void CState::makeAtoms(ivec3 N, vec3 L, mat r, double sites_per_cell, string atomType)
{
cout << "CState::makeAtoms" << endl;
vec3 cellPos;
atoms = vector<CAtom*>();
atoms.reserve(nAtoms); // don't want resize, since we're using "push_back" to add item
for (int ix = 0; ix < N(0); ix++)
{
for (int iy = 0; iy < N(1); iy++)
{
for (int iz = 0; iz < N(2); iz++)
{
for (int i = 0; i < sites_per_cell; i++)
{
CAtom* atom = new CAtom;
cellPos << L(0)*ix << L(1)*iy << L(2)*iz;
atom->setPosition(cellPos + r.row(i).t());
atom->setAtomType(atomType);
if (atom->matrixAtom)
{
nMatrixAtoms++;
atoms.push_back(atom);
}
else
{
nMovingAtoms++;
movingAtoms.push_back(atom);
atoms.push_back(atom);
}
}
}
}
}
cout << "Exiting CState::makeAtoms" << endl;
}
