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#include "nonbonded/LJ.hpp" |
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#include "utils/simError.h" |
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|
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|
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namespace OpenMD { |
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|
| 51 |
< |
bool LJ::initialized_ = false; |
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< |
bool LJ::shiftedPot_ = false; |
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< |
bool LJ::shiftedFrc_ = false; |
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< |
ForceField* LJ::forceField_ = NULL; |
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< |
std::map<int, AtomType*> LJ::LJMap; |
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< |
std::map<std::pair<AtomType*, AtomType*>, LJInteractionData> LJ::MixingMap; |
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|
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LJ* LJ::_instance = NULL; |
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> |
LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), |
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> |
shiftedFrc_(false), forceField_(NULL) {} |
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|
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LJ* LJ::Instance() { |
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if (!_instance) { |
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_instance = new LJ(); |
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} |
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return _instance; |
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} |
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|
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LJParam LJ::getLJParam(AtomType* atomType) { |
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|
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// Do sanity checking on the AtomType we were passed before |
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return ljParam.sigma; |
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} |
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|
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RealType LJ::getSigma(int atid) { |
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std::map<int, AtomType*> :: const_iterator it; |
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it = LJMap.find(atid); |
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if (it == LJMap.end()) { |
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sprintf( painCave.errMsg, |
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"LJ::getSigma could not find atid %d in LJMap\n", |
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(atid)); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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AtomType* atype = it->second; |
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|
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return getSigma(atype); |
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} |
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|
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RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
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RealType sigma1 = getSigma(atomType1); |
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RealType sigma2 = getSigma(atomType2); |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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std::string DistanceMix = fopts.getDistanceMixingRule(); |
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> |
string DistanceMix = fopts.getDistanceMixingRule(); |
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toUpper(DistanceMix); |
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|
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if (DistanceMix == "GEOMETRIC") |
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return ljParam.epsilon; |
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} |
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|
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RealType LJ::getEpsilon(int atid) { |
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std::map<int, AtomType*> :: const_iterator it; |
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it = LJMap.find(atid); |
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if (it == LJMap.end()) { |
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sprintf( painCave.errMsg, |
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"LJ::getEpsilon could not find atid %d in LJMap\n", |
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(atid)); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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AtomType* atype = it->second; |
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|
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return getEpsilon(atype); |
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} |
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|
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RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
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RealType epsilon1 = getEpsilon(atomType1); |
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RealType epsilon2 = getEpsilon(atomType2); |
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} |
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|
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void LJ::initialize() { |
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ForceField::AtomTypeContainer atomTypes = forceField_->getAtomTypes(); |
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ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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|
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for (at = atomTypes.beginType(i); at != NULL; |
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at = atomTypes.nextType(i)) { |
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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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|
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if (at->isLennardJones()) |
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addType(at); |
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} |
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|
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ForceField::NonBondedInteractionTypeContainer nbiTypes = forceField_->getNonBondedInteractionTypes(); |
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
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NonBondedInteractionType* nbt; |
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for (nbt = nbiTypes.beginType(j); nbt != NULL; |
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nbt = nbiTypes.nextType(j)) { |
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
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nbt = nbiTypes->nextType(j)) { |
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if (nbt->isLennardJones()) { |
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std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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|
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GenericData* data = nbt->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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void LJ::addType(AtomType* atomType){ |
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RealType sigma1 = getSigma(atomType); |
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RealType epsilon1 = getEpsilon(atomType); |
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|
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|
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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std::pair<std::map<int,AtomType*>::iterator,bool> ret; |
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ret = LJMap.insert( std::pair<int, AtomType*>(atp.ident, atomType) ); |
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> |
|
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> |
pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"LJ already had a previous entry with ident %d\n", |
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} |
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} |
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|
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void LJ::calcForce(AtomType* at1, AtomType* at2, Vector3d d, RealType rij, |
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RealType r2, RealType rcut, RealType sw, RealType vdwMult, |
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RealType vpair, RealType pot, Vector3d f1) { |
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|
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> |
void LJ::calcForce(InteractionData idat) { |
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|
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if (!initialized_) initialize(); |
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RealType ros; |
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RealType rcos; |
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RealType myPot = 0.0; |
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RealType myPotC = 0.0; |
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RealType myDeriv = 0.0; |
