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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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|
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using namespace std; |
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namespace OpenMD { |
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ForceManager::ForceManager(SimInfo * info) : info_(info) { |
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forceField_ = info_->getForceField(); |
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fDecomp_ = new ForceMatrixDecomposition(info_); |
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interactionMan_ = new InteractionManager(); |
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fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
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} |
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/** |
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painCave.isFatal = 0; |
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painCave.severity = OPENMD_INFO; |
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simError(); |
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} |
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} |
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} |
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|
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fDecomp_->setUserCutoff(rCut_); |
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|
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map<string, CutoffMethod> stringToCutoffMethod; |
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stringToCutoffMethod["HARD"] = HARD; |
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stringToCutoffMethod["SWITCHED"] = SWITCHED; |
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simError(); |
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cutoffPolicy_ = TRADITIONAL; |
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} |
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fDecomp_->setCutoffPolicy(cutoffPolicy_); |
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} |
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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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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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RealType* rc; |
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|
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//calculate the center of mass of cutoff group |
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if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
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rc = cgConfig->getArrayPointer(DataStorage::dslPosition); |
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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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|
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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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rc = pos; |
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cgConfig->position = config->position; |
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} |
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// new stuff starts here: |
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fDecomp_->zeroWorkArrays(); |
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fDecomp_->distributeData(); |
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|
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int cg1, cg2, atom1, atom2; |
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Vector3d d_grp, dag; |
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RealType rgrpsq, rgrp; |
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|
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int cg1, cg2, atom1, atom2, topoDist; |
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Vector3d d_grp, dag, d; |
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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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|
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for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) { |
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for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
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if (iLoop == loopStart) { |
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bool update_nlist = fDecomp_->checkNeighborList(); |
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if (update_nlist) |
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neighborList = fDecomp_->buildNeighborList(); |
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} |
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} |
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for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
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it != neighborList.end(); ++it) { |
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cg1 = (*it).first; |
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cg2 = (*it).second; |
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rCutSq = cuts.second; |
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if (rgrpsq < rCutSq) { |
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*(idat.rcut) = cuts.first; |
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idat.rcut = &cuts.first; |
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if (iLoop == PAIR_LOOP) { |
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vij *= 0.0; |
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fij = V3Zero; |
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} |
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in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr, |
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in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
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rgrp); |
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atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
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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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> |
|
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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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|
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fDecomp_->fillInteractionData(idat, atom1, atom2); |
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pot *= 0.0; |
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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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|
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idat = fDecomp_->fillInteractionData(atom1, atom2); |
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*(idat.pot) = pot; |
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|
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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.d = &d_grp; |
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idat.r2 = &rgrpsq; |
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} else { |
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*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2); |
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curSnapshot->wrapVector( *(idat.d) ); |
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*(idat.r2) = idat.d->lengthSquare(); |
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> |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
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> |
curSnapshot->wrapVector( d ); |
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> |
r2 = d.lengthSquare(); |
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> |
idat.d = &d; |
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> |
idat.r2 = &r2; |
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} |
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|
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*(idat.rij) = sqrt( *(idat.r2) ); |
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> |
r = sqrt( *(idat.r2) ); |
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> |
idat.rij = &r; |
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|
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if (iLoop == PREPAIR_LOOP) { |
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interactionMan_->doPrePair(idat); |
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} else { |
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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(); |
| 689 |
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|
| 690 |
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for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 691 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 691 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
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interactionMan_->doPreForce(sdat); |
| 693 |
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} |
| 694 |
< |
|
| 694 |
> |
|
| 695 |
> |
|
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fDecomp_->distributeIntermediateData(); |
| 697 |
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} |
| 698 |
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} |
| 705 |
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|
| 706 |
|
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 707 |
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|
| 708 |
< |
vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 ); |
| 708 |
> |
vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 ); |
| 709 |
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|
| 710 |
|
for (vector<int>::iterator jb = skipList.begin(); |
| 711 |
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jb != skipList.end(); ++jb) { |
| 712 |
|
|
| 713 |
|
atom2 = (*jb); |
| 714 |
< |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 714 |
> |
fDecomp_->fillSkipData(idat, atom1, atom2); |
| 715 |
|
interactionMan_->doSkipCorrection(idat); |
| 716 |
+ |
fDecomp_->unpackSkipData(idat, atom1, atom2); |
| 717 |
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|
| 718 |
|
} |
| 719 |
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} |
| 722 |
|
if (info_->requiresSelfCorrection()) { |
| 723 |
|
|
| 724 |
|
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 725 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 725 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 726 |
|
interactionMan_->doSelfCorrection(sdat); |
| 727 |
|
} |
| 728 |
|
|
| 729 |
|
} |
| 730 |
|
|
| 731 |
< |
longRangePotential = fDecomp_->getLongRangePotential(); |
| 731 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 732 |
> |
*(fDecomp_->getPairwisePotential()); |
| 733 |
> |
|
| 734 |
|
lrPot = longRangePotential.sum(); |
| 735 |
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|
| 736 |
|
//store the tau and long range potential |
