mdevaluate_examples/examples/selector.py

from functools import partial

import matplotlib.pyplot as plt
from matplotlib import cm

import mdevaluate as md

data_dir = "/data/skloth/python_packages/mdevaluate_examples/plots"
path_to_sim = (
    "/data/skloth/sim/silica_pore/tip4p2005/D3_L6_S4.9_R0/T300_isochor/T250_nvt_short"
)
trajectory = md.open(path_to_sim, topology="run.tpr", trajectory="out/traj_full.xtc")

oxygen_water = trajectory.subset(atom_name="OW", residue_name="SOL")

time, result_all = md.correlation.shifted_correlation(
    partial(md.correlation.isf, q=22.7), oxygen_water, segments=100, skip=0.1
)
time, result_wall = md.correlation.shifted_correlation(
    partial(md.correlation.isf, q=22.7),
    oxygen_water,
    selector=partial(md.coordinates.selector_radial_cylindrical, r_min=1.0, r_max=1.5),
    segments=100,
    skip=0.1,
)
time, result_center = md.correlation.shifted_correlation(
    partial(md.correlation.isf, q=22.7),
    oxygen_water,
    selector=partial(md.coordinates.selector_radial_cylindrical, r_min=0.0, r_max=0.5),
    segments=100,
    skip=0.1,
)

plt.figure()
plt.plot(time, result_all, "k-", label="all")
plt.plot(time, result_wall, "r.", label="wall")
plt.plot(time, result_center, "b.", label="center")
plt.legend()
plt.xscale("log")
plt.xlabel(r"$t$ / ps")
plt.ylabel(r"S_q(t)")
plt.savefig(f"{data_dir}/selector.png", dpi=300, bbox_inches="tight")
plt.show()