--- branches/development/src/nonbonded/LJ.cpp 2010/07/20 15:43:00 1473 +++ branches/development/src/nonbonded/LJ.cpp 2012/02/29 20:33:01 1683 @@ -36,7 +36,8 @@ * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -45,26 +46,12 @@ #include #include "nonbonded/LJ.hpp" #include "utils/simError.h" +#include "types/LennardJonesInteractionType.hpp" - namespace OpenMD { - bool LJ::initialized_ = false; - bool LJ::shiftedPot_ = false; - bool LJ::shiftedFrc_ = false; - ForceField* LJ::forceField_ = NULL; - std::map LJ::LJMap; - std::map, LJInteractionData> LJ::MixingMap; - - LJ* LJ::_instance = NULL; + LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {} - LJ* LJ::Instance() { - if (!_instance) { - _instance = new LJ(); - } - return _instance; - } - LJParam LJ::getLJParam(AtomType* atomType) { // Do sanity checking on the AtomType we were passed before @@ -106,29 +93,12 @@ namespace OpenMD { return ljParam.sigma; } - RealType LJ::getSigma(int atid) { - if (!initialized_) initialize(); - std::map :: const_iterator it; - it = LJMap.find(atid); - if (it == LJMap.end()) { - sprintf( painCave.errMsg, - "LJ::getSigma could not find atid %d in LJMap\n", - (atid)); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - AtomType* atype = it->second; - - return getSigma(atype); - } - RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { RealType sigma1 = getSigma(atomType1); RealType sigma2 = getSigma(atomType2); ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); - std::string DistanceMix = fopts.getDistanceMixingRule(); + string DistanceMix = fopts.getDistanceMixingRule(); toUpper(DistanceMix); if (DistanceMix == "GEOMETRIC") @@ -142,23 +112,6 @@ namespace OpenMD { return ljParam.epsilon; } - RealType LJ::getEpsilon(int atid) { - if (!initialized_) initialize(); - std::map :: const_iterator it; - it = LJMap.find(atid); - if (it == LJMap.end()) { - sprintf( painCave.errMsg, - "LJ::getEpsilon could not find atid %d in LJMap\n", - (atid)); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - AtomType* atype = it->second; - - return getEpsilon(atype); - } - RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { RealType epsilon1 = getEpsilon(atomType1); RealType epsilon2 = getEpsilon(atomType2); @@ -166,57 +119,46 @@ namespace OpenMD { } void LJ::initialize() { - ForceField::AtomTypeContainer atomTypes = forceField_->getAtomTypes(); + ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); ForceField::AtomTypeContainer::MapTypeIterator i; AtomType* at; - for (at = atomTypes.beginType(i); at != NULL; - at = atomTypes.nextType(i)) { - - if (at->isLennardJones()) - addType(at); + for (at = atomTypes->beginType(i); at != NULL; + at = atomTypes->nextType(i)) { + if (at->isLennardJones()){ + addType(at); + } } - - ForceField::NonBondedInteractionTypeContainer nbiTypes = forceField_->getNonBondedInteractionTypes(); + ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; NonBondedInteractionType* nbt; + ForceField::NonBondedInteractionTypeContainer::KeyType keys; - for (nbt = nbiTypes.beginType(j); nbt != NULL; - nbt = nbiTypes.nextType(j)) { - + + for (nbt = nbiTypes->beginType(j); nbt != NULL; + nbt = nbiTypes->nextType(j)) { + if (nbt->isLennardJones()) { - - std::pair atypes = nbt->getAtomTypes(); - - GenericData* data = nbt->getPropertyByName("LennardJones"); - if (data == NULL) { - sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n" - "\tLennard-Jones parameters for %s - %s interaction.\n", - atypes.first->getName().c_str(), - atypes.second->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - LJParamGenericData* ljData = dynamic_cast(data); - if (ljData == NULL) { + keys = nbiTypes->getKeys(j); + AtomType* at1 = forceField_->getAtomType(keys[0]); + AtomType* at2 = forceField_->getAtomType(keys[1]); + + LennardJonesInteractionType* ljit = dynamic_cast(nbt); + + if (ljit == NULL) { sprintf( painCave.errMsg, - "LJ::rebuildMixingMap could not convert GenericData to\n" - "\tLJParam for %s - %s interaction.\n", - atypes.first->getName().c_str(), - atypes.second->getName().c_str()); + "LJ::initialize could not convert NonBondedInteractionType\n" + "\tto LennardJonesInteractionType for %s - %s interaction.