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* @file ForceManager.cpp |
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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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*/ |
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| 57 |
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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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+ |
#include "perturbations/ElectricField.hpp" |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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| 63 |
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#include <cstdio> |
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} |
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switcher_->setSwitchType(sft_); |
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switcher_->setSwitch(rSwitch_, rCut_); |
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interactionMan_->setSwitchingRadius(rSwitch_); |
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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(); |
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if (doHeatFlux_) doParticlePot_ = true; |
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+ |
|
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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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|
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if (info_->getSimParams()->haveElectricField()) { |
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ElectricField* eField = new ElectricField(info_); |
| 429 |
+ |
perturbations_.push_back(eField); |
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} |
| 431 |
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|
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fDecomp_->distributeInitialData(); |
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initialized_ = true; |
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InteractionData idat; |
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SelfData sdat; |
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RealType mf; |
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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); |
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Vector3d eField2(0.0); |
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vector<int>::iterator ia, jb; |
| 693 |
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int loopStart, loopEnd; |
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idat.vpair = &vpair; |
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idat.dVdFQ1 = &dVdFQ1; |
| 704 |
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idat.dVdFQ2 = &dVdFQ2; |
| 705 |
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idat.eField1 = &eField1; |
| 706 |
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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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loopEnd = PAIR_LOOP; |
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if (iLoop == PAIR_LOOP) { |
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vij = 0.0; |
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fij = V3Zero; |
| 748 |
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eField1 = V3Zero; |
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eField2 = V3Zero; |
| 750 |
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} |
| 751 |
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in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
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fij += fg; |
| 822 |
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| 823 |
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if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
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< |
stressTensor -= outProduct( *(idat.d), fg); |
| 825 |
< |
if (doHeatFlux_) |
| 826 |
< |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 827 |
< |
|
| 824 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 825 |
> |
atomListColumn[0], |
| 826 |
> |
cg1, cg2)) { |
| 827 |
> |
stressTensor -= outProduct( *(idat.d), fg); |
| 828 |
> |
if (doHeatFlux_) |
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> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 830 |
> |
} |
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} |
| 832 |
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for (ia = atomListRow.begin(); |
| 884 |
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fDecomp_->collectIntermediateData(); |
| 886 |
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for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 887 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 888 |
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fDecomp_->fillSelfData(sdat, atom1); |
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interactionMan_->doPreForce(sdat); |
| 890 |
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} |
| 899 |
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fDecomp_->collectData(); |
| 900 |
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if (info_->requiresSelfCorrection()) { |
| 902 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 902 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 903 |
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fDecomp_->fillSelfData(sdat, atom1); |
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interactionMan_->doSelfCorrection(sdat); |
| 905 |
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} |
| 913 |
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| 914 |
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curSnapshot->setLongRangePotential(longRangePotential); |
| 915 |
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| 916 |
< |
// lrPot = longRangePotential.sum(); |
| 916 |
> |
// collects single-atom information |
| 917 |
> |
fDecomp_->collectSelfData(); |
| 918 |
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| 919 |
< |
// //store the long range potential |
| 920 |
< |
// curSnapshot->setLongRangePotential(lrPot); |
| 919 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 920 |
> |
*(fDecomp_->getPairwisePotential()); |
| 921 |
> |
|
| 922 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 923 |
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|
| 924 |
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curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 925 |
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*(fDecomp_->getExcludedPotential())); |
| 928 |
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| 929 |
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| 930 |
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void ForceManager::postCalculation() { |
| 931 |
+ |
|
| 932 |
+ |
vector<Perturbation*>::iterator pi; |
| 933 |
+ |
for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) { |
| 934 |
+ |
(*pi)->applyPerturbation(); |
| 935 |
+ |
} |
| 936 |
+ |
|
| 937 |
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SimInfo::MoleculeIterator mi; |
| 938 |
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Molecule* mol; |
| 939 |
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Molecule::RigidBodyIterator rbIter; |
| 958 |
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curSnapshot->setStressTensor(stressTensor); |
| 959 |
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|
| 960 |
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} |
| 937 |
– |
|
| 961 |
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} //end namespace OpenMD |
