mdtraj.utils.box_vectors_to_lengths_and_angles¶

mdtraj.utils.box_vectors_to_lengths_and_angles(a, b, c)¶

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

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.

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