skloth/mdevaluate_examples
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added example for single selector

Browse Source
This commit is contained in:
Sebastian Kloth 2024-01-20 12:52:30 +01:00
parent 0f6f293090
commit 8c246af1b5
1 changed files with 24 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

29
examples/selector.py
View File

@ -6,19 +6,38 @@ 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/"
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,
segments=10,
skip=0.1
)
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)
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()