| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 44 |
|
* @file ForceManager.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/09/2004 |
| 47 |
– |
* @time 10:39am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 57 |
|
#include "primitives/Torsion.hpp" |
| 58 |
|
#include "primitives/Inversion.hpp" |
| 59 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
+ |
#include "perturbations/ElectricField.hpp" |
| 61 |
|
#include "parallel/ForceMatrixDecomposition.hpp" |
| 62 |
|
|
| 63 |
|
#include <cstdio> |
| 117 |
|
else |
| 118 |
|
mdFileVersion = 0; |
| 119 |
|
|
| 120 |
+ |
// We need the list of simulated atom types to figure out cutoffs |
| 121 |
+ |
// as well as long range corrections. |
| 122 |
+ |
|
| 123 |
+ |
set<AtomType*>::iterator i; |
| 124 |
+ |
set<AtomType*> atomTypes_; |
| 125 |
+ |
atomTypes_ = info_->getSimulatedAtomTypes(); |
| 126 |
+ |
|
| 127 |
|
if (simParams_->haveCutoffRadius()) { |
| 128 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 129 |
|
} else { |
| 138 |
|
rCut_ = 12.0; |
| 139 |
|
} else { |
| 140 |
|
RealType thisCut; |
| 141 |
< |
set<AtomType*>::iterator i; |
| 135 |
< |
set<AtomType*> atomTypes; |
| 136 |
< |
atomTypes = info_->getSimulatedAtomTypes(); |
| 137 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 141 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 142 |
|
thisCut = interactionMan_->getSuggestedCutoffRadius((*i)); |
| 143 |
|
rCut_ = max(thisCut, rCut_); |
| 144 |
|
} |
| 373 |
|
} |
| 374 |
|
switcher_->setSwitchType(sft_); |
| 375 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 372 |
– |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 376 |
|
} |
| 377 |
|
|
| 378 |
|
|
| 396 |
|
doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
| 397 |
|
doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux(); |
| 398 |
|
if (doHeatFlux_) doParticlePot_ = true; |
| 399 |
+ |
|
| 400 |
+ |
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 401 |
|
|
| 402 |
|
} |
| 403 |
|
|
| 428 |
|
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 429 |
|
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 430 |
|
|
| 431 |
+ |
if (info_->getSimParams()->haveElectricField()) { |
| 432 |
+ |
ElectricField* eField = new ElectricField(info_); |
| 433 |
+ |
perturbations_.push_back(eField); |
| 434 |
+ |
} |
| 435 |
+ |
|
| 436 |
|
fDecomp_->distributeInitialData(); |
| 437 |
|
|
| 438 |
|
initialized_ = true; |
| 459 |
|
Molecule::CutoffGroupIterator ci; |
| 460 |
|
CutoffGroup* cg; |
| 461 |
|
|
| 462 |
< |
// forces are zeroed here, before any are accumulated. |
| 462 |
> |
// forces and potentials are zeroed here, before any are |
| 463 |
> |
// accumulated. |
| 464 |
|
|
| 465 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 466 |
+ |
|
| 467 |
+ |
snap->setBondPotential(0.0); |
| 468 |
+ |
snap->setBendPotential(0.0); |
| 469 |
+ |
snap->setTorsionPotential(0.0); |
| 470 |
+ |
snap->setInversionPotential(0.0); |
| 471 |
+ |
|
| 472 |
+ |
potVec zeroPot(0.0); |
| 473 |
+ |
snap->setLongRangePotential(zeroPot); |
| 474 |
+ |
snap->setExcludedPotentials(zeroPot); |
| 475 |
+ |
|
| 476 |
+ |
snap->setRestraintPotential(0.0); |
| 477 |
+ |
snap->setRawPotential(0.0); |
| 478 |
+ |
|
| 479 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 480 |
|
mol = info_->nextMolecule(mi)) { |
| 481 |
|
for(atom = mol->beginAtom(ai); atom != NULL; |
| 611 |
|
} |
| 612 |
|
} |
| 613 |
|
} |
| 614 |
< |
|
| 615 |
< |
RealType shortRangePotential = bondPotential + bendPotential + |
| 616 |
< |
torsionPotential + inversionPotential; |
| 614 |
> |
|
| 615 |
> |
#ifdef IS_MPI |
| 616 |
> |
// Collect from all nodes. This should eventually be moved into a |
