coords.py 文件源码

def eval(self, coords, grad=False):
        v1 = (coords[self.i]-coords[self.j])/bohr
        v2 = (coords[self.k]-coords[self.j])/bohr
        dot_product = np.dot(v1, v2)/(norm(v1)*norm(v2))
        if dot_product < -1:
            dot_product = -1
        elif dot_product > 1:
            dot_product = 1
        phi = np.arccos(dot_product)
        if not grad:
            return phi
        if abs(phi) > pi-1e-6:
            grad = [
                (pi-phi)/(2*norm(v1)**2)*v1,
                (1/norm(v1)-1/norm(v2))*(pi-phi)/(2*norm(v1))*v1,
                (pi-phi)/(2*norm(v2)**2)*v2
            ]
        else:
            grad = [
                1/np.tan(phi)*v1/norm(v1)**2-v2/(norm(v1)*norm(v2)*np.sin(phi)),
                (v1+v2)/(norm(v1)*norm(v2)*np.sin(phi)) -
                1/np.tan(phi)*(v1/norm(v1)**2+v2/norm(v2)**2),
                1/np.tan(phi)*v2/norm(v2)**2-v1/(norm(v1)*norm(v2)*np.sin(phi))
            ]
        return phi, grad