moleculekit.unitcell module#
- moleculekit.unitcell.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
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.
- moleculekit.unitcell.lengths_and_angles_to_box_vectors(a_length, b_length, c_length, alpha, beta, gamma, reduced=False)#
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)
Examples
>>> import numpy as np >>> result = lengths_and_angles_to_box_vectors(1, 1, 1, 90.0, 90.0, 90.0)
Notes
This code is adapted from gyroid, which is licensed under the BSD http://pythonhosted.org/gyroid/_modules/gyroid/unitcell.html
- moleculekit.unitcell.lengths_and_angles_to_tilt_factors(a_length, b_length, c_length, alpha, beta, gamma)#
- 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:
lx (scalar) – Extent in x direction
ly (scalar) – Extent in y direction
lz (scalar) – Extent in z direction
xy (scalar) – Unit vector b tilt with respect to a
xz (scalar) – Unit vector of c tilt with respect to a
yz (scalar) – Unit vector of c tilt with respect to b