internal.py 文件源码

def value(self, xyz):
        xyz = xyz.reshape(-1,3)
        a = np.array(self.a)
        b = self.b
        c = np.array(self.c)
        xyza = np.mean(xyz[a], axis=0)
        xyzc = np.mean(xyz[c], axis=0)
        # vector from first atom to central atom
        vector1 = xyza - xyz[b]
        # vector from last atom to central atom
        vector2 = xyzc - xyz[b]
        # norm of the two vectors
        norm1 = np.sqrt(np.sum(vector1**2))
        norm2 = np.sqrt(np.sum(vector2**2))
        dot = np.dot(vector1, vector2)
        # Catch the edge case that very rarely this number is -1.
        if dot / (norm1 * norm2) <= -1.0:
            if (np.abs(dot / (norm1 * norm2)) + 1.0) < -1e-6:
                raise RuntimeError('Encountered invalid value in angle')
            return np.pi
        return np.arccos(dot / (norm1 * norm2))