void EAM::initialize() {
// set up the mixing method:
ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
string EAMMixMeth = fopts.getEAMMixingMethod();
toUpper(EAMMixMeth);
if (EAMMixMeth == "JOHNSON")
mixMeth_ = eamJohnson;
else if (EAMMixMeth == "DAW")
mixMeth_ = eamDaw;
else
mixMeth_ = eamUnknown;
// find all of the EAM atom Types:
EAMtypes.clear();
EAMtids.clear();
EAMdata.clear();
MixingMap.clear();
nEAM_ = 0;
EAMtids.resize( forceField_->getNAtomType(), -1);
set<AtomType*>::iterator at;
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
if ((*at)->isEAM()) nEAM_++;
}
EAMdata.resize(nEAM_);
MixingMap.resize(nEAM_);
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
if ((*at)->isEAM()) addType(*at);
}
// find all of the explicit EAM interactions (setfl):
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
NonBondedInteractionType* nbt;
for (nbt = nbiTypes->beginType(j); nbt != NULL;
nbt = nbiTypes->nextType(j)) {
if (nbt->isEAM()) {
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
GenericData* data = nbt->getPropertyByName("EAM");
if (data == NULL) {
sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
"\tEAM parameters for %s - %s interaction.\n",
atypes.first->getName().c_str(),
atypes.second->getName().c_str());
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
if (eamData == NULL) {
sprintf( painCave.errMsg,
"EAM::rebuildMixingMap could not convert GenericData to\n"
"\tEAMMixingData for %s - %s interaction.\n",
atypes.first->getName().c_str(),
atypes.second->getName().c_str());
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
EAMMixingParam eamParam = eamData->getData();
vector<RealType> phiAB = eamParam.phi;
RealType dr = eamParam.dr;
int nr = eamParam.nr;
addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
}
}
initialized_ = true;
}
