| 110 |
|
Globals* simParams_ = info_->getSimParams(); |
| 111 |
|
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 112 |
|
int mdFileVersion; |
| 113 |
+ |
rCut_ = 0.0; //Needs a value for a later max() call; |
| 114 |
|
|
| 115 |
|
if (simParams_->haveMDfileVersion()) |
| 116 |
|
mdFileVersion = simParams_->getMDfileVersion(); |
| 476 |
|
// Zero out the stress tensor |
| 477 |
|
stressTensor *= 0.0; |
| 478 |
|
// Zero out the heatFlux |
| 479 |
< |
fDecomp_->setHeatFlux( V3Zero ); |
| 479 |
> |
fDecomp_->setHeatFlux( Vector3d(0.0) ); |
| 480 |
|
} |
| 481 |
|
|
| 482 |
|
void ForceManager::shortRangeInteractions() { |
| 586 |
|
} |
| 587 |
|
} |
| 588 |
|
} |
| 589 |
< |
|
| 590 |
< |
RealType shortRangePotential = bondPotential + bendPotential + |
| 591 |
< |
torsionPotential + inversionPotential; |
| 589 |
> |
|
| 590 |
> |
#ifdef IS_MPI |
| 591 |
> |
// Collect from all nodes. This should eventually be moved into a |
| 592 |
> |
// SystemDecomposition, but this is a better place than in |
| 593 |
> |
// Thermo to do the collection. |
| 594 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
| 595 |
> |
MPI::SUM); |
| 596 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 597 |
> |
MPI::SUM); |
| 598 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
| 599 |
> |
MPI::REALTYPE, MPI::SUM); |
| 600 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
| 601 |
> |
MPI::REALTYPE, MPI::SUM); |
| 602 |
> |
#endif |
| 603 |
> |
|
| 604 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 605 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 606 |
< |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 607 |
< |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 608 |
< |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 609 |
< |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 605 |
> |
|
| 606 |
> |
curSnapshot->setBondPotential(bondPotential); |
| 607 |
> |
curSnapshot->setBendPotential(bendPotential); |
| 608 |
> |
curSnapshot->setTorsionPotential(torsionPotential); |
| 609 |
> |
curSnapshot->setInversionPotential(inversionPotential); |
| 610 |
> |
|
| 611 |
> |
RealType shortRangePotential = bondPotential + bendPotential + |
| 612 |
> |
torsionPotential + inversionPotential; |
| 613 |
> |
|
| 614 |
> |
curSnapshot->setShortRangePotential(shortRangePotential); |
| 615 |
|
} |
| 616 |
|
|
| 617 |
|
void ForceManager::longRangeInteractions() { |
| 666 |
|
RealType dVdFQ2(0.0); |
| 667 |
|
potVec longRangePotential(0.0); |
| 668 |
|
potVec workPot(0.0); |
| 669 |
+ |
potVec exPot(0.0); |
| 670 |
|
vector<int>::iterator ia, jb; |
| 671 |
|
|
| 672 |
|
int loopStart, loopEnd; |
| 674 |
|
idat.vdwMult = &vdwMult; |
| 675 |
|
idat.electroMult = &electroMult; |
| 676 |
|
idat.pot = &workPot; |
| 677 |
+ |
idat.excludedPot = &exPot; |
| 678 |
|
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 679 |
+ |
sdat.excludedPot = fDecomp_->getExcludedSelfPotential(); |
| 680 |
|
idat.vpair = &vpair; |
| 681 |
|
idat.dVdFQ1 = &dVdFQ1; |
| 682 |
|
idat.dVdFQ2 = &dVdFQ2; |
| 693 |
|
} else { |
| 694 |
|
loopStart = PAIR_LOOP; |
| 695 |
|
} |
| 675 |
– |
|
| 696 |
|
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 697 |
|
|
| 698 |
|
if (iLoop == loopStart) { |
| 724 |
|
|
| 725 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 726 |
|
rgrp); |
| 727 |
< |
|
| 727 |
> |
|
| 728 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 729 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 730 |
|
|
| 731 |
|
if (doHeatFlux_) |
| 732 |
|
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 733 |
< |
|
| 733 |
> |
|
| 734 |
|
for (ia = atomListRow.begin(); |
| 735 |
|
ia != atomListRow.end(); ++ia) { |
| 736 |
|
atom1 = (*ia); |
| 737 |
< |
|
| 737 |
> |
|
| 738 |
|
for (jb = atomListColumn.begin(); |
| 739 |
|
jb != atomListColumn.end(); ++jb) { |
| 740 |
|
atom2 = (*jb); |
| 741 |
|
|
| 742 |
< |
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 742 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 743 |
> |
|
| 744 |
|
vpair = 0.0; |
| 745 |
|
workPot = 0.0; |
| 746 |
+ |
exPot = 0.0; |
| 747 |
|
f1 = V3Zero; |
| 748 |
|
dVdFQ1 = 0.0; |
| 749 |
|
dVdFQ2 = 0.0; |
| 750 |
|
|
| 751 |
|
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 752 |
< |
|
| 752 |
> |
|
| 753 |
|
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 754 |
|
vdwMult = vdwScale_[topoDist]; |
| 755 |
|
electroMult = electrostaticScale_[topoDist]; |
| 865 |
|
} |
| 866 |
|
} |
| 867 |
|
|
| 868 |
+ |
// collects pairwise information |
| 869 |
|
fDecomp_->collectData(); |
| 870 |
|
|
| 871 |
|
if (info_->requiresSelfCorrection()) { |
| 872 |
< |
|
| 850 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 872 |
> |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 873 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 874 |
|
interactionMan_->doSelfCorrection(sdat); |
| 875 |
|
} |
| 854 |
– |
|
| 876 |
|
} |
| 877 |
|
|
| 878 |
+ |
// collects single-atom information |
| 879 |
+ |
fDecomp_->collectSelfData(); |
| 880 |
+ |
|
| 881 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 882 |
|
*(fDecomp_->getPairwisePotential()); |
| 883 |
|
|
| 884 |
+ |
curSnapshot->setLongRangePotentialFamilies(longRangePotential); |
| 885 |
+ |
|
| 886 |
|
lrPot = longRangePotential.sum(); |
| 887 |
|
|
| 888 |
< |
//store the stressTensor and long range potential |
| 889 |
< |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 890 |
< |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 891 |
< |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 888 |
> |
//store the long range potential |
| 889 |
> |
curSnapshot->setLongRangePotential(lrPot); |
| 890 |
> |
|
| 891 |
> |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 892 |
> |
*(fDecomp_->getExcludedPotential())); |
| 893 |
> |
|
| 894 |
|
} |
| 895 |
|
|
| 896 |
|
|
| 913 |
|
} |
| 914 |
|
|
| 915 |
|
#ifdef IS_MPI |
| 888 |
– |
|
| 916 |
|
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 917 |
|
MPI::REALTYPE, MPI::SUM); |
| 918 |
|
#endif |
