44 lines
1.3 KiB
Python
44 lines
1.3 KiB
Python
from functools import partial
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import matplotlib.pyplot as plt
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from matplotlib import cm
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import mdevaluate as md
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data_dir = "/data/skloth/python_packages/mdevaluate_examples/plots"
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path_to_sim = (
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"/data/skloth/sim/silica_pore/tip4p2005/D3_L6_S4.9_R0/T300_isochor/T250_nvt_short"
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)
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trajectory = md.open(path_to_sim, topology="run.tpr", trajectory="out/traj_full.xtc")
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oxygen_water = trajectory.subset(atom_name="OW", residue_name="SOL")
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time, result_all = md.correlation.shifted_correlation(
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partial(md.correlation.isf, q=22.7), oxygen_water, segments=100, skip=0.1
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)
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time, result_wall = md.correlation.shifted_correlation(
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partial(md.correlation.isf, q=22.7),
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oxygen_water,
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selector=partial(md.coordinates.selector_radial_cylindrical, r_min=1.0, r_max=1.5),
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segments=100,
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skip=0.1,
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)
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time, result_center = md.correlation.shifted_correlation(
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partial(md.correlation.isf, q=22.7),
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oxygen_water,
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selector=partial(md.coordinates.selector_radial_cylindrical, r_min=0.0, r_max=0.5),
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segments=100,
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skip=0.1,
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)
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plt.figure()
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plt.plot(time, result_all, "k-", label="all")
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plt.plot(time, result_wall, "r.", label="wall")
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plt.plot(time, result_center, "b.", label="center")
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plt.legend()
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plt.xscale("log")
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plt.xlabel(r"$t$ / ps")
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plt.ylabel(r"S_q(t)")
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plt.savefig(f"{data_dir}/selector.png", dpi=300, bbox_inches="tight")
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plt.show()
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