48 |
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49 |
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#include <algorithm> |
50 |
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#include <set> |
51 |
+ |
#include <map> |
52 |
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|
53 |
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#include "brains/SimInfo.hpp" |
54 |
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#include "math/Vector3.hpp" |
55 |
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#include "primitives/Molecule.hpp" |
56 |
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#include "UseTheForce/fCutoffPolicy.h" |
57 |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
58 |
+ |
#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
59 |
+ |
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
60 |
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#include "UseTheForce/doForces_interface.h" |
61 |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
62 |
< |
#include "UseTheForce/notifyCutoffs_interface.h" |
62 |
> |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
63 |
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#include "utils/MemoryUtils.hpp" |
64 |
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#include "utils/simError.h" |
65 |
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#include "selection/SelectionManager.hpp" |
70 |
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#endif |
71 |
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|
72 |
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namespace oopse { |
73 |
+ |
std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
74 |
+ |
std::map<int, std::set<int> >::iterator i = container.find(index); |
75 |
+ |
std::set<int> result; |
76 |
+ |
if (i != container.end()) { |
77 |
+ |
result = i->second; |
78 |
+ |
} |
79 |
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|
80 |
+ |
return result; |
81 |
+ |
} |
82 |
+ |
|
83 |
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SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
84 |
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ForceField* ff, Globals* simParams) : |
85 |
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stamps_(stamps), forceField_(ff), simParams_(simParams), |
354 |
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int b; |
355 |
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int c; |
356 |
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int d; |
357 |
+ |
|
358 |
+ |
std::map<int, std::set<int> > atomGroups; |
359 |
+ |
|
360 |
+ |
Molecule::RigidBodyIterator rbIter; |
361 |
+ |
RigidBody* rb; |
362 |
+ |
Molecule::IntegrableObjectIterator ii; |
363 |
+ |
StuntDouble* integrableObject; |
364 |
|
|
365 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
366 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
367 |
+ |
|
368 |
+ |
if (integrableObject->isRigidBody()) { |
369 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
370 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
371 |
+ |
std::set<int> rigidAtoms; |
372 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
373 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
374 |
+ |
} |
375 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
376 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
377 |
+ |
} |
378 |
+ |
} else { |
379 |
+ |
std::set<int> oneAtomSet; |
380 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
381 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
382 |
+ |
} |
383 |
+ |
} |
384 |
+ |
|
385 |
+ |
|
386 |
+ |
|
387 |
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for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
388 |
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a = bond->getAtomA()->getGlobalIndex(); |
389 |
