Reorientation lifetime of vectors#

from fishmol import trj, utils, funcs, style
from cage_data import cage1_info

Read trajectory file#

%%time
cell = cage1_info.cell
traj = trj.Trajectory(timestep = 5, data = "/nobackup/rhtp48/data_ana/cage1-500K.xyz", index = ":", cell = cell)

CPU times: user 2min 17s, sys: 7.39 s, total: 2min 24s
Wall time: 2min 27s

Vector reorientation dynamics (VRD) of water O-H bonds#

Sepearately calculate the O-H bonds#

water_vrd = funcs.VRD(traj = traj, spec = [14, [15, 16]], num = 500, sampling = 5, skip = 2)
results = water_vrd.calculate(l = 1, mean = False, fit = True, plot = True)

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_images/cfa68e1b3ff38923f5ad8d1a9b3153cd7f116f50b46280f88f099bbe03df255e.png

Average the O-H bonds of the same water molecule#

water_vrd = funcs.VRD(traj = traj, spec = [14, [15, 16]], num = 500, sampling = 5, skip = 2)
results = water_vrd.calculate(l = 1, mean = True, fit = True, plot = True)

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_images/9d9e8d3f7938ca30a802f66ceed6171e226127f1dae5c762cdd1e6eb82953b71.png

Plot the results by yourself#

fig, ax = plt.subplots()

ax.scatter(results.t, results.C_t)
ax.plot(results.t_fit, results.C_t_fit, color = "#252525")

ax.set_xlabel(r"$t$ (ps)")
ax.set_ylabel(r"$C^1_t$")
plt.show()
_images/f8830bb4f171473ea16b159707a15824f41fb3f71c4aa9d5d01533289acdad68.png

VRD of trifluoroacetate ion C-C bond#

Calculate the C-C bond reorientation dynamics in one TFA anion#

TFAs = cage1_info.TFAs
spec = [*TFAs[0].values()]

spec

[0, 1, 2, 3, 4, 5, 6]

print([x for x in spec if traj.frames[0][x].symbs == "O"])

[3, 4]

vrd = new_VRD(traj = traj, spec = [3, 4], num = 2000, sampling = 10, skip = 5)
results = vrd.calculate(l = 3, mean = False, fit = True, plot = True)

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_images/33ffd0000620866f9c8dda19018dcc273a680f64a4ac85f2ead086aad3b816b7.png 
all_oxygen = [x for spec in TFAs for x in [*spec.values()] if traj.frames[0][x].symbs == "O"]

specs = [[x for x in all_oxygen[::2]], [x for x in all_oxygen[1::2]]]
specs

[[3, 10, 132, 139, 261, 268, 390, 397], [4, 11, 133, 140, 262, 269, 391, 398]]

Calculate the average VRD of all TFA C-C bonds#

vrd = funcs.VRD(traj = traj, spec = specs, num = 2000, sampling = 10, skip = 5)
results = vrd.calculate(l = 3, mean = True, fit = True, plot = True)

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