mdtraj.utils.lengths_and_angles_to_box_vectors¶

mdtraj.utils.lengths_and_angles_to_box_vectors(a_length, b_length, c_length, alpha, beta, gamma)¶

Convert from the lengths/angles of the unit cell to the box vectors (Bravais vectors). The angles should be in degrees.

Parameters:

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.

Returns:

a : np.ndarray

If the inputs are scalar, the vectors will one dimesninoal (length 3). If the inputs are one dimension, shape=(n_frames, ), then the output will be (n_frames, 3)

b : np.ndarray

If the inputs are scalar, the vectors will one dimesninoal (length 3). If the inputs are one dimension, shape=(n_frames, ), then the output will be (n_frames, 3)

c : np.ndarray

If the inputs are scalar, the vectors will one dimesninoal (length 3). If the inputs are one dimension, shape=(n_frames, ), then the output will be (n_frames, 3)

Notes

This code is adapted from gyroid, which is licensed under the BSD http://pythonhosted.org/gyroid/_modules/gyroid/unitcell.html

Examples

>>> import numpy as np
>>> result = lengths_and_angles_to_box_vectors(1, 1, 1, 90.0, 90.0, 90.0)