mdtraj.utils.box_vectors_to_lengths_and_angles¶
- mdtraj.utils.box_vectors_to_lengths_and_angles(a, b, c)[source]¶
Convert box vectors into the lengths and angles defining the box.
- Parameters:
a (np.ndarray) – the vector defining the first edge of the periodic box (length 3), or an array of this vector in multiple frames, where a[i,:] gives the length 3 array of vector a in each frame of a simulation
b (np.ndarray) – the vector defining the second edge of the periodic box (length 3), or an array of this vector in multiple frames, where b[i,:] gives the length 3 array of vector a in each frame of a simulation
c (np.ndarray) – the vector defining the third edge of the periodic box (length 3), or an array of this vector in multiple frames, where c[i,:] gives the length 3 array of vector a in each frame of a simulation
Examples
>>> a = np.array([2,0,0], dtype=float) >>> b = np.array([0,1,0], dtype=float) >>> c = np.array([0,1,1], dtype=float) >>> l1, l2, l3, alpha, beta, gamma = box_vectors_to_lengths_and_angles(a, b, c) >>> (l1 == 2.0) and (l2 == 1.0) and (l3 == np.sqrt(2)) True >>> np.abs(alpha - 45) < 1e-6 True >>> np.abs(beta - 90.0) < 1e-6 True >>> np.abs(gamma - 90.0) < 1e-6 True
- Returns:
a_length (scalar or np.ndarray) – length of Bravais unit vector a
b_length (scalar or np.ndarray) – length of Bravais unit vector b
c_length (scalar or np.ndarray) – length of Bravais unit vector c
alpha (scalar or np.ndarray) – angle between vectors b and c, in degrees.
beta (scalar or np.ndarray) – angle between vectors c and a, in degrees.
gamma (scalar or np.ndarray) – angle between vectors a and b, in degrees.