
|
951 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
952 |
|
|
953 |
< |
if (!simParams_->haveRcut()){ |
953 |
> |
if (!simParams_->haveCutoffRadius()){ |
954 |
|
sprintf(painCave.errMsg, |
955 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
956 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
959 |
|
simError(); |
960 |
|
rcut = 15.0; |
961 |
|
} else{ |
962 |
< |
rcut = simParams_->getRcut(); |
962 |
> |
rcut = simParams_->getCutoffRadius(); |
963 |
|
} |
964 |
|
|
965 |
< |
if (!simParams_->haveRsw()){ |
965 |
> |
if (!simParams_->haveSwitchingRadius()){ |
966 |
|
sprintf(painCave.errMsg, |
967 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
968 |
|
"\tOOPSE will use a default value of\n" |
969 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
969 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
970 |
|
painCave.isFatal = 0; |
971 |
|
simError(); |
972 |
< |
rsw = 0.95 * rcut; |
972 |
> |
rsw = 0.85 * rcut; |
973 |
|
} else{ |
974 |
< |
rsw = simParams_->getRsw(); |
974 |
> |
rsw = simParams_->getSwitchingRadius(); |
975 |
|
} |
976 |
|
|
977 |
|
} else { |
978 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
979 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
980 |
|
|
981 |
< |
if (simParams_->haveRcut()) { |
982 |
< |
rcut = simParams_->getRcut(); |
981 |
> |
if (simParams_->haveCutoffRadius()) { |
982 |
> |
rcut = simParams_->getCutoffRadius(); |
983 |
|
} else { |
984 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
985 |
|
rcut = calcMaxCutoffRadius(); |
986 |
|
} |
987 |
|
|
988 |
< |
if (simParams_->haveRsw()) { |
989 |
< |
rsw = simParams_->getRsw(); |
988 |
> |
if (simParams_->haveSwitchingRadius()) { |
989 |
> |
rsw = simParams_->getSwitchingRadius(); |
990 |
|
} else { |
991 |
|
rsw = rcut; |
992 |
|
} |
1003 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
1004 |
|
if (simParams_->haveCutoffPolicy()) { |
1005 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
1006 |
+ |
toUpper(myPolicy); |
1007 |
|
if (myPolicy == "MIX") { |
1008 |
|
cp = MIX_CUTOFF_POLICY; |
1009 |
|
} else { |
1022 |
|
} |
1023 |
|
} |
1024 |
|
} |
1025 |
+ |
|
1026 |
+ |
|
1027 |
+ |
if (simParams_->haveSkinThickness()) { |
1028 |
+ |
double skinThickness = simParams_->getSkinThickness(); |
1029 |
+ |
} |
1030 |
+ |
|
1031 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
1032 |
|
// also send cutoff notification to electrostatics |
1033 |
< |
setElectrostaticCutoffRadius(&rcut_); |
1033 |
> |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
1034 |
|
} |
1035 |
|
|
1036 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1037 |
|
|
1038 |
|
int errorOut; |
1039 |
|
int esm = NONE; |
1040 |
+ |
int sm = UNDAMPED; |
1041 |
|
double alphaVal; |
1042 |
|
double dielectric; |
1043 |
|
|
1047 |
|
|
1048 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
1049 |
|
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
1050 |
+ |
toUpper(myMethod); |
1051 |
|
if (myMethod == "NONE") { |
1052 |
|
esm = NONE; |
1053 |
|
} else { |
1054 |
< |
if (myMethod == "UNDAMPED_WOLF") { |
1055 |
< |
esm = UNDAMPED_WOLF; |
1054 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
1055 |
> |
esm = SWITCHING_FUNCTION; |
1056 |
|
} else { |
1057 |
< |
if (myMethod == "DAMPED_WOLF") { |
1058 |
< |
esm = DAMPED_WOLF; |
1059 |
< |
if (!simParams_->haveDampingAlpha()) { |
1060 |
