coords.py 文件源码

def __init__(self, geom, allowed=None):
        self._coords = []
        geom = geom.supercell()
        dist = geom.dist(geom)
        radii = np.array([get_property(sp, 'covalent_radius') for sp in geom.species])
        bondmatrix = dist < 1.3*(radii[None, :]+radii[:, None])
        self.fragments, C = get_clusters(bondmatrix)
        radii = np.array([get_property(sp, 'vdw_radius') for sp in geom.species])
        shift = 0.
        C_total = C.copy()
        while not C_total.all():
            bondmatrix |= ~C_total & (dist < radii[None, :]+radii[:, None]+shift)
            C_total = get_clusters(bondmatrix)[1]
            shift += 1.
        for i, j in combinations(range(len(geom)), 2):
            if bondmatrix[i, j]:
                bond = Bond(i, j, C=C)
                self.append(bond)
        for j in range(len(geom)):
            for i, k in combinations(np.flatnonzero(bondmatrix[j, :]), 2):
                ang = Angle(i, j, k, C=C)
                if ang.eval(geom.coords) > pi/4:
                    self.append(ang)
        for bond in self.bonds:
            self.extend(get_dihedrals([bond.i, bond.j], geom.coords, bondmatrix, C))