| 617 |
> |
// SystemDecomposition, but this is a better place than in |
| 618 |
> |
// Thermo to do the collection. |
| 619 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
| 620 |
> |
MPI::SUM); |
| 621 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 622 |
> |
MPI::SUM); |
| 623 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
| 624 |
> |
MPI::REALTYPE, MPI::SUM); |
| 625 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
| 626 |
> |
MPI::REALTYPE, MPI::SUM); |
| 627 |
> |
#endif |
| 628 |
> |
|
| 629 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 630 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 631 |
< |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 632 |
< |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 633 |
< |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 634 |
< |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 630 |
> |
|
| 631 |
> |
curSnapshot->setBondPotential(bondPotential); |
| 632 |
> |
curSnapshot->setBendPotential(bendPotential); |
| 633 |
> |
curSnapshot->setTorsionPotential(torsionPotential); |
| 634 |
> |
curSnapshot->setInversionPotential(inversionPotential); |
| 635 |
> |
|
| 636 |
> |
// RealType shortRangePotential = bondPotential + bendPotential + |
| 637 |
> |
// torsionPotential + inversionPotential; |
| 638 |
> |
|
| 639 |
> |
// curSnapshot->setShortRangePotential(shortRangePotential); |
| 640 |
|
} |
| 641 |
|
|
| 642 |
|
void ForceManager::longRangeInteractions() { |
| 685 |
|
InteractionData idat; |
| 686 |
|
SelfData sdat; |
| 687 |
|
RealType mf; |
| 646 |
– |
RealType lrPot; |
| 688 |
|
RealType vpair; |
| 689 |
|
RealType dVdFQ1(0.0); |
| 690 |
|
RealType dVdFQ2(0.0); |
| 691 |
|
potVec longRangePotential(0.0); |
| 692 |
|
potVec workPot(0.0); |
| 693 |
+ |
potVec exPot(0.0); |
| 694 |
+ |
Vector3d eField1(0.0); |
| 695 |
+ |
Vector3d eField2(0.0); |
| 696 |
|
vector<int>::iterator ia, jb; |
| 697 |
|
|
| 698 |
|
int loopStart, loopEnd; |
| 700 |
|
idat.vdwMult = &vdwMult; |
| 701 |
|
idat.electroMult = &electroMult; |
| 702 |
|
idat.pot = &workPot; |
| 703 |
+ |
idat.excludedPot = &exPot; |
| 704 |
|
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 705 |
+ |
sdat.excludedPot = fDecomp_->getExcludedSelfPotential(); |
| 706 |
|
idat.vpair = &vpair; |
| 707 |
|
idat.dVdFQ1 = &dVdFQ1; |
| 708 |
|
idat.dVdFQ2 = &dVdFQ2; |
| 709 |
+ |
idat.eField1 = &eField1; |
| 710 |
+ |
idat.eField2 = &eField2; |
| 711 |
|
idat.f1 = &f1; |
| 712 |
|
idat.sw = &sw; |
| 713 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 714 |
|
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 715 |
|
idat.doParticlePot = doParticlePot_; |
| 716 |
+ |
idat.doElectricField = doElectricField_; |
| 717 |
|
sdat.doParticlePot = doParticlePot_; |
| 718 |
|
|
| 719 |
|
loopEnd = PAIR_LOOP; |
| 749 |
|
if (iLoop == PAIR_LOOP) { |
| 750 |
|
vij = 0.0; |
| 751 |
|
fij = V3Zero; |
| 752 |
+ |
eField1 = V3Zero; |
| 753 |
+ |
eField2 = V3Zero; |
| 754 |
|
} |
| 755 |
|
|
| 756 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 774 |
|
|
| 775 |
|
vpair = 0.0; |
| 776 |
|
workPot = 0.0; |
| 777 |
+ |
exPot = 0.0; |
| 778 |
|
f1 = V3Zero; |
| 779 |
|
dVdFQ1 = 0.0; |
| 780 |
|
dVdFQ2 = 0.0; |
| 825 |
|
fij += fg; |
| 826 |
|
|
| 827 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 828 |
< |
stressTensor -= outProduct( *(idat.d), fg); |
| 829 |
< |
if (doHeatFlux_) |
| 830 |
< |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 831 |
< |
|
| 828 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 829 |
> |
atomListColumn[0], |
| 830 |
> |
cg1, cg2)) { |
| 831 |
> |
stressTensor -= outProduct( *(idat.d), fg); |
