| 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> |
| 67 |
|
using namespace std; |
| 68 |
|
namespace OpenMD { |
| 69 |
|
|
| 70 |
< |
ForceManager::ForceManager(SimInfo * info) : info_(info) { |
| 70 |
> |
ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL), |
| 71 |
> |
initialized_(false) { |
| 72 |
|
forceField_ = info_->getForceField(); |
| 73 |
|
interactionMan_ = new InteractionManager(); |
| 74 |
|
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 75 |
+ |
thermo = new Thermo(info_); |
| 76 |
|
} |
| 77 |
|
|
| 78 |
+ |
ForceManager::~ForceManager() { |
| 79 |
+ |
perturbations_.clear(); |
| 80 |
+ |
|
| 81 |
+ |
delete switcher_; |
| 82 |
+ |
delete interactionMan_; |
| 83 |
+ |
delete fDecomp_; |
| 84 |
+ |
delete thermo; |
| 85 |
+ |
} |
| 86 |
+ |
|
| 87 |
|
/** |
| 88 |
|
* setupCutoffs |
| 89 |
|
* |
| 98 |
|
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 99 |
|
* Use the maximum suggested value that was found. |
| 100 |
|
* |
| 101 |
< |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, |
| 101 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED, |
| 102 |
|
* or SHIFTED_POTENTIAL) |
| 103 |
|
* If cutoffMethod was explicitly set, use that choice. |
| 104 |
|
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 121 |
|
Globals* simParams_ = info_->getSimParams(); |
| 122 |
|
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 123 |
|
int mdFileVersion; |
| 124 |
+ |
rCut_ = 0.0; //Needs a value for a later max() call; |
| 125 |
|
|
| 126 |
|
if (simParams_->haveMDfileVersion()) |
| 127 |
|
mdFileVersion = simParams_->getMDfileVersion(); |
| 128 |
|
else |
| 129 |
|
mdFileVersion = 0; |
| 130 |
|
|
| 131 |
+ |
// We need the list of simulated atom types to figure out cutoffs |
| 132 |
+ |
// as well as long range corrections. |
| 133 |
+ |
|
| 134 |
+ |
set<AtomType*>::iterator i; |
| 135 |
+ |
set<AtomType*> atomTypes_; |
| 136 |
+ |
atomTypes_ = info_->getSimulatedAtomTypes(); |
| 137 |
+ |
|
| 138 |
|
if (simParams_->haveCutoffRadius()) { |
| 139 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 140 |
|
} else { |
| 149 |
|
rCut_ = 12.0; |
| 150 |
|
} else { |
| 151 |
|
RealType thisCut; |
| 152 |
< |
set<AtomType*>::iterator i; |
| 134 |
< |
set<AtomType*> atomTypes; |
| 135 |
< |
atomTypes = info_->getSimulatedAtomTypes(); |
| 136 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 152 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 153 |
|
thisCut = interactionMan_->getSuggestedCutoffRadius((*i)); |
| 154 |
|
rCut_ = max(thisCut, rCut_); |
| 155 |
|
} |
| 171 |
|
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 172 |
|
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 173 |
|
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 174 |
+ |
stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED; |
| 175 |
|
|
| 176 |
|
if (simParams_->haveCutoffMethod()) { |
| 177 |
|
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 181 |
|
sprintf(painCave.errMsg, |
| 182 |
|
"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 183 |
|
"\tShould be one of: " |
| 184 |
< |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 184 |
> |
"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n" |
| 185 |
> |
"\tor SHIFTED_FORCE\n", |
| 186 |
|
cutMeth.c_str()); |
| 187 |
|
painCave.isFatal = 1; |
| 188 |
|
painCave.severity = OPENMD_ERROR; |
| 226 |
|
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 227 |
|
} else if (myMethod == "SHIFTED_FORCE") { |
| 228 |
|
cutoffMethod_ = SHIFTED_FORCE; |
| 229 |
+ |
} else if (myMethod == "TAYLOR_SHIFTED") { |
| 230 |
+ |
cutoffMethod_ = TAYLOR_SHIFTED; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
