--- branches/development/src/nonbonded/EAM.cpp 2011/05/27 16:45:44 1571 +++ branches/development/src/nonbonded/EAM.cpp 2011/11/22 20:38:56 1665 @@ -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 @@ -51,7 +52,7 @@ namespace OpenMD { namespace OpenMD { EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), - mixMeth_(eamJohnson), eamRcut_(0.0) {} + mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {} EAMParam EAM::getEAMParam(AtomType* atomType) { @@ -193,6 +194,11 @@ namespace OpenMD { CubicSpline* cs = new CubicSpline(); cs->addPoints(rvals, phivals); return cs; + } + + void EAM::setCutoffRadius( RealType rCut ) { + eamRcut_ = rCut; + haveCutoffRadius_ = true; } void EAM::initialize() { @@ -353,18 +359,22 @@ namespace OpenMD { EAMAtomData data1 = EAMMap[idat.atypes.first]; EAMAtomData data2 = EAMMap[idat.atypes.second]; - - if ( *(idat.rij) < data1.rcut) - *(idat.rho_i_at_j) = data1.rho->getValueAt( *(idat.rij)); - + + if (haveCutoffRadius_) + if ( *(idat.rij) > eamRcut_) return; + + if ( *(idat.rij) < data1.rcut) + *(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); + + if ( *(idat.rij) < data2.rcut) - *(idat.rho_j_at_i) = data2.rho->getValueAt( *(idat.rij)); - - return; + *(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); + + return; } - + void EAM::calcFunctional(SelfData &sdat) { - + if (!initialized_) initialize(); EAMAtomData data1 = EAMMap[ sdat.atype ]; @@ -373,6 +383,10 @@ namespace OpenMD { *(sdat.frho) = result.first; *(sdat.dfrhodrho) = result.second; + + (*(sdat.pot))[METALLIC_FAMILY] += result.first; + *(sdat.particlePot) += result.first; + return; } @@ -381,108 +395,107 @@ namespace OpenMD { if (!initialized_) initialize(); + if (haveCutoffRadius_) + if ( *(idat.rij) > eamRcut_) return; + pair res; - if ( *(idat.rij) < eamRcut_) { - - EAMAtomData data1 = EAMMap[idat.atypes.first]; - EAMAtomData data2 = EAMMap[idat.atypes.second]; - - // get type-specific cutoff radii - - RealType rci = data1.rcut; - RealType rcj = data2.rcut; + EAMAtomData data1 = EAMMap[idat.atypes.first]; + EAMAtomData data2 = EAMMap[idat.atypes.second]; + + // get type-specific cutoff radii + + RealType rci = data1.rcut; + RealType rcj = data2.rcut; + + RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); + RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); + RealType phab(0.0), dvpdr(0.0); + RealType drhoidr, drhojdr, dudr; + + if ( *(idat.rij) < rci) { + res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); + rha = res.first; + drha = res.second; - RealType rha, drha, rhb, drhb; - RealType pha, dpha, phb, dphb; - RealType phab, dvpdr; - RealType drhoidr, drhojdr, dudr; + res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); + pha = res.first; + dpha = res.second; + } + + if ( *(idat.rij) < rcj) { + res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); + rhb = res.first; + drhb = res.second; - if ( *(idat.rij) < rci) { - res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); - rha = res.first; - drha = res.second; + res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); + phb = res.first; + dphb = res.second; + } - res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); - pha = res.first; - dpha = res.second; + switch(mixMeth_) { + case eamJohnson: + + if ( *(idat.rij) < rci) { + phab = phab + 0.5 * (rhb / rha) * pha; + dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + + pha*((drhb/rha) - (rhb*drha/rha/rha))); } - + + + if ( *(idat.rij) < rcj) { - res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); - rhb = res.first; - drhb = res.second; - - res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); - phb = res.first; - dphb = res.second; - } - - phab = 0.0; - dvpdr = 0.0; - - switch(mixMeth_) { - case eamJohnson: - - if ( *(idat.rij) < rci) { - phab = phab + 0.5 * (rhb / rha) * pha; - dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + - pha*((drhb/rha) - (rhb*drha/rha/rha))); - } - - if ( *(idat.rij) < rcj) { - phab = phab + 0.5 * (rha / rhb) * phb; - dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + - phb*((drha/rhb) - (rha*drhb/rhb/rhb))); - } - - break; - - case eamDaw: - res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); - phab = res.first; - dvpdr = res.second; - - break; - case eamUnknown: - default: - - sprintf(painCave.errMsg, - "EAM::calcForce hit a mixing method it doesn't know about!\n" - ); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - + phab = phab + 0.5 * (rha / rhb) * phb; + dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + + phb*((drha/rhb) - (rha*drhb/rhb/rhb))); } - drhoidr = drha; - drhojdr = drhb; - - dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; - - *(idat.f1) = *(idat.d) * dudr / *(idat.rij); - - // particle_pot is the difference between the full potential - // and the full potential without the presence of a particular - // particle (atom1). - // - // This reduces the density at other particle locations, so - // we need to recompute the density at atom2 assuming atom1 - // didn't contribute. This then requires recomputing the - // density functional for atom2 as well. - // - // Most of the particle_pot heavy lifting comes from the - // pair interaction, and will be handled by vpair. - - *(idat.fshift1) = data1.F->getValueAt( *(idat.rho1) - rhb ); - *(idat.fshift2) = data1.F->getValueAt( *(idat.rho2) - rha ); - - idat.pot[METALLIC_FAMILY] += phab; - - *(idat.vpair) += phab; + break; + + case eamDaw: + res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); + phab = res.first; + dvpdr = res.second; + + break; + case eamUnknown: + default: + + sprintf(painCave.errMsg, + "EAM::calcForce hit a mixing method it doesn't know about!\n" + ); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } - + + drhoidr = drha; + drhojdr = drhb; + + dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; + + *(idat.f1) += *(idat.d) * dudr / *(idat.rij); + + // particlePot is the difference between the full potential and + // the full potential without the presence of a particular + // particle (atom1). + // + // This reduces the density at other particle locations, so we + // need to recompute the density at atom2 assuming atom1 didn't + // contribute. This then requires recomputing the density + // functional for atom2 as well. + + *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) + - *(idat.frho2); + + *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) + - *(idat.frho1); + + (*(idat.pot))[METALLIC_FAMILY] += phab; + + *(idat.vpair) += phab; + return; }