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b = bond->getAtomB()->getGlobalIndex(); |
394 |
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a = bend->getAtomA()->getGlobalIndex(); |
395 |
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b = bend->getAtomB()->getGlobalIndex(); |
396 |
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c = bend->getAtomC()->getGlobalIndex(); |
397 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
398 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
399 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
400 |
|
|
401 |
< |
exclude_.addPair(a, b); |
402 |
< |
exclude_.addPair(a, c); |
403 |
< |
exclude_.addPair(b, c); |
401 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
402 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
403 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
404 |
> |
|
405 |
> |
//exclude_.addPair(a, b); |
406 |
> |
//exclude_.addPair(a, c); |
407 |
> |
//exclude_.addPair(b, c); |
408 |
|
} |
409 |
|
|
410 |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
412 |
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b = torsion->getAtomB()->getGlobalIndex(); |
413 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
414 |
|
d = torsion->getAtomD()->getGlobalIndex(); |
415 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
416 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
417 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
418 |
+ |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
419 |
|
|
420 |
+ |
exclude_.addPairs(rigidSetA, rigidSetB); |
421 |
+ |
exclude_.addPairs(rigidSetA, rigidSetC); |
422 |
+ |
exclude_.addPairs(rigidSetA, rigidSetD); |
423 |
+ |
exclude_.addPairs(rigidSetB, rigidSetC); |
424 |
+ |
exclude_.addPairs(rigidSetB, rigidSetD); |
425 |
+ |
exclude_.addPairs(rigidSetC, rigidSetD); |
426 |
+ |
|
427 |
+ |
/* |
428 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
429 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
430 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
431 |
+ |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
432 |
+ |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
433 |
+ |
exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
434 |
+ |
|
435 |
+ |
|
436 |
|
exclude_.addPair(a, b); |
437 |
|
exclude_.addPair(a, c); |
438 |
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exclude_.addPair(a, d); |
439 |
|
exclude_.addPair(b, c); |
440 |
|
exclude_.addPair(b, d); |
441 |
|
exclude_.addPair(c, d); |
442 |
+ |
*/ |
443 |
|
} |
444 |
|
|
376 |
– |
Molecule::RigidBodyIterator rbIter; |
377 |
– |
RigidBody* rb; |
445 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
446 |
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std::vector<Atom*> atoms = rb->getAtoms(); |
447 |
|
for (int i = 0; i < atoms.size() -1 ; ++i) { |
466 |
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int b; |
467 |
|
int c; |
468 |
|
int d; |
469 |
+ |
|
470 |
+ |
std::map<int, std::set<int> > atomGroups; |
471 |
+ |
|
472 |
+ |
Molecule::RigidBodyIterator rbIter; |
473 |
+ |
RigidBody* rb; |
474 |
+ |
Molecule::IntegrableObjectIterator ii; |
475 |
+ |
StuntDouble* integrableObject; |
476 |
|
|
477 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
478 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
479 |
+ |
|
480 |
+ |
if (integrableObject->isRigidBody()) { |
481 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
482 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
483 |
+ |
std::set<int> rigidAtoms; |
484 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
485 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
486 |
+ |
} |
487 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
488 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
489 |
+ |
} |
490 |
+ |
} else { |
491 |
+ |
std::set<int> oneAtomSet; |