|
if (simParams_->haveSwitchingRadius()) |
| 234 |
|
rSwitch_ = simParams_->getSwitchingRadius(); |
| 235 |
|
|
| 236 |
< |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 236 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" || |
| 237 |
> |
myMethod == "TAYLOR_SHIFTED") { |
| 238 |
|
if (simParams_->haveSwitchingRadius()){ |
| 239 |
|
sprintf(painCave.errMsg, |
| 240 |
|
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 389 |
|
} |
| 390 |
|
switcher_->setSwitchType(sft_); |
| 391 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 371 |
– |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 392 |
|
} |
| 393 |
|
|
| 394 |
|
|
| 410 |
|
info_->prepareTopology(); |
| 411 |
|
|
| 412 |
|
doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
| 413 |
< |
cerr << "dPP = " << doParticlePot_ << "\n"; |
| 413 |
> |
doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux(); |
| 414 |
> |
if (doHeatFlux_) doParticlePot_ = true; |
| 415 |
> |
|
| 416 |
> |
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 417 |
|
|
| 418 |
|
} |
| 419 |
|
|
| 444 |
|
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 445 |
|
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 446 |
|
|
| 447 |
+ |
if (info_->getSimParams()->haveElectricField()) { |
| 448 |
+ |
ElectricField* eField = new ElectricField(info_); |
| 449 |
+ |
perturbations_.push_back(eField); |
| 450 |
+ |
} |
| 451 |
+ |
|
| 452 |
+ |
usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 453 |
+ |
|
| 454 |
|
fDecomp_->distributeInitialData(); |
| 455 |
< |
|
| 455 |
> |
|
| 456 |
|
initialized_ = true; |
| 457 |
< |
|
| 457 |
> |
|
| 458 |
|
} |
| 459 |
< |
|
| 459 |
> |
|
| 460 |
|
void ForceManager::calcForces() { |
| 461 |
|
|
| 462 |
|
if (!initialized_) initialize(); |
| 463 |
< |
|
| 463 |
> |
|
| 464 |
|
preCalculation(); |
| 465 |
|
shortRangeInteractions(); |
| 466 |
|
longRangeInteractions(); |
| 477 |
|
Molecule::CutoffGroupIterator ci; |
| 478 |
|
CutoffGroup* cg; |
| 479 |
|
|
| 480 |
< |
// forces are zeroed here, before any are accumulated. |
| 480 |
> |
// forces and potentials are zeroed here, before any are |
| 481 |
> |
// accumulated. |
| 482 |
|
|
| 483 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 484 |
+ |
|
| 485 |
+ |
snap->setBondPotential(0.0); |
| 486 |
+ |
snap->setBendPotential(0.0); |
| 487 |
+ |
snap->setTorsionPotential(0.0); |
| 488 |
+ |
snap->setInversionPotential(0.0); |
| 489 |
+ |
|
| 490 |
+ |
potVec zeroPot(0.0); |
| 491 |
+ |
snap->setLongRangePotential(zeroPot); |
| 492 |
+ |
snap->setExcludedPotentials(zeroPot); |
| 493 |
+ |
|
| 494 |
+ |
snap->setRestraintPotential(0.0); |
| 495 |
+ |
snap->setRawPotential(0.0); |
| 496 |
+ |
|
| 497 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 498 |
|
mol = info_->nextMolecule(mi)) { |
| 499 |
|
for(atom = mol->beginAtom(ai); atom != NULL; |
| 517 |
|
} |
| 518 |
|
|
| 519 |
|
// Zero out the stress tensor |
| 520 |
< |
tau *= 0.0; |
| 521 |
< |
|
| 520 |
> |
stressTensor *= 0.0; |
| 521 |
> |
// Zero out the heatFlux |
| 522 |
> |
fDecomp_->setHeatFlux( Vector3d(0.0) ); |
| 523 |
|
} |
| 524 |
|
|
| 525 |
|
void ForceManager::shortRangeInteractions() { |
| 552 |
|
|
| 553 |
|
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 554 |
|
bond = mol->nextBond(bondIter)) { |
| 555 |
< |
bond->calcForce(); |
| 555 |
> |
bond->calcForce(doParticlePot_); |
| 556 |
|
bondPotential += bond->getPotential(); |
| 557 |
|
} |
| 558 |
|
|
| 560 |
|
bend = mol->nextBend(bendIter)) { |
| 561 |
|
|
| 562 |
|
RealType angle; |
| 563 |
< |
bend->calcForce(angle); |
| 563 |
> |
