internal.py 文件源码

def value(self, xyz):
        xyz = xyz.reshape(-1,3)
        a = self.a
        b = self.b
        c = self.c
        # vector from first atom to central atom
        vector1 = xyz[a] - xyz[b]
        # vector from last atom to central atom
        vector2 = xyz[c] - 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
        if dot / (norm1 * norm2) >= 1.0:
            if (np.abs(dot / (norm1 * norm2)) - 1.0) > 1e-6:
                raise RuntimeError('Encountered invalid value in angle')
            return 0.0
        return np.arccos(dot / (norm1 * norm2))