492 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
493 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
494 |
+ |
} |
495 |
+ |
} |
496 |
+ |
|
497 |
+ |
|
498 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
499 |
|
a = bond->getAtomA()->getGlobalIndex(); |
500 |
|
b = bond->getAtomB()->getGlobalIndex(); |
506 |
|
b = bend->getAtomB()->getGlobalIndex(); |
507 |
|
c = bend->getAtomC()->getGlobalIndex(); |
508 |
|
|
509 |
< |
exclude_.removePair(a, b); |
510 |
< |
exclude_.removePair(a, c); |
511 |
< |
exclude_.removePair(b, c); |
509 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
510 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
511 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
512 |
> |
|
513 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
514 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
515 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
516 |
> |
|
517 |
> |
//exclude_.removePair(a, b); |
518 |
> |
//exclude_.removePair(a, c); |
519 |
> |
//exclude_.removePair(b, c); |
520 |
|
} |
521 |
|
|
522 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
525 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
526 |
|
d = torsion->getAtomD()->getGlobalIndex(); |
527 |
|
|
528 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
529 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
530 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
531 |
+ |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
532 |
+ |
|
533 |
+ |
exclude_.removePairs(rigidSetA, rigidSetB); |
534 |
+ |
exclude_.removePairs(rigidSetA, rigidSetC); |
535 |
+ |
exclude_.removePairs(rigidSetA, rigidSetD); |
536 |
+ |
exclude_.removePairs(rigidSetB, rigidSetC); |
537 |
+ |
exclude_.removePairs(rigidSetB, rigidSetD); |
538 |
+ |
exclude_.removePairs(rigidSetC, rigidSetD); |
539 |
+ |
|
540 |
+ |
/* |
541 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
542 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
543 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
544 |
+ |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
545 |
+ |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
546 |
+ |
exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
547 |
+ |
|
548 |
+ |
|
549 |
|
exclude_.removePair(a, b); |
550 |
|
exclude_.removePair(a, c); |
551 |
|
exclude_.removePair(a, d); |
552 |
|
exclude_.removePair(b, c); |
553 |
|
exclude_.removePair(b, d); |
554 |
|
exclude_.removePair(c, d); |
555 |
+ |
*/ |
556 |
|
} |
557 |
|
|
433 |
– |
Molecule::RigidBodyIterator rbIter; |
434 |
– |
RigidBody* rb; |
558 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
559 |
|
std::vector<Atom*> atoms = rb->getAtoms(); |
560 |
|
for (int i = 0; i < atoms.size() -1 ; ++i) { |
594 |
|
int isError = 0; |
595 |
|
|
596 |
|
setupElectrostaticSummationMethod( isError ); |
597 |
+ |
setupSwitchingFunction(); |
598 |
|
|
599 |
|
if(isError){ |
600 |
|
sprintf( painCave.errMsg, |
639 |
|
int useLennardJones = 0; |
640 |
|
int useElectrostatic = 0; |
641 |
|
int useEAM = 0; |
642 |
+ |
int useSC = 0; |
643 |
|
int useCharge = 0; |
644 |
|
int useDirectional = 0; |
645 |
|
int useDipole = 0; |
653 |
|
//usePBC and useRF are from simParams |
654 |
|
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
655 |
|
int useRF; |
656 |
< |
int useDW; |
656 |
> |
int useSF; |
657 |
|
std::string myMethod; |
658 |
|
|
659 |
|
// set the useRF logical |
660 |
|
useRF = 0; |
661 |
< |
useDW = 0; |
661 |
> |
useSF = 0; |
662 |
|
|
663 |
|
|
664 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
667 |
|
if (myMethod == "REACTION_FIELD") { |
668 |
|
useRF=1; |
669 |
|
} else { |
670 |
< |
if (myMethod == "DAMPED_WOLF") { |
671 |
< |
useDW = 1; |
670 |
> |
if (myMethod == "SHIFTED_FORCE") { |
671 |
> |
useSF = 1; |
672 |
|
} |
673 |
|
} |
674 |
|
} |
678 |
|
useLennardJones |= (*i)->isLennardJones(); |
679 |