bend->calcForce(angle, doParticlePot_); |
| 564 |
|
RealType currBendPot = bend->getPotential(); |
| 565 |
|
|
| 566 |
|
bendPotential += bend->getPotential(); |
| 585 |
|
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 586 |
|
torsion = mol->nextTorsion(torsionIter)) { |
| 587 |
|
RealType angle; |
| 588 |
< |
torsion->calcForce(angle); |
| 588 |
> |
torsion->calcForce(angle, doParticlePot_); |
| 589 |
|
RealType currTorsionPot = torsion->getPotential(); |
| 590 |
|
torsionPotential += torsion->getPotential(); |
| 591 |
|
map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion); |
| 609 |
|
inversion != NULL; |
| 610 |
|
inversion = mol->nextInversion(inversionIter)) { |
| 611 |
|
RealType angle; |
| 612 |
< |
inversion->calcForce(angle); |
| 612 |
> |
inversion->calcForce(angle, doParticlePot_); |
| 613 |
|
RealType currInversionPot = inversion->getPotential(); |
| 614 |
|
inversionPotential += inversion->getPotential(); |
| 615 |
|
map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 629 |
|
} |
| 630 |
|
} |
| 631 |
|
} |
| 632 |
< |
|
| 633 |
< |
RealType shortRangePotential = bondPotential + bendPotential + |
| 634 |
< |
torsionPotential + inversionPotential; |
| 632 |
> |
|
| 633 |
> |
#ifdef IS_MPI |
| 634 |
> |
// Collect from all nodes. This should eventually be moved into a |
| 635 |
> |
// SystemDecomposition, but this is a better place than in |
| 636 |
> |
// Thermo to do the collection. |
| 637 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
| 638 |
> |
MPI::SUM); |
| 639 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 640 |
> |
MPI::SUM); |
| 641 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
| 642 |
> |
MPI::REALTYPE, MPI::SUM); |
| 643 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
| 644 |
> |
MPI::REALTYPE, MPI::SUM); |
| 645 |
> |
#endif |
| 646 |
> |
|
| 647 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 648 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 649 |
< |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 650 |
< |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 651 |
< |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 652 |
< |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 648 |
> |
|
| 649 |
> |
curSnapshot->setBondPotential(bondPotential); |
| 650 |
> |
curSnapshot->setBendPotential(bendPotential); |
| 651 |
> |
curSnapshot->setTorsionPotential(torsionPotential); |
| 652 |
> |
curSnapshot->setInversionPotential(inversionPotential); |
| 653 |
> |
|
| 654 |
> |
// RealType shortRangePotential = bondPotential + bendPotential + |
| 655 |
> |
// torsionPotential + inversionPotential; |
| 656 |
> |
|
| 657 |
> |
// curSnapshot->setShortRangePotential(shortRangePotential); |
| 658 |
|
} |
| 659 |
|
|
| 660 |
|
void ForceManager::longRangeInteractions() { |
| 682 |
|
// center of mass of the group is the same as position of the atom |
| 683 |
|
// if cutoff group does not exist |
| 684 |
|
cgConfig->position = config->position; |
| 685 |
+ |
cgConfig->velocity = config->velocity; |
| 686 |
|
} |
| 687 |
|
|
| 688 |
|
fDecomp_->zeroWorkArrays(); |
| 689 |
|
fDecomp_->distributeData(); |
| 690 |
|
|
| 691 |
|
int cg1, cg2, atom1, atom2, topoDist; |
| 692 |
< |
Vector3d d_grp, dag, d; |
| 692 |
> |
Vector3d d_grp, dag, d, gvel2, vel2; |
| 693 |
|
RealType rgrpsq, rgrp, r2, r; |
| 694 |
|
RealType electroMult, vdwMult; |
| 695 |
|
RealType vij; |
| 698 |
|
RealType rCutSq; |
| 699 |
|
bool in_switching_region; |
| 700 |
|
RealType sw, dswdr, swderiv; |
| 701 |
< |
vector<int> atomListColumn, atomListRow, atomListLocal; |
| 701 |
> |
vector<int> atomListColumn, atomListRow; |
