mdtraj.utils.box_vectors_to_lengths_and_angles¶
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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