|
useElectrostatic |= (*i)->isElectrostatic(); |
680 |
|
useEAM |= (*i)->isEAM(); |
681 |
+ |
useSC |= (*i)->isSC(); |
682 |
|
useCharge |= (*i)->isCharge(); |
683 |
|
useDirectional |= (*i)->isDirectional(); |
684 |
|
useDipole |= (*i)->isDipole(); |
729 |
|
temp = useEAM; |
730 |
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
731 |
|
|
732 |
+ |
temp = useSC; |
733 |
+ |
MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
734 |
+ |
|
735 |
|
temp = useShape; |
736 |
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
737 |
|
|
741 |
|
temp = useRF; |
742 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
743 |
|
|
744 |
< |
temp = useDW; |
745 |
< |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
744 |
> |
temp = useSF; |
745 |
> |
MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
746 |
|
|
747 |
|
#endif |
748 |
|
|
756 |
|
fInfo_.SIM_uses_StickyPower = useStickyPower; |
757 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
758 |
|
fInfo_.SIM_uses_EAM = useEAM; |
759 |
+ |
fInfo_.SIM_uses_SC = useSC; |
760 |
|
fInfo_.SIM_uses_Shapes = useShape; |
761 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
762 |
|
fInfo_.SIM_uses_RF = useRF; |
763 |
< |
fInfo_.SIM_uses_DampedWolf = useDW; |
763 |
> |
fInfo_.SIM_uses_SF = useSF; |
764 |
|
|
765 |
|
if( myMethod == "REACTION_FIELD") { |
766 |
|
|
922 |
|
|
923 |
|
#endif |
924 |
|
|
925 |
< |
double SimInfo::calcMaxCutoffRadius() { |
796 |
< |
|
797 |
< |
|
798 |
< |
std::set<AtomType*> atomTypes; |
799 |
< |
std::set<AtomType*>::iterator i; |
800 |
< |
std::vector<double> cutoffRadius; |
801 |
< |
|
802 |
< |
//get the unique atom types |
803 |
< |
atomTypes = getUniqueAtomTypes(); |
804 |
< |
|
805 |
< |
//query the max cutoff radius among these atom types |
806 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
807 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
808 |
< |
} |
809 |
< |
|
810 |
< |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
811 |
< |
#ifdef IS_MPI |
812 |
< |
//pick the max cutoff radius among the processors |
813 |
< |
#endif |
814 |
< |
|
815 |
< |
return maxCutoffRadius; |
816 |
< |
} |
817 |
< |
|
818 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
925 |
> |
void SimInfo::setupCutoff() { |
926 |
|
|
927 |
< |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
821 |
< |
|
822 |
< |
if (!simParams_->haveCutoffRadius()){ |
823 |
< |
sprintf(painCave.errMsg, |
824 |
< |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
825 |
< |
"\tOOPSE will use a default value of 15.0 angstroms" |
826 |
< |
"\tfor the cutoffRadius.\n"); |
827 |
< |
painCave.isFatal = 0; |
828 |
< |
simError(); |
829 |
< |
rcut = 15.0; |
830 |
< |
} else{ |
831 |
< |
rcut = simParams_->getCutoffRadius(); |
832 |
< |
} |
833 |
< |
|
834 |
< |
if (!simParams_->haveSwitchingRadius()){ |
835 |
< |
sprintf(painCave.errMsg, |
836 |
< |
"SimCreator Warning: No value was set for switchingRadius.\n" |
837 |
< |
"\tOOPSE will use a default value of\n" |
838 |
< |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
839 |
< |
painCave.isFatal = 0; |
840 |
< |
simError(); |
841 |
< |
rsw = 0.85 * rcut; |
842 |
< |
} else{ |
843 |
< |
rsw = simParams_->getSwitchingRadius(); |
844 |
< |
} |
845 |
< |
|
846 |
< |
} else { |
847 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
848 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
849 |
< |
|
850 |
< |
if (simParams_->haveCutoffRadius()) { |
851 |
< |
rcut = simParams_->getCutoffRadius(); |
852 |
< |
} else { |
853 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
854 |
< |
rcut = calcMaxCutoffRadius(); |
855 |
< |
} |
856 |
< |
|
857 |
< |
if (simParams_->haveSwitchingRadius()) { |
858 |
< |
rsw = simParams_->getSwitchingRadius(); |
859 |
< |
} else { |
860 |
< |
rsw = rcut; |
861 |
< |
} |
862 |
< |
|
863 |
< |
} |
864 |
< |
} |
865 |
< |
|
866 |
< |
