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#include "nonbonded/NonBondedInteraction.hpp" |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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#include <cstdio> |
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#include <iostream> |
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#include <iomanip> |
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using namespace std; |
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namespace OpenMD { |
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painCave.severity = OPENMD_INFO; |
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simError(); |
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} |
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fDecomp_->setUserCutoff(rCut_); |
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} |
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fDecomp_->setUserCutoff(rCut_); |
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interactionMan_->setCutoffRadius(rCut_); |
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map<string, CutoffMethod> stringToCutoffMethod; |
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stringToCutoffMethod["HARD"] = HARD; |
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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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} |
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void ForceManager::initialize() { |
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} |
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void ForceManager::longRangeInteractions() { |
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// some of this initial stuff will go away: |
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|
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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DataStorage* config = &(curSnapshot->atomData); |
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DataStorage* cgConfig = &(curSnapshot->cgData); |
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RealType* frc = config->getArrayPointer(DataStorage::dslForce); |
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RealType* pos = config->getArrayPointer(DataStorage::dslPosition); |
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RealType* trq = config->getArrayPointer(DataStorage::dslTorque); |
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RealType* A = config->getArrayPointer(DataStorage::dslAmat); |
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RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
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RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
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// new stuff starts here: |
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//calculate the center of mass of cutoff group |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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if(info_->getNCutoffGroups() > 0){ |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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cg->updateCOM(); |
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} |
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} |
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} else { |
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// center of mass of the group is the same as position of the atom |
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// if cutoff group does not exist |
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cgConfig->position = config->position; |
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} |
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|
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fDecomp_->zeroWorkArrays(); |
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fDecomp_->distributeData(); |
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RealType rgrpsq, rgrp, r2, r; |
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RealType electroMult, vdwMult; |
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RealType vij; |
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Vector3d fij, fg; |
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Vector3d fij, fg, f1; |
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tuple3<RealType, RealType, RealType> cuts; |
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RealType rCutSq; |
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bool in_switching_region; |
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InteractionData idat; |
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SelfData sdat; |
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RealType mf; |
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potVec pot(0.0); |
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potVec longRangePotential(0.0); |
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RealType lrPot; |
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RealType vpair; |
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potVec longRangePotential(0.0); |
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potVec workPot(0.0); |
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int loopStart, loopEnd; |
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idat.vdwMult = &vdwMult; |
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idat.electroMult = &electroMult; |
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idat.pot = &workPot; |
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sdat.pot = fDecomp_->getEmbeddingPotential(); |
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idat.vpair = &vpair; |
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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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|
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loopEnd = PAIR_LOOP; |
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if (info_->requiresPrepair() ) { |
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loopStart = PREPAIR_LOOP; |
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} else { |
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loopStart = PAIR_LOOP; |
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} |
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for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
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if (iLoop == loopStart) { |
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in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
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rgrp); |
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idat.sw = &sw; |
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atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
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atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
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for (vector<int>::iterator jb = atomListColumn.begin(); |
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jb != atomListColumn.end(); ++jb) { |
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atom2 = (*jb); |
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cerr << "doing atoms " << atom1 << " " << atom2 << "\n"; |
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if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
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vpair = 0.0; |
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workPot = 0.0; |
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f1 = V3Zero; |
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cerr << "filling idat atoms " << atom1 << " " << atom2 << "\n"; |
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idat = fDecomp_->fillInteractionData(atom1, atom2); |
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cerr << "done with idat\n"; |
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fDecomp_->fillInteractionData(idat, atom1, atom2); |
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topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
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vdwMult = vdwScale_[topoDist]; |
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electroMult = electrostaticScale_[topoDist]; |
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idat.vdwMult = &vdwMult; |
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idat.electroMult = &electroMult; |
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idat.pot = &pot; |
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idat.vpair = &vpair; |
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if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
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idat.d = &d_grp; |
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idat.r2 = &rgrpsq; |
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idat.r2 = &r2; |
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} |
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cerr << "d = " << d << "\n"; |
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cerr << "r2 = " << r2 << "\n"; |
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r = sqrt( r2 ); |
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r = sqrt( *(idat.r2) ); |
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idat.rij = &r; |
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if (iLoop == PREPAIR_LOOP) { |
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interactionMan_->doPrePair(idat); |
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} else { |
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cerr << "doing doPair " << atom1 << " " << atom2 << " " << r << "\n"; |
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interactionMan_->doPair(idat); |
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fDecomp_->unpackInteractionData(idat, atom1, atom2); |
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vij += *(idat.vpair); |
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fij += *(idat.f1); |
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tau -= outProduct( *(idat.d), *(idat.f1)); |
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vij += vpair; |
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fij += f1; |
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tau -= outProduct( *(idat.d), f1); |
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} |
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} |
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} |
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fDecomp_->collectIntermediateData(); |
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for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 693 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
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> |
fDecomp_->fillSelfData(sdat, atom1); |
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interactionMan_->doPreForce(sdat); |
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} |
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< |
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| 696 |
> |
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> |
|
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fDecomp_->distributeIntermediateData(); |
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} |
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} |
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jb != skipList.end(); ++jb) { |
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atom2 = (*jb); |
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< |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 716 |
> |
fDecomp_->fillSkipData(idat, atom1, atom2); |
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interactionMan_->doSkipCorrection(idat); |
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fDecomp_->unpackSkipData(idat, atom1, atom2); |
| 719 |
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} |
| 721 |
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} |
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if (info_->requiresSelfCorrection()) { |
| 725 |
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|
| 726 |
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for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
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< |
sdat = fDecomp_->fillSelfData(atom1); |
| 727 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 728 |
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interactionMan_->doSelfCorrection(sdat); |
| 729 |
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} |
| 730 |
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| 731 |
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} |
| 732 |
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|
| 733 |
< |
longRangePotential = fDecomp_->getLongRangePotential(); |
| 733 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 734 |
> |
*(fDecomp_->getPairwisePotential()); |
| 735 |
> |
|
| 736 |
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lrPot = longRangePotential.sum(); |
| 737 |
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|
| 738 |
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//store the tau and long range potential |
