--- branches/development/src/nonbonded/EAM.cpp 2010/07/23 20:45:40 1478 +++ branches/development/src/nonbonded/EAM.cpp 2010/07/27 14:55:15 1482 @@ -45,15 +45,19 @@ #include #include "nonbonded/EAM.hpp" #include "utils/simError.h" +#include "types/NonBondedInteractionType.hpp" namespace OpenMD { bool EAM::initialized_ = false; + RealType EAM::eamRcut_ = 0.0; + EAMMixingMethod EAM::mixMeth_ = eamJohnson; ForceField* EAM::forceField_ = NULL; - std::map EAM::EAMlist; - std::map EAM::EAMMap; - std::map, EAMInteractionData> EAM::MixingMap; + map EAM::EAMlist; + map EAM::EAMMap; + map, EAMInteractionData> EAM::MixingMap; + EAM* EAM::_instance = NULL; @@ -107,20 +111,25 @@ namespace OpenMD { RealType dr = eamParam.dr; vector rvals; - for (int i = 0; i < nr; i++) rvals.push_back(i * dr); + 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(i * dr); + for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); CubicSpline* cs = new CubicSpline(); cs->addPoints(rvals, eamParam.rho); @@ -135,12 +144,12 @@ namespace OpenMD { vector scaledF; for (int i = 0; i < nrho; i++) { - rhovals.push_back(i * drho); + rhovals.push_back(RealType(i) * drho); scaledF.push_back( eamParam.F[i] * 23.06054 ); } CubicSpline* cs = new CubicSpline(); - cs->addPoints(rhovals, eamParam.F); + cs->addPoints(rhovals, scaledF); return cs; } @@ -152,17 +161,24 @@ namespace OpenMD { // make the r grid: - // set rcut to be the smaller of the two atomic rcuts - RealType rcut = eamParam1.rcut < eamParam2.rcut ? - eamParam1.rcut : eamParam2.rcut; + // 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, eamParam2.rcut); + rmax = max(rmax, eamParam2.nr * eamParam2.dr); + // use the smallest dr (finest grid) to build our grid: - RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr; - int nr = int(rcut/dr); + RealType dr = min(eamParam1.dr, eamParam2.dr); + + int nr = int(rmax/dr + 0.5); + vector rvals; - for (int i = 0; i < nr; i++) rvals.push_back(i*dr); + for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr)); // construct the pair potential: @@ -175,10 +191,15 @@ namespace OpenMD { for (int i = 1; i < rvals.size(); i++ ) { r = rvals[i]; - zi = z1->getValueAt(r); - zj = z2->getValueAt(r); + // only use z(r) if we're inside this atoms cutoff radius, otherwise, we'll use zero for the charge. + // This effectively 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; + phi = 331.999296 * (zi * zj) / r; + phivals.push_back(phi); } @@ -190,9 +211,10 @@ namespace OpenMD { void EAM::initialize() { // set up the mixing method: - ForceFieldOptions ffo = forceField_->getForceFieldOptions(); - string EAMMixMeth = toUpperCopy(ffo.getEAMMixingMethod()); - + ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); + string EAMMixMeth = fopts.getEAMMixingMethod(); + toUpper(EAMMixMeth); + if (EAMMixMeth == "JOHNSON") mixMeth_ = eamJohnson; else if (EAMMixMeth == "DAW") @@ -222,7 +244,7 @@ namespace OpenMD { if (nbt->isEAM()) { - std::pair atypes = nbt->getAtomTypes(); + pair atypes = nbt->getAtomTypes(); GenericData* data = nbt->getPropertyByName("EAM"); if (data == NULL) { @@ -247,9 +269,9 @@ namespace OpenMD { simError(); } - EAMMix eamParam = eamData->getData(); + EAMMixingParam eamParam = eamData->getData(); - vector phiAB = eamParam.phiAB; + vector phiAB = eamParam.phi; RealType dr = eamParam.dr; int nr = eamParam.nr; @@ -264,7 +286,7 @@ namespace OpenMD { void EAM::addType(AtomType* atomType){ EAMAtomData eamAtomData; - + eamAtomData.rho = getRho(atomType); eamAtomData.F = getF(atomType); eamAtomData.Z = getZ(atomType); @@ -273,8 +295,8 @@ namespace OpenMD { // add it to the map: AtomTypeProperties atp = atomType->getATP(); - std::pair::iterator,bool> ret; - ret = EAMlist.insert( std::pair(atp.ident, atomType) ); + pair::iterator,bool> ret; + ret = EAMlist.insert( pair(atp.ident, atomType) ); if (ret.second == false) { sprintf( painCave.errMsg, "EAM already had a previous entry with ident %d\n", @@ -288,18 +310,18 @@ namespace OpenMD { // Now, iterate over all known types and add to the mixing map: - std::map::iterator it; + map::iterator it; for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { - AtomType* atype2 = (*it).second; + AtomType* atype2 = (*it).first; EAMInteractionData mixer; mixer.phi = getPhi(atomType, atype2); mixer.explicitlySet = false; - std::pair key1, key2; - key1 = std::make_pair(atomType, atype2); - key2 = std::make_pair(atype2, atomType); + pair key1, key2; + key1 = make_pair(atomType, atype2); + key2 = make_pair(atype2, atomType); MixingMap[key1] = mixer; if (key2 != key1) { @@ -319,17 +341,17 @@ namespace OpenMD { EAMInteractionData mixer; CubicSpline* cs = new CubicSpline(); - vector rvals; + vector rVals; - for (int i = 0; i < nr; i++) rvals.push_back(i * dr); + for (int i = 0; i < nr; i++) rVals.push_back(i * dr); cs->addPoints(rVals, phiVals); mixer.phi = cs; mixer.explicitlySet = true; - std::pair key1, key2; - key1 = std::make_pair(atype1, atype2); - key2 = std::make_pair(atype2, atype1); + pair key1, key2; + key1 = make_pair(atype1, atype2); + key2 = make_pair(atype2, atype1); MixingMap[key1] = mixer; if (key2 != key1) { @@ -338,12 +360,11 @@ namespace OpenMD { return; } - void EAM::calcDensity(AtomType* at1, AtomType* at2, Vector3d d, - RealType rij, RealType r2, RealType rho_i_at_j, - RealType rho_j_at_i) { - + void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij, + RealType &rho_i_at_j, RealType &rho_j_at_i) { + if (!initialized_) initialize(); - + EAMAtomData data1 = EAMMap[at1]; EAMAtomData data2 = EAMMap[at2]; @@ -352,8 +373,8 @@ namespace OpenMD { return; } - void EAM::calcFunctional(AtomType* at1, RealType rho, RealType frho, - RealType dfrhodrho) { + void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho, + RealType &dfrhodrho) { if (!initialized_) initialize(); @@ -370,11 +391,12 @@ namespace OpenMD { void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d, RealType rij, RealType r2, RealType sw, RealType &vpair, RealType &pot, Vector3d &f1, - RealType rho1, RealType rho2, RealType dfrho1, - RealType dfrho2, RealType fshift1, RealType fshift2) { + RealType rho_i, RealType rho_j, + RealType dfrhodrho_i, RealType dfrhodrho_j, + RealType &fshift_i, RealType &fshift_j) { if (!initialized_) initialize(); - + pair res; if (rij < eamRcut_) { @@ -433,7 +455,6 @@ namespace OpenMD { break; case eamDaw: - res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij); phab = res.first; dvpdr = res.second; @@ -483,18 +504,16 @@ namespace OpenMD { } - void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *d, - RealType *rij, RealType *r2, + void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij, RealType* rho_i_at_j, RealType* rho_j_at_i){ - if (!initialized_) initialize(); + if (!initialized_) initialize(); + AtomType* atype1 = EAMlist[*atid1]; AtomType* atype2 = EAMlist[*atid2]; - Vector3d disp(d[0], d[1], d[2]); + calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); - calcDensity(atype1, atype2, disp, *rij, *r2, *rho_i_at_j, *rho_j_at_i); - return; } @@ -509,7 +528,15 @@ namespace OpenMD { return; } + RealType EAM::getEAMcut(int *atid1) { + if (!initialized_) initialize(); + + AtomType* atype1 = EAMlist[*atid1]; + + return getRcut(atype1); + } + void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij, RealType *r2, RealType *sw, RealType *vpair, RealType *pot, RealType *f1, RealType *rho1, @@ -518,8 +545,8 @@ namespace OpenMD { if (!initialized_) initialize(); - AtomType* atype1 = EAMMap[*atid1]; - AtomType* atype2 = EAMMap[*atid2]; + AtomType* atype1 = EAMlist[*atid1]; + AtomType* atype2 = EAMlist[*atid2]; Vector3d disp(d[0], d[1], d[2]); Vector3d frc(f1[0], f1[1], f1[2]); @@ -535,7 +562,7 @@ namespace OpenMD { } void EAM::setCutoffEAM(RealType *thisRcut) { - eamRcut_ = thisRcut; + eamRcut_ = *thisRcut; } } @@ -545,38 +572,40 @@ extern "C" { #define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO) #define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR) #define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM) - - RealType fortranCalcDensity(int *atid1, int *atid2, RealType *d, - RealType *rij, RealType *r2, - RealType *rho_i_at_j, RealType *rho_j_at_i) { +#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT) - return OpenMD::EAM::Instance()->calc_eam_prepair_rho(*atid1, *atid2, *d, - *rij, *r2, - *rho_i_at_j, - *rho_j_at_i); + + void fortranCalcDensity(int *atid1, int *atid2, RealType *rij, + RealType *rho_i_at_j, RealType *rho_j_at_i) { + + return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij, + rho_i_at_j, + rho_j_at_i); } - RealType fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho, - RealType *dfrhodrho) { - - return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(*atid1, - *rho, - *frho, - *dfrhodrho); - + void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho, + RealType *dfrhodrho) { + + return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho, + dfrhodrho); + } - void fortranSetEAMCutoff(RealType *rcut) { + void fortranSetCutoffEAM(RealType *rcut) { return OpenMD::EAM::Instance()->setCutoffEAM(rcut); } - void fortranDoEAMPair(int *atid1, int *atid2, RealType *d, RealType *rij, + void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij, RealType *r2, RealType *sw, RealType *vpair, RealType *pot, RealType *f1, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){ - return OpenMD::EAM::Instance()->do_eam_pair(*atid1, *atid2, *d, *rij, - *r2, *sw, *vpair, - *pot, *f1, *rho1, - *rho2, *dfrho1, *dfrho2, - *fshift1, *fshift2); + return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij, + r2, sw, vpair, + pot, f1, rho1, + rho2, dfrho1, dfrho2, + fshift1, fshift2); } + RealType fortranGetEAMcut(int* atid) { + return OpenMD::EAM::Instance()->getEAMcut(atid); + } + }