| 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 |
|
|
| 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, |
| 102 |
< |
* or SHIFTED_POTENTIAL) |
| 101 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED, |
| 102 |
> |
* SHIFTED_POTENTIAL, or EWALD_FULL) |
| 103 |
|
* If cutoffMethod was explicitly set, use that choice. |
| 104 |
|
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 105 |
|
* |
| 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; |
| 136 |
< |
set<AtomType*> atomTypes; |
| 137 |
< |
atomTypes = info_->getSimulatedAtomTypes(); |
| 138 |
< |
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 |
+ |
stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL; |
| 176 |
|
|
| 177 |
|
if (simParams_->haveCutoffMethod()) { |
| 178 |
|
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 182 |
|
sprintf(painCave.errMsg, |
| 183 |
|
"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 184 |
|
"\tShould be one of: " |
| 185 |
< |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 185 |
> |
"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n" |
| 186 |
> |
"\tSHIFTED_FORCE, or EWALD_FULL\n", |
| 187 |
|
cutMeth.c_str()); |
| 188 |
|
painCave.isFatal = 1; |
| 189 |
|
painCave.severity = OPENMD_ERROR; |
| 227 |
|
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 228 |
|
} else if (myMethod == "SHIFTED_FORCE") { |
| 229 |
|
cutoffMethod_ = SHIFTED_FORCE; |
| 230 |
+ |
} else if (myMethod == "TAYLOR_SHIFTED") { |
| 231 |
+ |
cutoffMethod_ = TAYLOR_SHIFTED; |
| 232 |
+ |
} else if (myMethod == "EWALD_FULL") { |
| 233 |
+ |
cutoffMethod_ = EWALD_FULL; |
| 234 |
|
} |
| 235 |
|
|
| 236 |
|
if (simParams_->haveSwitchingRadius()) |
| 237 |
|
rSwitch_ = simParams_->getSwitchingRadius(); |
| 238 |
|
|
| 239 |
< |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 239 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" || |
| 240 |
> |
myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") { |
| 241 |
|
if (simParams_->haveSwitchingRadius()){ |
| 242 |
|
sprintf(painCave.errMsg, |
| 243 |
|
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 392 |
|
} |
| 393 |
|
switcher_->setSwitchType(sft_); |
| 394 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 373 |
– |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 395 |
|
} |
| 396 |
|
|
| 397 |
|
|
| 415 |
|
doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
| 416 |
|
doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux(); |
| 417 |
|
if (doHeatFlux_) doParticlePot_ = true; |
| 418 |
+ |
|
| 419 |
+ |
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 420 |
|
|
| 421 |
|
} |
| 422 |
|
|
| 452 |
|
perturbations_.push_back(eField); |
| 453 |
|
} |
| 454 |
|
|
| 455 |
+ |
usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 456 |
+ |
|
| 457 |
|
fDecomp_->distributeInitialData(); |
| 458 |
< |
|
| 458 |
> |
|
| 459 |
|
initialized_ = true; |
| 460 |
< |
|
| 460 |
> |
|
| 461 |
|
} |
| 462 |
< |
|
| 462 |
> |
|
| 463 |
|
void ForceManager::calcForces() { |
| 464 |
|
|
| 465 |
|
if (!initialized_) initialize(); |
| 466 |
< |
|
| 466 |
> |
|
| 467 |
|
preCalculation(); |
| 468 |
|
shortRangeInteractions(); |
| 469 |
|
longRangeInteractions(); |
| 662 |
|
|
| 663 |
|
void ForceManager::longRangeInteractions() { |
| 664 |
|
|
| 640 |
– |
|
| 665 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 666 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 667 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 668 |
|
|
| 669 |
+ |
|
| 670 |
|