| 702 |
|
InteractionData idat; |
| 703 |
|
SelfData sdat; |
| 704 |
|
RealType mf; |
| 641 |
– |
RealType lrPot; |
| 705 |
|
RealType vpair; |
| 706 |
+ |
RealType dVdFQ1(0.0); |
| 707 |
+ |
RealType dVdFQ2(0.0); |
| 708 |
|
potVec longRangePotential(0.0); |
| 709 |
|
potVec workPot(0.0); |
| 710 |
+ |
potVec exPot(0.0); |
| 711 |
+ |
Vector3d eField1(0.0); |
| 712 |
+ |
Vector3d eField2(0.0); |
| 713 |
+ |
vector<int>::iterator ia, jb; |
| 714 |
|
|
| 715 |
|
int loopStart, loopEnd; |
| 716 |
|
|
| 717 |
|
idat.vdwMult = &vdwMult; |
| 718 |
|
idat.electroMult = &electroMult; |
| 719 |
|
idat.pot = &workPot; |
| 720 |
+ |
idat.excludedPot = &exPot; |
| 721 |
|
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 722 |
+ |
sdat.excludedPot = fDecomp_->getExcludedSelfPotential(); |
| 723 |
|
idat.vpair = &vpair; |
| 724 |
+ |
idat.dVdFQ1 = &dVdFQ1; |
| 725 |
+ |
idat.dVdFQ2 = &dVdFQ2; |
| 726 |
+ |
idat.eField1 = &eField1; |
| 727 |
+ |
idat.eField2 = &eField2; |
| 728 |
|
idat.f1 = &f1; |
| 729 |
|
idat.sw = &sw; |
| 730 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 731 |
< |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 731 |
> |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
| 732 |
|
idat.doParticlePot = doParticlePot_; |
| 733 |
+ |
idat.doElectricField = doElectricField_; |
| 734 |
|
sdat.doParticlePot = doParticlePot_; |
| 735 |
|
|
| 736 |
|
loopEnd = PAIR_LOOP; |
| 739 |
|
} else { |
| 740 |
|
loopStart = PAIR_LOOP; |
| 741 |
|
} |
| 666 |
– |
|
| 742 |
|
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 743 |
|
|
| 744 |
|
if (iLoop == loopStart) { |
| 745 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 746 |
< |
if (update_nlist) |
| 746 |
> |
if (update_nlist) { |
| 747 |
> |
if (!usePeriodicBoundaryConditions_) |
| 748 |
> |
Mat3x3d bbox = thermo->getBoundingBox(); |
| 749 |
|
neighborList = fDecomp_->buildNeighborList(); |
| 750 |
< |
} |
| 750 |
> |
} |
| 751 |
> |
} |
| 752 |
|
|
| 753 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 754 |
|
it != neighborList.end(); ++it) { |
| 768 |
|
idat.rcut = &cuts.first; |
| 769 |
|
if (iLoop == PAIR_LOOP) { |
| 770 |
|
vij = 0.0; |
| 771 |
< |
fij = V3Zero; |
| 771 |
> |
fij.zero(); |
| 772 |
> |
eField1.zero(); |
| 773 |
> |
eField2.zero(); |
| 774 |
|
} |
| 775 |
|
|
| 776 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 777 |
|
rgrp); |
| 778 |
< |
|
| 778 |
> |
|
| 779 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 780 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 781 |
|
|
| 782 |
< |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 782 |
> |
if (doHeatFlux_) |
| 783 |
> |
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 784 |
> |
|
| 785 |
> |
for (ia = atomListRow.begin(); |
| 786 |
|
ia != atomListRow.end(); ++ia) { |
| 787 |
|
atom1 = (*ia); |
| 788 |
< |
|
| 789 |
< |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 788 |
> |
|
| 789 |
> |
for (jb = atomListColumn.begin(); |
| 790 |
|
jb != atomListColumn.end(); ++jb) { |
| 791 |
|
atom2 = (*jb); |
| 792 |
|
|
| 793 |
< |
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 793 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 794 |
> |
|
| 795 |
|
vpair = 0.0; |
| 796 |
|
workPot = 0.0; |
| 797 |
< |
f1 = V3Zero; |
| 797 |
> |
exPot = 0.0; |
| 798 |
> |
f1.zero(); |
| 799 |
> |
dVdFQ1 = 0.0; |
| 800 |
> |
dVdFQ2 = 0.0; |
| 801 |
|
|
| 802 |
|
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 803 |
< |
|
| 803 |
> |
|
| 804 |
|
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 805 |
|
vdwMult = vdwScale_[topoDist]; |
| 806 |
|
electroMult = electrostaticScale_[topoDist]; |
