| 44 |
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* @file ForceManager.cpp |
| 45 |
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* @author tlin |
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* @date 11/09/2004 |
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– |
* @time 10:39am |
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* @version 1.0 |
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*/ |
| 49 |
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|
| 57 |
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#include "primitives/Torsion.hpp" |
| 58 |
|
#include "primitives/Inversion.hpp" |
| 59 |
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#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
+ |
#include "perturbations/ElectricField.hpp" |
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#include "parallel/ForceMatrixDecomposition.hpp" |
| 62 |
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|
| 63 |
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#include <cstdio> |
| 369 |
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} |
| 370 |
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switcher_->setSwitchType(sft_); |
| 371 |
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switcher_->setSwitch(rSwitch_, rCut_); |
| 372 |
– |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 372 |
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} |
| 373 |
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|
| 374 |
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|
| 392 |
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doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
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doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux(); |
| 394 |
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if (doHeatFlux_) doParticlePot_ = true; |
| 395 |
+ |
|
| 396 |
+ |
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 397 |
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|
| 398 |
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} |
| 399 |
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|
| 424 |
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electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
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electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 426 |
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|
| 427 |
+ |
if (info_->getSimParams()->haveElectricField()) { |
| 428 |
+ |
ElectricField* eField = new ElectricField(info_); |
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+ |
perturbations_.push_back(eField); |
| 430 |
+ |
} |
| 431 |
+ |
|
| 432 |
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fDecomp_->distributeInitialData(); |
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|
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initialized_ = true; |
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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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|
| 458 |
< |
// forces are zeroed here, before any are accumulated. |
| 458 |
> |
// forces and potentials are zeroed here, before any are |
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> |
// accumulated. |
| 460 |
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|
| 461 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 462 |
+ |
|
| 463 |
+ |
snap->setBondPotential(0.0); |
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+ |
snap->setBendPotential(0.0); |
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+ |
snap->setTorsionPotential(0.0); |
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+ |
snap->setInversionPotential(0.0); |
| 467 |
+ |
|
| 468 |
+ |
potVec zeroPot(0.0); |
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snap->setLongRangePotential(zeroPot); |
| 470 |
+ |
snap->setExcludedPotentials(zeroPot); |
| 471 |
+ |
|
| 472 |
+ |
snap->setRestraintPotential(0.0); |
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snap->setRawPotential(0.0); |
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+ |
|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; |
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} |
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} |
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} |
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< |
|
| 611 |
< |
RealType shortRangePotential = bondPotential + bendPotential + |
| 612 |
< |
torsionPotential + inversionPotential; |
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> |
|
| 611 |
> |
#ifdef IS_MPI |
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> |
// Collect from all nodes. This should eventually be moved into a |
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> |
// SystemDecomposition, but this is a better place than in |
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> |
// Thermo to do the collection. |
| 615 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
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> |
MPI::SUM); |
| 617 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 618 |
> |
MPI::SUM); |
| 619 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
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> |
MPI::REALTYPE, MPI::SUM); |
| 621 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
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> |
MPI::REALTYPE, MPI::SUM); |
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> |
#endif |
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> |
|
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
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< |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 628 |
< |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
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< |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
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< |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
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> |
|
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> |
curSnapshot->setBondPotential(bondPotential); |
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> |
curSnapshot->setBendPotential(bendPotential); |
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> |
curSnapshot->setTorsionPotential(torsionPotential); |
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> |
curSnapshot->setInversionPotential(inversionPotential); |
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> |
|
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> |
// RealType shortRangePotential = bondPotential + bendPotential + |
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> |
// torsionPotential + inversionPotential; |
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> |
|
| 635 |
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// curSnapshot->setShortRangePotential(shortRangePotential); |
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} |
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|
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void ForceManager::longRangeInteractions() { |