< |
//throw error |
1061 |
< |
sprintf( painCave.errMsg, |
901 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal); |
902 |
< |
painCave.isFatal = 0; |
903 |
< |
simError(); |
904 |
< |
} |
905 |
< |
} else { |
906 |
< |
if (myMethod == "REACTION_FIELD") { |
907 |
< |
esm = REACTION_FIELD; |
1057 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
1058 |
> |
esm = SHIFTED_POTENTIAL; |
1059 |
> |
} else { |
1060 |
> |
if (myMethod == "SHIFTED_FORCE") { |
1061 |
> |
esm = SHIFTED_FORCE; |
1062 |
|
} else { |
1063 |
< |
// throw error |
1064 |
< |
sprintf( painCave.errMsg, |
1065 |
< |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() ); |
1066 |
< |
painCave.isFatal = 1; |
1067 |
< |
simError(); |
1068 |
< |
} |
1069 |
< |
} |
1063 |
> |
if (myMethod == "REACTION_FIELD") { |
1064 |
> |
esm = REACTION_FIELD; |
1065 |
> |
} else { |
1066 |
> |
// throw error |
1067 |
> |
sprintf( painCave.errMsg, |
1068 |
> |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() ); |
1069 |
> |
painCave.isFatal = 1; |
1070 |
> |
simError(); |
1071 |
> |
} |
1072 |
> |
} |
1073 |
> |
} |
1074 |
|
} |
1075 |
|
} |
1076 |
|
} |
1077 |
+ |
|
1078 |
+ |
if (simParams_->haveElectrostaticScreeningMethod()) { |
1079 |
+ |
std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
1080 |
+ |
toUpper(myScreen); |
1081 |
+ |
if (myScreen == "UNDAMPED") { |
1082 |
+ |
sm = UNDAMPED; |
1083 |
+ |
} else { |
1084 |
+ |
if (myScreen == "DAMPED") { |
1085 |
+ |
sm = DAMPED; |
1086 |
+ |
if (!simParams_->haveDampingAlpha()) { |
1087 |
+ |
//throw error |
1088 |
+ |
sprintf( painCave.errMsg, |
1089 |
+ |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
1090 |
+ |
painCave.isFatal = 0; |
1091 |
+ |
simError(); |
1092 |
+ |
} |
1093 |
+ |
} else { |
1094 |
+ |
// throw error |
1095 |
+ |
sprintf( painCave.errMsg, |
1096 |
+ |
"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
1097 |
+ |
painCave.isFatal = 1; |
1098 |
+ |
simError(); |
1099 |
+ |
} |
1100 |
+ |
} |
1101 |
+ |
} |
1102 |
+ |
|
1103 |
|
// let's pass some summation method variables to fortran |
1104 |
|
setElectrostaticSummationMethod( &esm ); |
1105 |
< |
setDampedWolfAlpha( &alphaVal ); |
1105 |
> |
setScreeningMethod( &sm ); |
1106 |
> |
setDampingAlpha( &alphaVal ); |
1107 |
|
setReactionFieldDielectric( &dielectric ); |
1108 |
|
initFortranFF( &esm, &errorOut ); |
1109 |
|
} |
1110 |
|
|
1111 |
+ |
void SimInfo::setupSwitchingFunction() { |
1112 |
+ |
int ft = CUBIC; |
1113 |
+ |
|
1114 |
+ |
if (simParams_->haveSwitchingFunctionType()) { |
1115 |
+ |
std::string funcType = simParams_->getSwitchingFunctionType(); |
1116 |
+ |
toUpper(funcType); |
1117 |
+ |
if (funcType == "CUBIC") { |
1118 |
+ |
ft = CUBIC; |
1119 |
+ |
} else { |
1120 |
+ |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
1121 |
+ |
ft = FIFTH_ORDER_POLY; |
1122 |
+ |
} else { |
1123 |
+ |
// throw error |
1124 |
+ |
sprintf( painCave.errMsg, |
1125 |
+ |
"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
1126 |
+ |
painCave.isFatal = 1; |
1127 |
+ |
simError(); |
1128 |
+ |
} |
1129 |
+ |
} |
1130 |
+ |
} |
1131 |
+ |
|
1132 |
+ |
// send switching function notification to switcheroo |
1133 |
+ |
setFunctionType(&ft); |
1134 |
+ |
|
1135 |
+ |
} |
1136 |
+ |
|
1137 |
|
void SimInfo::addProperty(GenericData* genData) { |
1138 |
|
properties_.addProperty(genData); |
1139 |
|
} |