\n", + at1->getName().c_str(), + at2->getName().c_str()); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } - - LJParam ljParam = ljData->getData(); - RealType sigma = ljParam.sigma; - RealType epsilon = ljParam.epsilon; - - addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon); + RealType sigma = ljit->getSigma(); + RealType epsilon = ljit->getEpsilon(); + addExplicitInteraction(at1, at2, sigma, epsilon); } } initialized_ = true; @@ -227,12 +169,12 @@ namespace OpenMD { void LJ::addType(AtomType* atomType){ RealType sigma1 = getSigma(atomType); RealType epsilon1 = getEpsilon(atomType); - + // add it to the map: AtomTypeProperties atp = atomType->getATP(); - std::pair::iterator,bool> ret; - ret = LJMap.insert( std::pair(atp.ident, atomType) ); + pair::iterator,bool> ret; + ret = LJMap.insert( pair(atp.ident, atomType) ); if (ret.second == false) { sprintf( painCave.errMsg, "LJ already had a previous entry with ident %d\n", @@ -268,10 +210,6 @@ namespace OpenMD { void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){ - // in case these weren't already in the map - addType(atype1); - addType(atype2); - LJInteractionData mixer; mixer.sigma = sigma; mixer.epsilon = epsilon; @@ -288,80 +226,53 @@ namespace OpenMD { } } - void LJ::calcForce(AtomType* at1, AtomType* at2, Vector3d d, - RealType rij, RealType r2, RealType rcut, RealType sw, - RealType vdwMult, RealType &vpair, RealType &pot, - Vector3d &f1) { - + void LJ::calcForce(InteractionData &idat) { if (!initialized_) initialize(); + map, LJInteractionData>::iterator it; + it = MixingMap.find( idat.atypes ); - RealType ros; - RealType rcos; - RealType myPot = 0.0; - RealType myPotC = 0.0; - RealType myDeriv = 0.0; - RealType myDerivC = 0.0; + if (it != MixingMap.end()) { + + LJInteractionData mixer = (*it).second; + + RealType sigmai = mixer.sigmai; + RealType epsilon = mixer.epsilon; + + RealType ros; + RealType rcos; + RealType myPot = 0.0; + RealType myPotC = 0.0; + RealType myDeriv = 0.0; + RealType myDerivC = 0.0; + + ros = *(idat.rij) * sigmai; + + getLJfunc(ros, myPot, myDeriv); + + if (idat.shiftedPot) { + rcos = *(idat.rcut) * sigmai; + getLJfunc(rcos, myPotC, myDerivC); + myDerivC = 0.0; + } else if (idat.shiftedForce) { + rcos = *(idat.rcut) * sigmai; + getLJfunc(rcos, myPotC, myDerivC); + myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; + } else { + myPotC = 0.0; + myDerivC = 0.0; + } - std::pair key = std::make_pair(at1, at2); - LJInteractionData mixer = MixingMap[key]; + RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); + *(idat.vpair) += pot_temp; + + RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - + myDerivC)*sigmai; - RealType sigmai = mixer.sigmai; - RealType epsilon = mixer.epsilon; - - - ros = rij * sigmai; - - getLJfunc(ros, myPot, myDeriv); - - if (shiftedPot_) { - rcos = rcut * sigmai; - getLJfunc(rcos, myPotC, myDerivC); - myDerivC = 0.0; - } else if (LJ::shiftedFrc_) { - rcos = rcut * sigmai; - getLJfunc(rcos, myPotC, myDerivC); - myPotC = myPotC + myDerivC * (rij - rcut) * sigmai; - } else { - myPotC = 0.0; - myDerivC = 0.0; + (*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; + *(idat.f1) += *(idat.d) * dudr / *(idat.rij); } - - RealType pot_temp = vdwMult * epsilon * (myPot - myPotC); - vpair += pot_temp; - - RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai; - - pot += sw * pot_temp; - f1 = d * dudr / rij; - return; - - - } - - void LJ::do_lj_pair(int *atid1, int *atid2, RealType *d, RealType *rij, - RealType *r2, RealType *rcut, RealType *sw, - RealType *vdwMult, - RealType *vpair, RealType *pot, RealType *f1) { - - if (!initialized_) initialize(); - - AtomType* atype1 = LJMap[*atid1]; - AtomType* atype2 = LJMap[*atid2]; - - Vector3d disp(d[0], d[1], d[2]); - Vector3d frc(f1[0], f1[1], f1[2]); - - calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, - *pot, frc); - - f1[0] = frc.x(); - f1[1] = frc.y(); - f1[2] = frc.z(); - - return; - } void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) { @@ -378,36 +289,16 @@ namespace OpenMD { return; } - - void LJ::setLJDefaultCutoff(RealType *thisRcut, int *sP, int *sF) { - shiftedPot_ = (bool)(*sP); - shiftedFrc_ = (bool)(*sF); + RealType LJ::getSuggestedCutoffRadius(pair atypes) { + if (!initialized_) initialize(); + map, LJInteractionData>::iterator it; + it = MixingMap.find(atypes); + if (it == MixingMap.end()) + return 0.0; + else { + LJInteractionData mixer = (*it).second; + return 2.5 * mixer.sigma; + } } -} -extern "C" { - -#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA) -#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON) -#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF) -#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR) - - RealType fortranGetSigma(int* atid) { - return OpenMD::LJ::Instance()->getSigma(*atid); - } - RealType fortranGetEpsilon(int* atid) { - return OpenMD::LJ::Instance()->getEpsilon(*atid); - } - void fortranSetLJCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) { - return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot, - shiftedFrc); - } - void fortranDoLJPair(int *atid1, int *atid2, RealType *d, RealType *rij, - RealType *r2, RealType *rcut, RealType *sw, - RealType *vdwMult, RealType* vpair, RealType* pot, - RealType *f1){ - - return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut, - sw, vdwMult, vpair, pot, f1); - } }