private void generateInterAtomDistances(IsopointalSet isopointalSet) {
int numAtoms = isopointalSet.getNumPositions();
interAtomicDistances = new List[numAtoms];
multiplicity = new int[numAtoms];
int dz = (int) Math.ceil(Rcutoff / isopointalSet.vecC.z);
int dy =
(int) Math.ceil((Rcutoff + Math.abs(dz * isopointalSet.vecC.y)) / isopointalSet.vecB.y);
int dx =
(int)
Math.ceil(
(Rcutoff
+ Math.abs(dz * isopointalSet.vecC.x)
+ Math.abs(dy * isopointalSet.vecB.x))
/ isopointalSet.vecA.x);
for (int i = 0; i < numAtoms; i++) {
interAtomicDistances[i] = new ArrayList<>();
for (int j = 0; j < numAtoms; j++) {
for (int x = -dx; x <= dx; x++) {
for (int y = -dy; y <= dy; y++) {
for (int z = -dz; z <= dz; z++) {
if (x == 0 && y == 0 && z == 0 && i == j) continue;
double rsq = isopointalSet.getDistSqBetweenPositions(i, j, x, y, z);
if (rsq <= RcutoffSq) interAtomicDistances[i].add(Math.sqrt(rsq));
}
}
}
}
multiplicity[i] = isopointalSet.getMultiplicity(i);
i += (multiplicity[i] - 1);
}
}
public double computeEnergy(IsopointalSet isopointalSet) {
double totalEnergy = 0;
generateInterAtomDistances(isopointalSet);
for (int i = 0; i < isopointalSet.getNumPositions(); i++) {
double energy = 0.0;
double phiSum = 0;
for (double dist : interAtomicDistances[i]) {
phiSum += computeOPP(dist);
}
energy += 0.5 * phiSum;
int mult = multiplicity[i];
totalEnergy += mult * energy;
i += (mult - 1); // Skip the positions with same energy;
}
return totalEnergy;
}
