--- branches/development/src/nonbonded/EAM.cpp 2010/10/02 19:53:32 1502 +++ branches/development/src/nonbonded/EAM.cpp 2012/05/18 21:44:02 1710 @@ -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 @@ -51,114 +52,29 @@ 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) { - - // Do sanity checking on the AtomType we were passed before - // building any data structures: - if (!atomType->isEAM()) { - sprintf( painCave.errMsg, - "EAM::getEAMParam was passed an atomType (%s) that does not\n" - "\tappear to be an embedded atom method (EAM) atom.\n", - atomType->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - GenericData* data = atomType->getPropertyByName("EAM"); - if (data == NULL) { - sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n" - "\tparameters for atomType %s.\n", - atomType->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - EAMParamGenericData* eamData = dynamic_cast(data); - if (eamData == NULL) { - sprintf( painCave.errMsg, - "EAM::getEAMParam could not convert GenericData to EAMParam for\n" - "\tatom type %s\n", atomType->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - return eamData->getData(); - } + CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { + EAMAdapter ea1 = EAMAdapter(atomType1); + EAMAdapter ea2 = EAMAdapter(atomType2); + CubicSpline* z1 = ea1.getZ(); + CubicSpline* z2 = ea2.getZ(); - CubicSpline* EAM::getZ(AtomType* atomType) { - EAMParam eamParam = getEAMParam(atomType); - int nr = eamParam.nr; - RealType dr = eamParam.dr; - vector rvals; - - for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); - - CubicSpline* cs = new CubicSpline(); - cs->addPoints(rvals, eamParam.Z); - return cs; - } - - RealType EAM::getRcut(AtomType* atomType) { - EAMParam eamParam = getEAMParam(atomType); - return eamParam.rcut; - } - - CubicSpline* EAM::getRho(AtomType* atomType) { - EAMParam eamParam = getEAMParam(atomType); - int nr = eamParam.nr; - RealType dr = eamParam.dr; - vector rvals; - - for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); - - CubicSpline* cs = new CubicSpline(); - cs->addPoints(rvals, eamParam.rho); - return cs; - } - - CubicSpline* EAM::getF(AtomType* atomType) { - EAMParam eamParam = getEAMParam(atomType); - int nrho = eamParam.nrho; - RealType drho = eamParam.drho; - vector rhovals; - vector scaledF; - - for (int i = 0; i < nrho; i++) { - rhovals.push_back(RealType(i) * drho); - scaledF.push_back( eamParam.F[i] * 23.06054 ); - } - - CubicSpline* cs = new CubicSpline(); - cs->addPoints(rhovals, scaledF); - return cs; - } - - CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { - EAMParam eamParam1 = getEAMParam(atomType1); - EAMParam eamParam2 = getEAMParam(atomType2); - CubicSpline* z1 = getZ(atomType1); - CubicSpline* z2 = getZ(atomType2); - // make the r grid: // we need phi out to the largest value we'll encounter in the radial space; RealType rmax = 0.0; - rmax = max(rmax, eamParam1.rcut); - rmax = max(rmax, eamParam1.nr * eamParam1.dr); + rmax = max(rmax, ea1.getRcut()); + rmax = max(rmax, ea1.getNr() * ea1.getDr()); - rmax = max(rmax, eamParam2.rcut); - rmax = max(rmax, eamParam2.nr * eamParam2.dr); + rmax = max(rmax, ea2.getRcut()); + rmax = max(rmax, ea2.getNr() * ea2.getDr()); // use the smallest dr (finest grid) to build our grid: - RealType dr = min(eamParam1.dr, eamParam2.dr); + RealType dr = min(ea1.getDr(), ea2.getDr()); int nr = int(rmax/dr + 0.5); @@ -182,8 +98,8 @@ namespace OpenMD { // means that our phi grid goes out beyond the cutoff of the // pair potential - zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0; - zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0; + zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0; + zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0; phi = 331.999296 * (zi * zj) / r; @@ -195,6 +111,11 @@ namespace OpenMD { return cs; } + void EAM::setCutoffRadius( RealType rCut ) { + eamRcut_ = rCut; + haveCutoffRadius_ = true; + } + void EAM::initialize() { // set up the