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Worked out example for static properties

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Sebastian Kloth 2024-02-10 14:53:47 +01:00
parent 7231dc53fd
commit 55ad026e7b
1 changed files with 38 additions and 4 deletions
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examples/static_properties.py
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@ -1,19 +1,53 @@
bins = np.linspace(0, 1, 101)
# %%
from functools import partial
import numpy as np
import matplotlib.pyplot as plt
import mdevaluate as md
data_dir = "/data/skloth/python_packages/mdevaluate_examples/plots"
path_to_sim = "/data/skloth/sim/IL_water/C4MIM_BF4_x50/T300_nvt"
trajectory = md.open(path_to_sim, topology="run.tpr", trajectory="out/traj_full.xtc")
oxygen_water = trajectory.subset(atom_name="OW", residue_name="SOL")
# %%
bins = np.arange(0, 1, 0.01)
result_rdf = md.distribution.rdf(oxygen_water[-1], bins=bins)
plt.figure()
plt.plot(bins[:-1], result_rdf)
plt.xlabel(r"$r$ in nm", fontsize=16)
plt.ylabel(r"$g(r)$", fontsize=16)
plt.savefig(f"{data_dir}/rdf.png", dpi=300, bbox_inches="tight")
plt.show()
plt.close()
# %%
bins = np.arange(0, 1, 0.01)
result_rdf = md.distribution.time_average(
partial(md.distribution.rdf, bins=bins), oxygen_water, segments=1000, skip=0.1
)
plt.figure()
plt.plot(bins[:-1], result_rdf)
plt.xlabel(r"$r$ in nm", fontsize=16)
plt.ylabel(r"$g(r)$", fontsize=16)
plt.show()
plt.close()
bins = np.linspace(0, 1, 101)
# %%
boron_anion = trajectory.subset(atom_name="B", residue_name="BF4")
bins = np.arange(0, 1, 0.01)
result_rdf = md.distribution.time_average(
partial(md.distribution.rdf, bins=bins), oxygen_water, segments=100, skip=0.1
partial(md.distribution.rdf, bins=bins),
oxygen_water,
coordinates_b=boron_anion,
segments=1000,
skip=0.1,
)
plt.figure()
plt.plot(bins[:-1], result_rdf)
plt.xlabel(r"$r$ in nm", fontsize=16)
plt.ylabel(r"$g(r)$", fontsize=16)
plt.show()
plt.close()
plt.close()