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

Worked out example for dynamic properties

Browse Source
This commit is contained in:
Sebastian Kloth 2024-02-10 14:53:35 +01:00
parent 6b99ed67ff
commit 7231dc53fd
1 changed files with 44 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

50
examples/dynamic_properties.py
View File

@ -1,19 +1,57 @@
# %%
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")
# %%
print(md.correlation.msd(trajectory[0], trajectory[-1]))
result_msd = md.correlation.shifted_correlation(
md.correlation.msd, oxygen_water, segments=10, skip=0.1, average=True
result_msd_pbc = md.correlation.shifted_correlation(
md.correlation.msd, oxygen_water, segments=100, skip=0.1, average=True
)
result_msd_nojump = md.correlation.shifted_correlation(
md.correlation.msd, oxygen_water.nojump, segments=10, skip=0.1, average=True
md.correlation.msd, oxygen_water.nojump, segments=100, skip=0.1, average=True
)
plt.figure()
plt.plot(result_msd[0], result_msd[1], ".", label="pbc")
plt.plot(result_msd_nojump[0], result_msd_nojump[1], "-", label="nojump")
plt.plot(result_msd_pbc[0], result_msd_pbc[1], ".", label="pbc")
plt.plot(result_msd_nojump[0], result_msd_nojump[1], ".", label="nojump")
plt.legend()
plt.xscale("log")
plt.yscale("log")
plt.xlabel(r"$t$ in ps", fontsize=16)
plt.ylabel(r"$\langle r^2\rangle(t)$ in nm$^2$", fontsize=16)
plt.show()
plt.close()
plt.close()
# %%
cation = trajectory.subset(residue_name="amim")
cation_indices = cation.atom_subset.indices
cation_com = md.coordinates.center_of_masses(trajectory, atom_indices=cation_indices)
result_msd_cation = md.correlation.shifted_correlation(
md.correlation.msd, cation.nojump, segments=100, skip=0.1, average=True
)
result_msd_cation_com = md.correlation.shifted_correlation(
md.correlation.msd, cation_com.nojump, segments=100, skip=0.1, average=True
)
plt.figure()
plt.plot(result_msd_cation[0], result_msd_cation[1], ".", label="cation all atoms")
plt.plot(result_msd_cation_com[0], result_msd_cation_com[1], ".", label="cation com")
plt.legend()
plt.xscale("log")
plt.yscale("log")
plt.xlabel(r"$t$ in ps", fontsize=16)
plt.ylabel(r"$\langle r^2\rangle(t)$ in nm$^2$", fontsize=16)
plt.show()
plt.close()