| 832 |
> |
if (doHeatFlux_) |
| 833 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 834 |
> |
} |
| 835 |
|
} |
| 836 |
|
|
| 837 |
|
for (ia = atomListRow.begin(); |
| 888 |
|
|
| 889 |
|
fDecomp_->collectIntermediateData(); |
| 890 |
|
|
| 891 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 891 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 892 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 893 |
|
interactionMan_->doPreForce(sdat); |
| 894 |
|
} |
| 903 |
|
fDecomp_->collectData(); |
| 904 |
|
|
| 905 |
|
if (info_->requiresSelfCorrection()) { |
| 906 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 906 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 907 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 908 |
|
interactionMan_->doSelfCorrection(sdat); |
| 909 |
|
} |
| 915 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 916 |
|
*(fDecomp_->getPairwisePotential()); |
| 917 |
|
|
| 918 |
< |
lrPot = longRangePotential.sum(); |
| 918 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 919 |
> |
|
| 920 |
> |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 921 |
> |
*(fDecomp_->getExcludedPotential())); |
| 922 |
|
|
| 865 |
– |
//store the stressTensor and long range potential |
| 866 |
– |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 867 |
– |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 868 |
– |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 923 |
|
} |
| 924 |
|
|
| 925 |
|
|
| 926 |
|
void ForceManager::postCalculation() { |
| 927 |
+ |
|
| 928 |
+ |
vector<Perturbation*>::iterator pi; |
| 929 |
+ |
for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) { |
| 930 |
+ |
(*pi)->applyPerturbation(); |
| 931 |
+ |
} |
| 932 |
+ |
|
| 933 |
|
SimInfo::MoleculeIterator mi; |
| 934 |
|
Molecule* mol; |
| 935 |
|
Molecule::RigidBodyIterator rbIter; |
| 936 |
|
RigidBody* rb; |
| 937 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 938 |
< |
|
| 938 |
> |
|
| 939 |
|
// collect the atomic forces onto rigid bodies |
| 940 |
|
|
| 941 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 953 |
|
#endif |
| 954 |
|
curSnapshot->setStressTensor(stressTensor); |
| 955 |
|
|
| 956 |
< |
} |
| 956 |
> |
if (info_->getSimParams()->getUseLongRangeCorrections()) { |
| 957 |
> |
/* |
| 958 |
> |
RealType vol = curSnapshot->getVolume(); |
| 959 |
> |
RealType Elrc(0.0); |
| 960 |
> |
RealType Wlrc(0.0); |
| 961 |
|
|
| 962 |
< |
} //end namespace OpenMD |
| 962 |
> |
set<AtomType*>::iterator i; |
| 963 |
> |
set<AtomType*>::iterator j; |
| 964 |
> |
|
| 965 |
> |
RealType n_i, n_j; |
| 966 |
> |
RealType rho_i, rho_j; |
| 967 |
> |
pair<RealType, RealType> LRI; |
| 968 |
> |
|
| 969 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 970 |
> |
n_i = RealType(info_->getGlobalCountOfType(*i)); |
| 971 |
> |
rho_i = n_i / vol; |
| 972 |
> |
for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) { |
| 973 |
> |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 974 |
> |
rho_j = n_j / vol; |
| 975 |
> |
|
| 976 |
> |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 977 |
> |
|
| 978 |
> |
Elrc += n_i * rho_j * LRI.first; |
| 979 |
> |
Wlrc -= rho_i * rho_j * LRI.second; |
| 980 |
> |
} |
| 981 |
> |
} |
| 982 |
> |
Elrc *= 2.0 * NumericConstant::PI; |
| 983 |
> |
Wlrc *= 2.0 * NumericConstant::PI; |
| 984 |
> |
|
| 985 |
> |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 986 |
> |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 987 |
> |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 988 |
> |
curSnapshot->setStressTensor(stressTensor); |
| 989 |
> |
*/ |
| 990 |
> |
|
| 991 |
> |
} |
| 992 |
> |
} |
| 993 |
> |
} |
