amep.pbc.pbc_points#

amep.pbc.pbc_points(coords: ndarray, box_boundary: ndarray, enforce_nd: int | None = None, thickness: float | None = None, width: float | None = None, index: bool = False, inclusive: bool = True, verbose: bool = False, fold_coords: bool = False) → ndarray#

Returns the points and their first periodic images.

Notes

Copied from mdevaluate’s pbc.py (data/robin/mdevaluate/mdevaluate) and slightly modified for 2D use.

Parameters:

coords (np.ndarray of shape (N,3)) – Particle coordinates.
box_boundary (np.ndarray of shape (3,2)) – Boundary of the simulation box in the form of np.array([[xmin, xmax], [ymin, ymax], [zmin, zmax]]).
enforce_nd (int, None, optional) – enforces the number of dimensions. 2 for 2d, 3 for 3d. If None is supplied, a best guess is used by checking if all particles have the same dimension in the last coordinate. See utils.dimension()
width (float or None, optional) – Width of the periodic images relative to the box dimensions. None means the original and all periodic images are returned; positive means points are cutoff at box*(1+width); negative values mean that less than the box is returned. At most one periodic image in each direction is returned. This keyword is preferred before thickness. The default is None.
thickness (float or None, optional) – Absolute width of the periodic images in each direction. None means the original and all periodic images are returned; positive means points are cutoff at box+thickness; negative values mean that less than the box is returned. If width is supplied, this keyword is ignored. The default is None.
index – If True, also the indices with indices of images being their original values are returned. The default is False.
inclusive (bool, optional) – If False, only the images are returned. The default is True.
fold_coords (bool, optional) – If True, points in coordinates are fold back into the box. The default is False.
verbose (bool, optional) – If True, some information is printed. The default is False.

Returns:

Array of all coordinates (including periodic images; array of floats)

Return type:

np.ndarray

Examples

>>> import amep
>>> traj = amep.load.traj("../examples/data/lammps.h5amep")
>>> frame = traj[-1]
>>> images = amep.pbc.pbc_points(
...     frame.coords(), frame.box, inclusive=False
... )
>>> perm_vectors = np.array([
...     [-1, -1,  0],
...     [-1,  0,  0],
...     [-1,  1,  0],
...     [ 0, -1,  0],
...     [ 0,  1,  0],
...     [ 1, -1,  0],
...     [ 1,  0,  0],
...     [ 1,  1,  0]
... ]).astype(float)
>>> fig, axs = amep.plot.new(figsize=(3,3))
>>> amep.plot.particles(
...     axs, images, frame.box, 0.5, color="tab:blue",
...     set_ax_limits=False
... )
>>> amep.plot.particles(
...     axs, frame.coords(), frame.box, 0.5, color="tab:orange",
...     set_ax_limits=False
... )
>>> amep.plot.box(axs, frame.box, color='k', linewidth=2)
>>> for p in perm_vectors:
...     shift = p*(frame.box[:,1]-frame.box[:,0])
...     amep.plot.box(
...         axs, frame.box+shift[:,None], color='k',
...         linewidth=1, linestyle='--'
...     )
>>> axs.set_xlabel(r'$x$')
>>> axs.set_ylabel(r'$y$')
>>> fig.savefig('./figures/pbc/pbc-pbc_points.png')
>>>