double Molecule::dist(Molecule &other) {
double minSqr = 1e9; //large value;
Bounds bounds = state->bounds;
for (int id : ids) {
Vector pos = state->idToAtom(id).pos;
for (int idOther : other.ids) {
minSqr = fmin(minSqr, bounds.minImage((pos - state->idToAtom(idOther).pos)).lenSqr() );
}
}
return sqrt(minSqr);
}
void Molecule::unwrap() {
Vector weightedPos(0, 0, 0);
double sumMass = 0;
Vector firstPos = state->idToAtom(ids[0]).pos;
Bounds bounds = state->bounds;
for (int id : ids) {
int idx = state->idToIdx[id];
Atom &a = state->atoms[idx];
a.pos = firstPos + bounds.minImage(a.pos - firstPos);
}
}
Vector Molecule::COM() {
Vector weightedPos(0, 0, 0);
double sumMass = 0;
Vector firstPos = state->idToAtom(ids[0]).pos;
Bounds bounds = state->bounds;
for (int id : ids) {
Atom &a = state->idToAtom(id);
Vector pos = firstPos + bounds.minImage(a.pos - firstPos);
double mass = a.mass;
weightedPos += pos * mass;
sumMass += mass;
}
return weightedPos / sumMass;
}
Vector Molecule::size() {
Vector firstPos = state->idToAtom(ids[0]).pos;
Vector lo = firstPos;
Vector hi = firstPos;
Bounds bounds = state->bounds;
for (int id : ids) {
Atom &a = state->idToAtom(id);
Vector pos = firstPos + bounds.minImage(a.pos - firstPos);
for (int i=0; i<3; i++) {
lo[i] = fmin(lo[i], pos[i]);
hi[i] = fmax(hi[i], pos[i]);
}
}
return hi - lo;
}