| 808 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 809 |
|
idat.d = &d_grp; |
| 810 |
|
idat.r2 = &rgrpsq; |
| 811 |
+ |
if (doHeatFlux_) |
| 812 |
+ |
vel2 = gvel2; |
| 813 |
|
} else { |
| 814 |
|
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 815 |
|
curSnapshot->wrapVector( d ); |
| 816 |
|
r2 = d.lengthSquare(); |
| 817 |
|
idat.d = &d; |
| 818 |
|
idat.r2 = &r2; |
| 819 |
+ |
if (doHeatFlux_) |
| 820 |
+ |
vel2 = fDecomp_->getAtomVelocityColumn(atom2); |
| 821 |
|
} |
| 822 |
|
|
| 823 |
|
r = sqrt( *(idat.r2) ); |
| 830 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 831 |
|
vij += vpair; |
| 832 |
|
fij += f1; |
| 833 |
< |
tau -= outProduct( *(idat.d), f1); |
| 833 |
> |
stressTensor -= outProduct( *(idat.d), f1); |
| 834 |
> |
if (doHeatFlux_) |
| 835 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2)); |
| 836 |
|
} |
| 837 |
|
} |
| 838 |
|
} |
| 845 |
|
fij += fg; |
| 846 |
|
|
| 847 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 848 |
< |
tau -= outProduct( *(idat.d), fg); |
| 848 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 849 |
> |
atomListColumn[0], |
| 850 |
> |
cg1, cg2)) { |
| 851 |
> |
stressTensor -= outProduct( *(idat.d), fg); |
| 852 |
> |
if (doHeatFlux_) |
| 853 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 854 |
> |
} |
| 855 |
|
} |
| 856 |
|
|
| 857 |
< |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 857 |
> |
for (ia = atomListRow.begin(); |
| 858 |
|
ia != atomListRow.end(); ++ia) { |
| 859 |
|
atom1 = (*ia); |
| 860 |
|
mf = fDecomp_->getMassFactorRow(atom1); |
| 867 |
|
// find the distance between the atom |
| 868 |
|
// and the center of the cutoff group: |
| 869 |
|
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 870 |
< |
tau -= outProduct(dag, fg); |
| 870 |
> |
stressTensor -= outProduct(dag, fg); |
| 871 |
> |
if (doHeatFlux_) |
| 872 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 873 |
|
} |
| 874 |
|
} |
| 875 |
|
} |
| 876 |
< |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 876 |
> |
for (jb = atomListColumn.begin(); |
| 877 |
|
jb != atomListColumn.end(); ++jb) { |
| 878 |
|
atom2 = (*jb); |
| 879 |
|
mf = fDecomp_->getMassFactorColumn(atom2); |
| 887 |
|
// find the distance between the atom |
| 888 |
|
// and the center of the cutoff group: |
| 889 |
|
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 890 |
< |
tau -= outProduct(dag, fg); |
| 890 |
> |
stressTensor -= outProduct(dag, fg); |
| 891 |
> |
if (doHeatFlux_) |
| 892 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 893 |
|
} |
| 894 |
|
} |
| 895 |
|
} |
| 896 |
|
} |
| 897 |
|
//if (!info_->usesAtomicVirial()) { |
| 898 |
< |
// tau -= outProduct(d_grp, fij); |
| 898 |
> |
// stressTensor -= outProduct(d_grp, fij); |
| 899 |
> |
// if (doHeatFlux_) |
| 900 |
> |
// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2)); |
| 901 |
|
//} |
| 902 |
|
} |
| 903 |
|
} |
| 908 |
|
|
| 909 |
|
fDecomp_->collectIntermediateData(); |
| 910 |
|
|
| 911 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 911 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 912 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 913 |
|
interactionMan_->doPreForce(sdat); |
| 914 |
|
} |
| 919 |
|
} |
| 920 |
|
} |
| 921 |
|
|
| 922 |
+ |
// collects pairwise information |
| 923 |
|
fDecomp_->collectData(); |
| 924 |
|
|
| 925 |
|
if (info_->requiresSelfCorrection()) { |
| 926 |
< |
|
| 821 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 926 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 927 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 928 |
|
interactionMan_->doSelfCorrection(sdat); |
