diff --git a/examples/selector.py b/examples/selector.py index ef7e295..2bf8903 100644 --- a/examples/selector.py +++ b/examples/selector.py @@ -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()