void SimInfo::setupCutoff() { |
867 |
< |
getCutoff(rcut_, rsw_); |
868 |
< |
double rnblist = rcut_ + 1; // skin of neighbor list |
869 |
< |
|
870 |
< |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
871 |
< |
|
927 |
> |
// Check the cutoff policy |
928 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
929 |
|
if (simParams_->haveCutoffPolicy()) { |
930 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
946 |
|
} |
947 |
|
} |
948 |
|
} |
949 |
< |
} |
949 |
> |
} |
950 |
> |
notifyFortranCutoffPolicy(&cp); |
951 |
|
|
952 |
< |
|
952 |
> |
// Check the Skin Thickness for neighborlists |
953 |
> |
double skin; |
954 |
|
if (simParams_->haveSkinThickness()) { |
955 |
< |
double skinThickness = simParams_->getSkinThickness(); |
956 |
< |
} |
955 |
> |
skin = simParams_->getSkinThickness(); |
956 |
> |
notifyFortranSkinThickness(&skin); |
957 |
> |
} |
958 |
> |
|
959 |
> |
// Check if the cutoff was set explicitly: |
960 |
> |
if (simParams_->haveCutoffRadius()) { |
961 |
> |
rcut_ = simParams_->getCutoffRadius(); |
962 |
> |
if (simParams_->haveSwitchingRadius()) { |
963 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
964 |
> |
} else { |
965 |
> |
rsw_ = rcut_; |
966 |
> |
} |
967 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
968 |
> |
|
969 |
> |
} else { |
970 |
> |
|
971 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
972 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
973 |
> |
sprintf(painCave.errMsg, |
974 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
975 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
976 |
> |
"\tfor the cutoffRadius.\n"); |
977 |
> |
painCave.isFatal = 0; |
978 |
> |
simError(); |
979 |
> |
rcut_ = 15.0; |
980 |
> |
|
981 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
982 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
983 |
> |
toUpper(myMethod); |
984 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
985 |
> |
if (simParams_->haveSwitchingRadius()){ |
986 |
> |
sprintf(painCave.errMsg, |
987 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
988 |
> |
"\teven though the electrostaticSummationMethod was\n" |
989 |
> |
"\tset to %s\n", myMethod.c_str()); |
990 |
> |
painCave.isFatal = 1; |
991 |
> |
simError(); |
992 |
> |
} |
993 |
> |
} |
994 |
> |
} |
995 |
> |
|
996 |
> |
if (simParams_->haveSwitchingRadius()){ |
997 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
998 |
> |
} else { |
999 |
> |
sprintf(painCave.errMsg, |
1000 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
1001 |
> |
"\tOOPSE will use a default value of\n" |
1002 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
1003 |
> |
painCave.isFatal = 0; |
1004 |
> |
simError(); |
1005 |
> |
rsw_ = 0.85 * rcut_; |
1006 |
> |
} |
1007 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1008 |
> |
} else { |
1009 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1010 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
1011 |
> |
|
1012 |
> |
notifyFortranYouAreOnYourOwn(); |
1013 |
|
|
1014 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
1015 |
< |
// also send cutoff notification to electrostatics |
902 |
< |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
1014 |
> |
} |
1015 |
> |
} |
1016 |
|
} |
1017 |
|
|
1018 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1019 |
|
|
1020 |
|
int errorOut; |
1021 |
|
int esm = NONE; |
1022 |
+ |
int sm = UNDAMPED; |
1023 |
|
double alphaVal; |
1024 |
|
double dielectric; |
1025 |
|
|
1033 |
|
if (myMethod == "NONE") { |
1034 |
|
esm = NONE; |
1035 |
|
} else { |
1036 |
< |
if (myMethod == "UNDAMPED_WOLF") { |
1037 |
< |
esm = UNDAMPED_WOLF; |
1036 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
1037 |
> |
esm = SWITCHING_FUNCTION; |
1038 |
|
} else { |
1039 |
< |
if (myMethod == "DAMPED_WOLF") { |
1040 |
< |
esm = DAMPED_WOLF; |
1041 |
< |