| 929 |
|
} |
| 825 |
– |
|
| 930 |
|
} |
| 931 |
|
|
| 932 |
+ |
// collects single-atom information |
| 933 |
+ |
fDecomp_->collectSelfData(); |
| 934 |
+ |
|
| 935 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 936 |
|
*(fDecomp_->getPairwisePotential()); |
| 937 |
|
|
| 938 |
< |
lrPot = longRangePotential.sum(); |
| 938 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 939 |
> |
|
| 940 |
> |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 941 |
> |
*(fDecomp_->getExcludedPotential())); |
| 942 |
|
|
| 833 |
– |
//store the tau and long range potential |
| 834 |
– |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 835 |
– |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 836 |
– |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 943 |
|
} |
| 944 |
|
|
| 945 |
|
|
| 946 |
|
void ForceManager::postCalculation() { |
| 947 |
+ |
|
| 948 |
+ |
vector<Perturbation*>::iterator pi; |
| 949 |
+ |
for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) { |
| 950 |
+ |
(*pi)->applyPerturbation(); |
| 951 |
+ |
} |
| 952 |
+ |
|
| 953 |
|
SimInfo::MoleculeIterator mi; |
| 954 |
|
Molecule* mol; |
| 955 |
|
Molecule::RigidBodyIterator rbIter; |
| 956 |
|
RigidBody* rb; |
| 957 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 958 |
< |
|
| 958 |
> |
|
| 959 |
|
// collect the atomic forces onto rigid bodies |
| 960 |
|
|
| 961 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 963 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 964 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 965 |
|
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 966 |
< |
tau += rbTau; |
| 966 |
> |
stressTensor += rbTau; |
| 967 |
|
} |
| 968 |
|
} |
| 969 |
|
|
| 970 |
|
#ifdef IS_MPI |
| 971 |
< |
Mat3x3d tmpTau(tau); |
| 972 |
< |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 861 |
< |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 971 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 972 |
> |
MPI::REALTYPE, MPI::SUM); |
| 973 |
|
#endif |
| 974 |
< |
curSnapshot->setTau(tau); |
| 975 |
< |
} |
| 974 |
> |
curSnapshot->setStressTensor(stressTensor); |
| 975 |
> |
|
| 976 |
> |
if (info_->getSimParams()->getUseLongRangeCorrections()) { |
| 977 |
> |
/* |
| 978 |
> |
RealType vol = curSnapshot->getVolume(); |
| 979 |
> |
RealType Elrc(0.0); |
| 980 |
> |
RealType Wlrc(0.0); |
| 981 |
|
|
| 982 |
< |
} //end namespace OpenMD |
| 982 |
> |
set<AtomType*>::iterator i; |
| 983 |
> |
set<AtomType*>::iterator j; |
| 984 |
> |
|
| 985 |
> |
RealType n_i, n_j; |
| 986 |
> |
RealType rho_i, rho_j; |
| 987 |
> |
pair<RealType, RealType> LRI; |
| 988 |
> |
|
| 989 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 990 |
> |
n_i = RealType(info_->getGlobalCountOfType(*i)); |
| 991 |
> |
rho_i = n_i / vol; |
| 992 |
> |
for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) { |
| 993 |
> |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 994 |
> |
rho_j = n_j / vol; |
| 995 |
> |
|
| 996 |
> |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 997 |
> |
|
| 998 |
> |
Elrc += n_i * rho_j * LRI.first; |
| 999 |
> |
Wlrc -= rho_i * rho_j * LRI.second; |
| 1000 |
> |
} |
| 1001 |
> |
} |
| 1002 |
> |
Elrc *= 2.0 * NumericConstant::PI; |
| 1003 |
> |
Wlrc *= 2.0 * NumericConstant::PI; |
| 1004 |
> |
|
| 1005 |
> |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 1006 |
> |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 1007 |
> |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 1008 |
> |
curSnapshot->setStressTensor(stressTensor); |
| 1009 |
> |
*/ |
| 1010 |
> |
|
| 1011 |
> |
} |
| 1012 |
> |
} |
| 1013 |
> |
} |