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InteractionData idat; |
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SelfData sdat; |
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RealType mf; |
| 646 |
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RealType lrPot; |
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RealType vpair; |
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RealType dVdFQ1(0.0); |
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RealType dVdFQ2(0.0); |
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potVec longRangePotential(0.0); |
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potVec workPot(0.0); |
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potVec exPot(0.0); |
| 690 |
+ |
Vector3d eField1(0.0); |
| 691 |
+ |
Vector3d eField2(0.0); |
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vector<int>::iterator ia, jb; |
| 693 |
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|
| 694 |
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int loopStart, loopEnd; |
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idat.vdwMult = &vdwMult; |
| 697 |
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idat.electroMult = &electroMult; |
| 698 |
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idat.pot = &workPot; |
| 699 |
+ |
idat.excludedPot = &exPot; |
| 700 |
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sdat.pot = fDecomp_->getEmbeddingPotential(); |
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+ |
sdat.excludedPot = fDecomp_->getExcludedSelfPotential(); |
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idat.vpair = &vpair; |
| 703 |
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idat.dVdFQ1 = &dVdFQ1; |
| 704 |
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idat.dVdFQ2 = &dVdFQ2; |
| 705 |
+ |
idat.eField1 = &eField1; |
| 706 |
+ |
idat.eField2 = &eField2; |
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idat.f1 = &f1; |
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idat.sw = &sw; |
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idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
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idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
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idat.doParticlePot = doParticlePot_; |
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+ |
idat.doElectricField = doElectricField_; |
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sdat.doParticlePot = doParticlePot_; |
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|
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loopEnd = PAIR_LOOP; |
| 749 |
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|
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in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 751 |
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rgrp); |
| 752 |
+ |
|
| 753 |
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atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 754 |
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atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 755 |
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|
| 764 |
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jb != atomListColumn.end(); ++jb) { |
| 765 |
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atom2 = (*jb); |
| 766 |
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|
| 767 |
< |
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 767 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 768 |
> |
|
| 769 |
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vpair = 0.0; |
| 770 |
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workPot = 0.0; |
| 771 |
+ |
exPot = 0.0; |
| 772 |
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f1 = V3Zero; |
| 773 |
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dVdFQ1 = 0.0; |
| 774 |
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dVdFQ2 = 0.0; |
| 879 |
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|
| 880 |
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fDecomp_->collectIntermediateData(); |
| 881 |
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|
| 882 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 882 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 883 |
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fDecomp_->fillSelfData(sdat, atom1); |
| 884 |
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interactionMan_->doPreForce(sdat); |
| 885 |
|
} |
| 890 |
|
} |
| 891 |
|
} |
| 892 |
|
|
| 893 |
+ |
// collects pairwise information |
| 894 |
|
fDecomp_->collectData(); |
| 895 |
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|
| 896 |
|
if (info_->requiresSelfCorrection()) { |
| 897 |
< |
|
| 849 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 897 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 898 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 899 |
|
interactionMan_->doSelfCorrection(sdat); |
| 900 |
|
} |
| 853 |
– |
|
| 901 |
|
} |
| 902 |
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|
| 903 |
+ |
// collects single-atom information |
| 904 |
+ |
fDecomp_->collectSelfData(); |
| 905 |
+ |
|
| 906 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 907 |
|
*(fDecomp_->getPairwisePotential()); |
| 908 |
|
|
| 909 |
< |
lrPot = longRangePotential.sum(); |
| 909 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 910 |
|
|
| 911 |
< |
//store the stressTensor and long range potential |
| 912 |
< |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 913 |
< |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 914 |
< |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 911 |
> |
// collects single-atom information |
| 912 |
> |
fDecomp_->collectSelfData(); |
| 913 |
> |
|
| 914 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 915 |
> |
*(fDecomp_->getPairwisePotential()); |
| 916 |
> |
|
| 917 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 918 |
> |
|
| 919 |
> |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 920 |
> |
*(fDecomp_->getExcludedPotential())); |
| 921 |
> |
|
| 922 |
|
} |
| 923 |
|
|
| 924 |
|
|
| 925 |
|
void ForceManager::postCalculation() { |
| 926 |
+ |
|
| 927 |
+ |
vector<Perturbation*>::iterator pi; |
| 928 |
+ |
for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) { |
| 929 |
+ |
(*pi)->applyPerturbation(); |
| 930 |
+ |
} |
| 931 |
+ |
|
| 932 |
|
SimInfo::MoleculeIterator mi; |
| 933 |
|
Molecule* mol; |
| 934 |
|
Molecule::RigidBodyIterator rbIter; |
| 935 |
|
RigidBody* rb; |
| 936 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 937 |
< |
|
| 937 |
> |
|
| 938 |
|
// collect the atomic forces onto rigid bodies |
| 939 |
|
|
| 940 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 947 |
|
} |
| 948 |
|
|
| 949 |
|
#ifdef IS_MPI |
| 887 |
– |
|
| 950 |
|
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 951 |
|
MPI::REALTYPE, MPI::SUM); |
| 952 |
|
#endif |
| 953 |
|
curSnapshot->setStressTensor(stressTensor); |
| 954 |
|
|
| 955 |
|
} |
| 894 |
– |
|
| 956 |
|
} //end namespace OpenMD |