//calculate the center of mass of cutoff group |
| 671 |
|
|
| 672 |
|
SimInfo::MoleculeIterator mi; |
| 699 |
|
RealType vij; |
| 700 |
|
Vector3d fij, fg, f1; |
| 701 |
|
tuple3<RealType, RealType, RealType> cuts; |
| 702 |
< |
RealType rCutSq; |
| 702 |
> |
RealType rCut, rCutSq, rListSq; |
| 703 |
|
bool in_switching_region; |
| 704 |
|
RealType sw, dswdr, swderiv; |
| 705 |
< |
vector<int> atomListColumn, atomListRow, atomListLocal; |
| 705 |
> |
vector<int> atomListColumn, atomListRow; |
| 706 |
|
InteractionData idat; |
| 707 |
|
SelfData sdat; |
| 708 |
|
RealType mf; |
| 709 |
|
RealType vpair; |
| 710 |
|
RealType dVdFQ1(0.0); |
| 711 |
|
RealType dVdFQ2(0.0); |
| 712 |
< |
Vector3d eField1(0.0); |
| 713 |
< |
Vector3d eField2(0.0); |
| 689 |
< |
potVec longRangePotential(0.0); |
| 712 |
> |
potVec longRangePotential(0.0); |
| 713 |
> |
potVec reciprocalPotential(0.0); |
| 714 |
|
potVec workPot(0.0); |
| 715 |
|
potVec exPot(0.0); |
| 716 |
+ |
Vector3d eField1(0.0); |
| 717 |
+ |
Vector3d eField2(0.0); |
| 718 |
|
vector<int>::iterator ia, jb; |
| 719 |
|
|
| 720 |
|
int loopStart, loopEnd; |
| 721 |
< |
|
| 721 |
> |
|
| 722 |
> |
idat.rcut = &rCut; |
| 723 |
|
idat.vdwMult = &vdwMult; |
| 724 |
|
idat.electroMult = &electroMult; |
| 725 |
|
idat.pot = &workPot; |
| 730 |
|
idat.dVdFQ1 = &dVdFQ1; |
| 731 |
|
idat.dVdFQ2 = &dVdFQ2; |
| 732 |
|
idat.eField1 = &eField1; |
| 733 |
< |
idat.eField2 = &eField2; |
| 733 |
> |
idat.eField2 = &eField2; |
| 734 |
|
idat.f1 = &f1; |
| 735 |
|
idat.sw = &sw; |
| 736 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 737 |
< |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 737 |
> |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
| 738 |
|
idat.doParticlePot = doParticlePot_; |
| 739 |
+ |
idat.doElectricField = doElectricField_; |
| 740 |
|
sdat.doParticlePot = doParticlePot_; |
| 741 |
|
|
| 742 |
|
loopEnd = PAIR_LOOP; |
| 749 |
|
|
| 750 |
|
if (iLoop == loopStart) { |
| 751 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 752 |
< |
if (update_nlist) |
| 753 |
< |
neighborList = fDecomp_->buildNeighborList(); |
| 754 |
< |
} |
| 752 |
> |
if (update_nlist) { |
| 753 |
> |
if (!usePeriodicBoundaryConditions_) |
| 754 |
> |
Mat3x3d bbox = thermo->getBoundingBox(); |
| 755 |
> |
fDecomp_->buildNeighborList(neighborList_); |
| 756 |
> |
} |
| 757 |
> |
} |
| 758 |
|
|
| 759 |
< |
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 760 |
< |
it != neighborList.end(); ++it) { |
| 759 |
> |
for (vector<pair<int, int> >::iterator it = neighborList_.begin(); |
| 760 |
> |
it != neighborList_.end(); ++it) { |
| 761 |
|
|
| 762 |
|
cg1 = (*it).first; |
| 763 |
|
cg2 = (*it).second; |
| 764 |
|
|
| 765 |
< |
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 765 |
> |
fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq); |
| 766 |
|
|
| 767 |
|
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 768 |
|
|
| 769 |
< |
curSnapshot->wrapVector(d_grp); |
| 769 |
> |
// already wrapped in the getIntergroupVector call: |
| 770 |
> |
// curSnapshot->wrapVector(d_grp); |
| 771 |
|
rgrpsq = d_grp.lengthSquare(); |
| 740 |
– |
rCutSq = cuts.second; |
| 772 |
|
|
| 773 |
|
if (rgrpsq < rCutSq) { |
| 743 |
– |
idat.rcut = &cuts.first; |
| 774 |
|
if (iLoop == PAIR_LOOP) { |
| 775 |
|
vij = 0.0; |
| 776 |
< |
fij = V3Zero; |
| 776 |
> |
fij.zero(); |
| 777 |
> |
eField1.zero(); |
| 778 |
> |
eField2.zero(); |
| 779 |
|
} |
| 780 |
|
|
| 781 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 800 |