mixing method: @@ -272,22 +193,22 @@ namespace OpenMD { void EAM::addType(AtomType* atomType){ + EAMAdapter ea = EAMAdapter(atomType); EAMAtomData eamAtomData; - - eamAtomData.rho = getRho(atomType); - eamAtomData.F = getF(atomType); - eamAtomData.Z = getZ(atomType); - eamAtomData.rcut = getRcut(atomType); + eamAtomData.rho = ea.getRho(); + eamAtomData.F = ea.getF(); + eamAtomData.Z = ea.getZ(); + eamAtomData.rcut = ea.getRcut(); + // add it to the map: - AtomTypeProperties atp = atomType->getATP(); pair::iterator,bool> ret; - ret = EAMlist.insert( pair(atp.ident, atomType) ); + ret = EAMlist.insert( pair(atomType->getIdent(), atomType) ); if (ret.second == false) { sprintf( painCave.errMsg, "EAM already had a previous entry with ident %d\n", - atp.ident); + atomType->getIdent()); painCave.severity = OPENMD_INFO; painCave.isFatal = 0; simError(); @@ -347,144 +268,174 @@ namespace OpenMD { return; } - void EAM::calcDensity(DensityData ddat) { + void EAM::calcDensity(InteractionData &idat) { if (!initialized_) initialize(); - EAMAtomData data1 = EAMMap[ddat.atype1]; - EAMAtomData data2 = EAMMap[ddat.atype2]; - - if (ddat.rij < data1.rcut) - ddat.rho_i_at_j = data1.rho->getValueAt(ddat.rij); - - if (ddat.rij < data2.rcut) - ddat.rho_j_at_i = data2.rho->getValueAt(ddat.rij); - - return; + EAMAtomData data1 = EAMMap[idat.atypes.first]; + EAMAtomData data2 = EAMMap[idat.atypes.second]; + + 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.rho2) += data2.rho->getValueAt( *(idat.rij)); + + return; } - - void EAM::calcFunctional(FunctionalData fdat) { - + + void EAM::calcFunctional(SelfData &sdat) { + if (!initialized_) initialize(); - EAMAtomData data1 = EAMMap[fdat.atype]; + EAMAtomData data1 = EAMMap[ sdat.atype ]; - pair result = data1.F->getValueAndDerivativeAt(fdat.rho); + pair result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); - fdat.frho = result.first; - fdat.dfrhodrho = result.second; + *(sdat.frho) = result.first; + *(sdat.dfrhodrho) = result.second; + + (*(sdat.pot))[METALLIC_FAMILY] += result.first; + *(sdat.particlePot) += result.first; + return; } - void EAM::calcForce(InteractionData idat) { + void EAM::calcForce(InteractionData &idat) { if (!initialized_) initialize(); + if (haveCutoffRadius_) + if ( *(idat.rij) > eamRcut_) return; + pair res; - if (idat.rij < eamRcut_) { - - EAMAtomData data1 = EAMMap[idat.atype1]; - EAMAtomData data2 = EAMMap[idat.atype2]; - - // get type-specific cutoff radii - - RealType rci = data1.rcut; - RealType rcj = data2.rcut; - - RealType rha, drha, rhb, drhb; - RealType pha, dpha, phb, dphb; - RealType phab, dvpdr; - RealType drhoidr, drhojdr, dudr; + 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; - if (idat.rij < rci) { - res = data1.rho->getValueAndDerivativeAt(idat.rij); - rha = res.first; - drha = res.second; + 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; + + 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.atype1, idat.atype1)].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.atype2, idat.atype2)].phi->getValueAndDerivativeAt(idat.rij); - phb = res.first; - dphb = res.second; + + + + 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))); } - - 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[make_pair(idat.atype1,idat.atype2)].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; + 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; + + } - dudr = drhojdr*idat.dfrho1 + drhoidr*idat.dfrho2 + dvpdr; + RealType EAM::getSuggestedCutoffRadius(pair atypes) { + if (!initialized_) initialize(); - 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 ); + RealType cut = 0.0; - idat.pot += phab; + map::iterator it; - idat.vpair += phab; + it = EAMMap.find(atypes.first); + if (it != EAMMap.end()) { + EAMAtomData data1 = (*it).second; + cut = data1.rcut; } - return; - + it = EAMMap.find(atypes.second); + if (it != EAMMap.end()) { + EAMAtomData data2 = (*it).second; + if (data2.rcut > cut) + cut = data2.rcut; + } + + return cut; } }