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vp.liquids.pair_distribution

The pair distribution function g(r) of a set of configurations of N atoms in a periodic cubic box: a histogram of every pair's separation (nearest image) out to half the box, divided by what an ideal gas of the same density would give in each spherical shell.

Part of the distribution vipyr-liquids; it runs from a checkout of the repository. Planned on PyPI as pip install vipyr-liquids.

Signature

vp.liquids.pair_distribution(*, n=32, box=3.4943, frames=..., dr=0.02)

Parameters

n : int, default 32
The atoms in each configuration. Range: >= 2, <= 1000000.
box : float, default 3.4943
The box side, in sigma. Range: > 0.
frames : ndarray[float64], default fcc_positions(32, 3.4943)
The configurations one after another, (frames x n, 3), positions in sigma; by default one fcc lattice of 32 atoms filling the box. Range: rank 2.
dr : float, default 0.02
The bin width, in sigma. Range: > 0.

Returns

A frozen PairDistributionResult. Iterating it gives the fields below in order; it also has params, tests, log and check().

r_mid : ndarray[float64]
The midpoints of the bins, in sigma.
g : ndarray[float64]
G(r) at those midpoints.
nframes_used : int
The configurations read.

Raises

vipyr.ParameterError
A ValueError: an argument outside its range, choices, rank or shape, or one of a group given without the rest; its .param names the argument.
TypeError
An argument of the wrong type, or an unknown keyword.
vipyr.VivBuildError
An ImportError: no C compiler, or the program's C does not build.
RuntimeError
The program stops with its own message (a combination it rejects, or no convergence where the program treats that as an error).

Examples

import vipyr as vp
m = vp.liquids.md_nve(n=108, nblock=1, nstep=50)
r = vp.liquids.pair_distribution(n=108, box=m.box, frames=m.r_final, dr=0.05)
print(r.r_mid[r.g.argmax()])               # the first peak, near 1.1 sigma
assert r.check()
1.075

Each example ran as written when these pages were generated, and the output shown is what it printed.

Checked against

Tests
ports/liquids/test_liquids.py: every tolerance is stated beside its check
Upstream
pair_distribution of https://github.com/Allen-Tildesley/examples at 4818bc82, built with gfortran -O2 by ports/liquids/oracle/build.py; same bits from the same start and random numbers

Credits

  • A port of the examples of Allen and Tildesley's Computer Simulation of Liquids, which are CC0-1.0.

Source