CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {
EAMAdapter ea1 = EAMAdapter(atomType1);
EAMAdapter ea2 = EAMAdapter(atomType2);
CubicSpline* z1 = ea1.getZ();
CubicSpline* z2 = ea2.getZ();
// Thise prefactors convert the charge-charge interactions into
// kcal / mol all were computed assuming distances are measured in
// angstroms Charge-Charge, assuming charges are measured in
// electrons. Matches value in Electrostatics.cpp
pre11_ = 332.0637778;
// 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, ea1.getRcut());
rmax = max(rmax, ea1.getNr() * ea1.getDr());
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(ea1.getDr(), ea2.getDr());
int nr = int(rmax/dr + 0.5);
vector<RealType> rvals;
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
// construct the pair potential:
vector<RealType> phivals;
RealType phi;
RealType r;
RealType zi, zj;
phivals.push_back(0.0);
for (unsigned int i = 1; i < rvals.size(); i++ ) {
r = rvals[i];
// only use z(r) if we're inside this atom's 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 <= ea1.getRcut() ? z1->getValueAt(r) : 0.0;
zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0;
phi = pre11_ * (zi * zj) / r;
phivals.push_back(phi);
}
CubicSpline* cs = new CubicSpline();
cs->addPoints(rvals, phivals);
return cs;
}
void EAM::addType(AtomType* atomType){
EAMAdapter ea = EAMAdapter(atomType);
EAMAtomData eamAtomData;
eamAtomData.rho = ea.getRho();
eamAtomData.F = ea.getF();
eamAtomData.Z = ea.getZ();
eamAtomData.rcut = ea.getRcut();
// add it to the map:
int atid = atomType->getIdent();
int eamtid = EAMtypes.size();
pair<set<int>::iterator,bool> ret;
ret = EAMtypes.insert( atid );
if (ret.second == false) {
sprintf( painCave.errMsg,
"EAM already had a previous entry with ident %d\n",
atid);
painCave.severity = OPENMD_INFO;
painCave.isFatal = 0;
simError();
}
EAMtids[atid] = eamtid;
EAMdata[eamtid] = eamAtomData;
MixingMap[eamtid].resize(nEAM_);
// Now, iterate over all known types and add to the mixing map:
std::set<int>::iterator it;
for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) {
int eamtid2 = EAMtids[ (*it) ];
AtomType* atype2 = forceField_->getAtomType( (*it) );
EAMInteractionData mixer;
mixer.phi = getPhi(atomType, atype2);
mixer.rcut = mixer.phi->getLimits().second;
mixer.explicitlySet = false;
MixingMap[eamtid2].resize( nEAM_ );
MixingMap[eamtid][eamtid2] = mixer;
if (eamtid2 != eamtid) {
MixingMap[eamtid2][eamtid] = mixer;
}
}
return;
}