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RealType myDerivC = 0.0; |
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|
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std::pair<AtomType*, AtomType*> key = std::make_pair(at1, at2); |
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LJInteractionData mixer = MixingMap[key]; |
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|
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RealType sigmai = mixer.sigmai; |
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RealType epsilon = mixer.epsilon; |
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> |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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> |
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
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> |
it = MixingMap.find(key); |
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< |
ros = rij * sigmai; |
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< |
|
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getLJfunc(ros, myPot, myDeriv); |
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> |
if (it != MixingMap.end()) { |
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|
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LJInteractionData mixer = (*it).second; |
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|
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> |
RealType sigmai = mixer.sigmai; |
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RealType epsilon = mixer.epsilon; |
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> |
|
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> |
RealType ros; |
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RealType rcos; |
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RealType myPot = 0.0; |
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RealType myPotC = 0.0; |
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> |
RealType myDeriv = 0.0; |
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> |
RealType myDerivC = 0.0; |
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> |
|
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> |
ros = idat.rij * sigmai; |
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> |
|
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> |
getLJfunc(ros, myPot, myDeriv); |
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> |
|
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> |
if (shiftedPot_) { |
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rcos = idat.rcut * sigmai; |
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> |
getLJfunc(rcos, myPotC, myDerivC); |
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> |
myDerivC = 0.0; |
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> |
} else if (LJ::shiftedFrc_) { |
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rcos = idat.rcut * sigmai; |
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getLJfunc(rcos, myPotC, myDerivC); |
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myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai; |
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} else { |
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myPotC = 0.0; |
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myDerivC = 0.0; |
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> |
} |
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|
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< |
if (shiftedPot_) { |
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< |
rcos = rcut * sigmai; |
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< |
getLJfunc(rcos, myPotC, myDerivC); |
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< |
myDerivC = 0.0; |
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< |
} else if (LJ::shiftedFrc_) { |
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< |
rcos = rcut * sigmai; |
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< |
getLJfunc(rcos, myPotC, myDerivC); |
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< |
myPotC = myPotC + myDerivC * (rij - rcut) * sigmai; |
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< |
} else { |
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< |
myPotC = 0.0; |
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< |
myDerivC = 0.0; |
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> |
RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC); |
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> |
idat.vpair += pot_temp; |
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> |
|
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> |
RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv - |
| 286 |
> |
myDerivC)*sigmai; |
| 287 |
> |
|
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> |
idat.pot += idat.sw * pot_temp; |
| 289 |
> |
idat.f1 = idat.d * dudr / idat.rij; |
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> |
|
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} |
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|
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RealType pot_temp = vdwMult * epsilon * (myPot - myPotC); |
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vpair += pot_temp; |
| 326 |
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|
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RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai; |
| 328 |
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|
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pot += sw * pot_temp; |
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f1 = d * dudr / rij; |
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– |
|
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return; |
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} |
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|
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void LJ::do_lj_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
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RealType *r2, RealType *rcut, RealType *sw, |
| 337 |
– |
RealType *vdwMult, |
| 338 |
– |
RealType *vpair, RealType *pot, RealType *f1) { |
| 339 |
– |
|
| 340 |
– |
if (!initialized_) initialize(); |
| 341 |
– |
|
| 342 |
– |
AtomType* atype1 = LJMap[*atid1]; |
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– |
AtomType* atype2 = LJMap[*atid2]; |
| 344 |
– |
|
| 345 |
– |
Vector3d disp(d[0], d[1], d[2]); |
| 346 |
– |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 347 |
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|
| 348 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, |
| 349 |
– |
*pot, frc); |
| 350 |
– |
return; |
| 351 |
– |
} |
| 294 |
|
|
| 295 |
< |
void LJ::getLJfunc(const RealType r, RealType pot, RealType deriv) { |
| 295 |
> |
void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) { |
| 296 |
> |
|
| 297 |
|
RealType ri = 1.0 / r; |
| 298 |
|
RealType ri2 = ri * ri; |
| 299 |
|
RealType ri6 = ri2 * ri2 * ri2; |
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RealType ri7 = ri6 * ri; |
| 301 |
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RealType ri12 = ri6 * ri6; |
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RealType ri13 = ri12 * ri; |
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< |
|
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> |
|
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|
pot = 4.0 * (ri12 - ri6); |
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|
deriv = 24.0 * (ri7 - 2.0 * ri13); |
| 306 |
+ |
|
| 307 |
|
return; |
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|
} |
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|
| 366 |
– |
|
| 367 |
– |
void LJ::setLJDefaultCutoff(RealType *thisRcut, int *sP, int *sF) { |
| 368 |
– |
shiftedPot_ = (bool)(*sP); |
| 369 |
– |
shiftedFrc_ = (bool)(*sF); |
| 370 |
– |
} |
| 371 |
– |
} |
| 372 |
– |
|
| 373 |
– |
extern "C" { |
| 309 |
|
|
| 310 |
< |
#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA) |
| 311 |
< |
#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON) |
| 312 |
< |
#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF) |
| 313 |
< |
#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR) |
| 314 |
< |
|
| 315 |
< |
RealType fortranGetSigma(int* atid) { |
| 316 |
< |
return OpenMD::LJ::Instance()->getSigma(*atid); |
| 310 |
> |
RealType LJ::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 311 |
> |
if (!initialized_) initialize(); |
| 312 |
> |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 313 |
> |
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 314 |
> |
it = MixingMap.find(key); |
| 315 |
> |
if (it == MixingMap.end()) |
| 316 |
> |
return 0.0; |
| 317 |
> |
else { |
| 318 |
> |
LJInteractionData mixer = (*it).second; |
| 319 |
> |
return 2.5 * mixer.sigma; |
| 320 |
> |
} |
| 321 |
|
} |
| 322 |
< |
RealType fortranGetEpsilon(int* atid) { |
| 384 |
< |
return OpenMD::LJ::Instance()->getEpsilon(*atid); |
| 385 |
< |
} |
| 386 |
< |
void fortranSetLJCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) { |
| 387 |
< |
return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot, |
| 388 |
< |
shiftedFrc); |
| 389 |
< |
} |
| 390 |
< |
void fortranDoLJPair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 391 |
< |
RealType *r2, RealType *rcut, RealType *sw, |
| 392 |
< |
RealType *vdwMult, RealType* vpair, RealType* pot, |
| 393 |
< |
RealType *f1){ |
| 394 |
< |
|
| 395 |
< |
return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut, |
| 396 |
< |
sw, vdwMult, vpair, pot, f1); |
| 397 |
< |
} |
| 322 |
> |
|
| 323 |
|
} |