if (!simParams_->haveDampingAlpha()) { |
1042 |
< |
//throw error |
1043 |
< |
sprintf( painCave.errMsg, |
930 |
< |
"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); |
931 |
< |
painCave.isFatal = 0; |
932 |
< |
simError(); |
933 |
< |
} |
934 |
< |
} else { |
935 |
< |
if (myMethod == "REACTION_FIELD") { |
936 |
< |
esm = REACTION_FIELD; |
1039 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
1040 |
> |
esm = SHIFTED_POTENTIAL; |
1041 |
> |
} else { |
1042 |
> |
if (myMethod == "SHIFTED_FORCE") { |
1043 |
> |
esm = SHIFTED_FORCE; |
1044 |
|
} else { |
1045 |
< |
// throw error |
1046 |
< |
sprintf( painCave.errMsg, |
1047 |
< |
"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() ); |
1048 |
< |
painCave.isFatal = 1; |
1049 |
< |
simError(); |
1050 |
< |
} |
1051 |
< |
} |
1045 |
> |
if (myMethod == "REACTION_FIELD") { |
1046 |
> |
esm = REACTION_FIELD; |
1047 |
> |
} else { |
1048 |
> |
// throw error |
1049 |
> |
sprintf( painCave.errMsg, |
1050 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1051 |
> |
"\t(Input file specified %s .)\n" |
1052 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1053 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1054 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1055 |
> |
painCave.isFatal = 1; |
1056 |
> |
simError(); |
1057 |
> |
} |
1058 |
> |
} |
1059 |
> |
} |
1060 |
> |
} |
1061 |
> |
} |
1062 |
> |
} |
1063 |
> |
|
1064 |
> |
if (simParams_->haveElectrostaticScreeningMethod()) { |
1065 |
> |
std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
1066 |
> |
toUpper(myScreen); |
1067 |
> |
if (myScreen == "UNDAMPED") { |
1068 |
> |
sm = UNDAMPED; |
1069 |
> |
} else { |
1070 |
> |
if (myScreen == "DAMPED") { |
1071 |
> |
sm = DAMPED; |
1072 |
> |
if (!simParams_->haveDampingAlpha()) { |
1073 |
> |
//throw error |
1074 |
> |
sprintf( painCave.errMsg, |
1075 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1076 |
> |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1077 |
> |
painCave.isFatal = 0; |
1078 |
> |
simError(); |
1079 |
> |
} |
1080 |
> |
} else { |
1081 |
> |
// throw error |
1082 |
> |
sprintf( painCave.errMsg, |
1083 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1084 |
> |
"\t(Input file specified %s .)\n" |
1085 |
> |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1086 |
> |
"or \"damped\".\n", myScreen.c_str() ); |
1087 |
> |
painCave.isFatal = 1; |
1088 |
> |
simError(); |
1089 |
|
} |
1090 |
|
} |
1091 |
|
} |
1092 |
+ |
|
1093 |
|
// let's pass some summation method variables to fortran |
1094 |
|
setElectrostaticSummationMethod( &esm ); |
1095 |
< |
setDampedWolfAlpha( &alphaVal ); |
1095 |
> |
notifyFortranElectrostaticMethod( &esm ); |
1096 |
> |
setScreeningMethod( &sm ); |
1097 |
> |
setDampingAlpha( &alphaVal ); |
1098 |
|
setReactionFieldDielectric( &dielectric ); |
1099 |
< |
initFortranFF( &esm, &errorOut ); |
1099 |
> |
initFortranFF( &errorOut ); |
1100 |
> |
} |
1101 |
> |
|
1102 |
> |
void SimInfo::setupSwitchingFunction() { |
1103 |
> |
int ft = CUBIC; |
1104 |
> |
|
1105 |
> |
if (simParams_->haveSwitchingFunctionType()) { |
1106 |
> |
std::string funcType = simParams_->getSwitchingFunctionType(); |
1107 |
> |
toUpper(funcType); |
1108 |
> |
if (funcType == "CUBIC") { |
1109 |
> |
ft = CUBIC; |
1110 |
> |
} else { |
1111 |
> |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
1112 |
> |
ft = FIFTH_ORDER_POLY; |
1113 |
> |
} else { |
1114 |
> |
// throw error |
1115 |
> |
sprintf( painCave.errMsg, |
1116 |
> |
"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
1117 |
> |
painCave.isFatal = 1; |
1118 |
> |
simError(); |
1119 |
> |
} |
1120 |
> |
} |
1121 |
> |
} |
1122 |
> |
|
1123 |
> |
// send switching function notification to switcheroo |
1124 |
> |
setFunctionType(&ft); |
1125 |
> |
|
1126 |
|
} |
1127 |
|
|
1128 |
|
void SimInfo::addProperty(GenericData* genData) { |