Overlapping atoms¶
mdapy.neighbor.find_overlapping selects the atoms closer than a distance
to another atom, as OVITO's find overlapping particles modifier does: by
default the atom of the higher index of each such pair, so that deleting the
selection leaves no pair that close, or all of them with keep_one=False.
It finds the atoms that clash where structures are put together.
import numpy as np
from mdapy.build import build_crystal
from mdapy.neighbor import find_overlapping
from mdapy.transform import affine, combine
crystal = build_crystal("fcc", 3.615, elements="Cu", repeat=(12, 12, 1))
center = crystal.box.matrix.sum(axis=0) / 2
inside = np.linalg.norm((crystal["positions"] - center)[:, :2], axis=1) < 14
c, s = np.cos(np.radians(25)), np.sin(np.radians(25))
rotation = np.array([[c, -s, 0], [s, c, 0], [0, 0, 1]])
grain = affine(crystal.filter(inside), rotation, center - rotation @ center, box=False)
merged = combine(crystal.filter(~inside), grain) # the grain turned by 25°
too_close = find_overlapping(merged, 2.0) # 16 atoms of the grain
every = find_overlapping(merged, 2.0, keep_one=False) # 36, of both
cleaned = merged.filter(~too_close) # no two atoms closer than 2 Å
The atoms of the grain that find_overlapping selects:
from mdapy.visualization import assign_color, render
grain_atoms = np.arange(len(merged)) >= len(merged) - len(grain)
shown = assign_color(merged, "#9ecae1")
shown = assign_color(shown, "#fdae6b", atoms=grain_atoms)
shown = assign_color(shown, "#d62728", atoms=too_close)
render(shown, "images/overlapping.png", view="top", width=600, height=600)
Copper seen along z: the crystal (blue), the grain turned by 25° in it (orange), and the atoms of the grain closer than 2 Å to an atom of the crystal (red).
Parameters¶
find_overlapping(system, distance, *, keep_one=True, atoms=None)
| Name | Type | Default | Unit | Meaning |
|---|---|---|---|---|
system |
System |
the atoms and the box | ||
distance |
float64 | Å | two atoms closer than this overlap | |
keep_one |
bool | True |
select only the atom of the higher index of each pair that overlaps; False selects both |
|
atoms |
(N,) bool or indices | all | the atoms considered; the others neither overlap nor are selected |
Distances are measured through the periodic boundaries, with the neighbor lists of MDAPY; atoms on top of each other overlap.
Results¶
A boolean mask of one value per atom. With keep_one, deleting the atoms
selected leaves no pair closer than distance, and of each group of atoms
that all overlap one another, as the copies of an atom, one is kept: that of
the lowest index. Along a chain of atoms each closer than distance to the
next only, every atom but the first is selected. OVITO keeps an atom of each
group picked at random, so the atoms it selects can differ from these, their
number in each group not.
Errors¶
InvalidParameter
when atoms is not a mask or indices of the system, and as
NeighborList.build for the distance.