void SC::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
RealType epsilon, RealType m, RealType n,
RealType alpha) {
// in case these weren't already in the map
addType(atype1);
addType(atype2);
SCInteractionData mixer;
mixer.epsilon = epsilon;
mixer.m = m;
mixer.n = n;
mixer.alpha = alpha;
mixer.rCut = 2.0 * mixer.alpha;
RealType dr = mixer.rCut / (np_ - 1);
vector<RealType> rvals;
vector<RealType> vvals;
vector<RealType> phivals;
rvals.push_back(0.0);
vvals.push_back(0.0);
phivals.push_back(0.0);
for (int k = 1; k < np_; k++) {
RealType r = dr * k;
rvals.push_back(r);
vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) );
phivals.push_back( pow(mixer.alpha/r, mixer.m) );
}
mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n);
CubicSpline* V = new CubicSpline();
V->addPoints(rvals, vvals);
CubicSpline* phi = new CubicSpline();
phi->addPoints(rvals, phivals);
mixer.V = V;
mixer.phi = phi;
mixer.explicitlySet = true;
int sctid1 = SCtids[ atype1->getIdent() ];
int sctid2 = SCtids[ atype2->getIdent() ];
MixingMap[sctid1][sctid2] = mixer;
if (sctid2 != sctid1) {
MixingMap[sctid2][sctid1] = mixer;
}
return;
}
void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
RealType dr, int nr,
vector<RealType> phiVals) {
// in case these weren't already in the map
addType(atype1);
addType(atype2);
EAMInteractionData mixer;
CubicSpline* cs = new CubicSpline();
vector<RealType> rVals;
for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
cs->addPoints(rVals, phiVals);
mixer.phi = cs;
mixer.rcut = mixer.phi->getLimits().second;
mixer.explicitlySet = true;
int eamtid1 = EAMtids[ atype1->getIdent() ];
int eamtid2 = EAMtids[ atype2->getIdent() ];
MixingMap[eamtid1][eamtid2] = mixer;
if (eamtid2 != eamtid1) {
MixingMap[eamtid2][eamtid1] = mixer;
}
return;
}
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 SC::addType(AtomType* atomType){
SuttonChenAdapter sca = SuttonChenAdapter(atomType);
SCAtomData scAtomData;
scAtomData.c = sca.getC();
scAtomData.m = sca.getM();
scAtomData.n = sca.getN();
scAtomData.alpha = sca.getAlpha();
scAtomData.epsilon = sca.getEpsilon();
scAtomData.rCut = 2.0 * scAtomData.alpha;
// add it to the map:
int atid = atomType->getIdent();
int sctid = SCtypes.size();
pair<set<int>::iterator,bool> ret;
ret = SCtypes.insert( atid );
if (ret.second == false) {
sprintf( painCave.errMsg,
"SC already had a previous entry with ident %d\n",
atid );
painCave.severity = OPENMD_INFO;
painCave.isFatal = 0;
simError();
}
SCtids[atid] = sctid;
SCdata[sctid] = scAtomData;
MixingMap[sctid].resize(nSC_);
// Now, iterate over all known types and add to the mixing map:
std::set<int>::iterator it;
for( it = SCtypes.begin(); it != SCtypes.end(); ++it) {
int sctid2 = SCtids[ (*it) ];
AtomType* atype2 = forceField_->getAtomType( (*it) );
SCInteractionData mixer;
mixer.alpha = getAlpha(atomType, atype2);
mixer.rCut = 2.0 * mixer.alpha;
mixer.epsilon = getEpsilon(atomType, atype2);
mixer.m = getM(atomType, atype2);
mixer.n = getN(atomType, atype2);
RealType dr = mixer.rCut / (np_ - 1);
vector<RealType> rvals;
vector<RealType> vvals;
vector<RealType> phivals;
rvals.push_back(0.0);
vvals.push_back(0.0);
phivals.push_back(0.0);
for (int k = 1; k < np_; k++) {
RealType r = dr * k;
rvals.push_back(r);
vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) );
phivals.push_back( pow(mixer.alpha/r, mixer.m) );
}
mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n);
CubicSpline* V = new CubicSpline();
V->addPoints(rvals, vvals);
CubicSpline* phi = new CubicSpline();
phi->addPoints(rvals, phivals);
mixer.V = V;
mixer.phi = phi;
mixer.explicitlySet = false;
MixingMap[sctid2].resize( nSC_ );
MixingMap[sctid][sctid2] = mixer;
if (sctid2 != sctid) {
MixingMap[sctid2][sctid] = mixer;
}
}
return;
}