|
vpair = 0.0; |
| 801 |
|
workPot = 0.0; |
| 802 |
|
exPot = 0.0; |
| 803 |
< |
f1 = V3Zero; |
| 803 |
> |
f1.zero(); |
| 804 |
|
dVdFQ1 = 0.0; |
| 805 |
|
dVdFQ2 = 0.0; |
| 806 |
|
|
| 827 |
|
|
| 828 |
|
r = sqrt( *(idat.r2) ); |
| 829 |
|
idat.rij = &r; |
| 830 |
< |
|
| 830 |
> |
|
| 831 |
|
if (iLoop == PREPAIR_LOOP) { |
| 832 |
|
interactionMan_->doPrePair(idat); |
| 833 |
|
} else { |
| 850 |
|
fij += fg; |
| 851 |
|
|
| 852 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 853 |
< |
stressTensor -= outProduct( *(idat.d), fg); |
| 854 |
< |
if (doHeatFlux_) |
| 855 |
< |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 856 |
< |
|
| 853 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 854 |
> |
atomListColumn[0], |
| 855 |
> |
cg1, cg2)) { |
| 856 |
> |
stressTensor -= outProduct( *(idat.d), fg); |
| 857 |
> |
if (doHeatFlux_) |
| 858 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 859 |
> |
} |
| 860 |
|
} |
| 861 |
|
|
| 862 |
|
for (ia = atomListRow.begin(); |
| 923 |
|
} |
| 924 |
|
} |
| 925 |
|
} |
| 926 |
< |
|
| 926 |
> |
|
| 927 |
|
// collects pairwise information |
| 928 |
|
fDecomp_->collectData(); |
| 929 |
+ |
if (cutoffMethod_ == EWALD_FULL) { |
| 930 |
+ |
interactionMan_->doReciprocalSpaceSum(reciprocalPotential); |
| 931 |
+ |
} |
| 932 |
|
|
| 933 |
|
if (info_->requiresSelfCorrection()) { |
| 934 |
|
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 941 |
|
fDecomp_->collectSelfData(); |
| 942 |
|
|
| 943 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 944 |
< |
*(fDecomp_->getPairwisePotential()); |
| 944 |
> |
*(fDecomp_->getPairwisePotential()) + reciprocalPotential; |
| 945 |
|
|
| 946 |
|
curSnapshot->setLongRangePotential(longRangePotential); |
| 947 |
|
|
| 950 |
|
|
| 951 |
|
} |
| 952 |
|
|
| 915 |
– |
|
| 953 |
|
void ForceManager::postCalculation() { |
| 954 |
|
|
| 955 |
|
vector<Perturbation*>::iterator pi; |
| 980 |
|
#endif |
| 981 |
|
curSnapshot->setStressTensor(stressTensor); |
| 982 |
|
|
| 983 |
+ |
if (info_->getSimParams()->getUseLongRangeCorrections()) { |
| 984 |
+ |
/* |
| 985 |
+ |
RealType vol = curSnapshot->getVolume(); |
| 986 |
+ |
RealType Elrc(0.0); |
| 987 |
+ |
RealType Wlrc(0.0); |
| 988 |
+ |
|
| 989 |
+ |
set<AtomType*>::iterator i; |
| 990 |
+ |
set<AtomType*>::iterator j; |
| 991 |
+ |
|
| 992 |
+ |
RealType n_i, n_j; |
| 993 |
+ |
RealType rho_i, rho_j; |
| 994 |
+ |
pair<RealType, RealType> LRI; |
| 995 |
+ |
|
| 996 |
+ |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 997 |
+ |
n_i = RealType(info_->getGlobalCountOfType(*i)); |
| 998 |
+ |
rho_i = n_i / vol; |
| 999 |
+ |
for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) { |
| 1000 |
+ |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 1001 |
+ |
rho_j = n_j / vol; |
| 1002 |
+ |
|
| 1003 |
+ |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 1004 |
+ |
|
| 1005 |
+ |
Elrc += n_i * rho_j * LRI.first; |
| 1006 |
+ |
Wlrc -= rho_i * rho_j * LRI.second; |
| 1007 |
+ |
} |
| 1008 |
+ |
} |
| 1009 |
+ |
Elrc *= 2.0 * NumericConstant::PI; |
| 1010 |
+ |
Wlrc *= 2.0 * NumericConstant::PI; |
| 1011 |
+ |
|
| 1012 |
+ |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 1013 |
+ |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 1014 |
+ |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 1015 |
+ |
curSnapshot->setStressTensor(stressTensor); |
| 1016 |
+ |
*/ |
| 1017 |
+ |
|
| 1018 |
+ |
} |
| 1019 |
|
} |
| 1020 |
< |
} //end namespace OpenMD |
| 1020 |
> |
} |
