Complete Python code¶

#!/usr/bin/env amspython
# coding: utf-8

# ## Initial imports

import scm.plams as plams
import os
import numpy as np


# ## Create initial benzene system

benzene_box = plams.packmol(plams.from_smiles("c1ccccc1", forcefield="uff"), density=0.875, n_molecules=40)
plams.plot_molecule(benzene_box)


# ## Equilibration MD simulation
#
# Short equilibration MD simulation at 300 K for 5 ps with the GAFF force field and automatic atom typing.

s = plams.Settings()
s.input.ForceField.Type = "GAFF"
s.input.ForceField.AnteChamberIntegration = "Yes"
eq_job = plams.AMSNVTJob(
    settings=s,
    molecule=benzene_box,
    name="equilibration",
    nsteps=5000,
    timestep=1.0,
    temperature=300,
    thermostat="Berendsen",
)
eq_job.run()


# ## Production MD simulation
#
# Enable the "Bin log" for Pressure tensor and Time. This stores these quantities at every time step of the simulation, even if the structure is not stored. It is required to be able to calculate viscosity from the Green-Kubo relation.
#
# Here, we run a very short MD simulation of 200 ps. Typically, to converge the viscosity you would need longer simulations.
#
# The time step is quite large at 1 fs. You may want to decrease it (and increase the number of MD steps correspondingly).

prod_job = plams.AMSNVTJob.restart_from(
    eq_job,
    name="production",
    nsteps=200000,
    timestep=1,
    temperature=300,
    thermostat="NHC",
    tau=100,
    binlog_pressuretensor=True,
    binlog_time=True,
)


prod_job.run()


# ## Calculate the viscosity autocorrelation integral

from scm.plams.recipes.md.trajectoryanalysis import AMSViscosityFromBinLogJob

job = AMSViscosityFromBinLogJob(previous_job=prod_job)
job.run()


# ## Plot the results
#
# The viscosity is the limiting value of the viscosity integral.
#
# The viscosity integral **must** converge to a near-constant value. If it is not close to converging, then you should run a longer MD simulation.
#
# To better estimate the viscosity, a double-exponential function is fitted to the viscosity integral curve. This makes it easier to get a numerical value for the viscosity.
#
# $\eta(t) = A(\lambda (1 - \exp(-t/\tau _1) + (1-\lambda) (1- \exp(-t/\tau _2))$
#
# The parameters $A$, $\lambda$, $\tau _1$, and $\tau _2$ are fitted and available as ``popt[0]``, ``popt[1]``, ``popt[2]``, and ``popt[3]``.
#
#

x, viscosity_integral = job.results.get_viscosity_integral()
popt, x_fit, fit_viscosity_integral = job.results.get_double_exponential_fit()


import matplotlib.pyplot as plt

fig, ax = plt.subplots()
ax.set_title(f"Limiting value: {popt[0]:.5f} Pa s")
ax.plot(x, viscosity_integral, color="tab:blue")
ax.plot(x_fit, fit_viscosity_integral, color="tab:red")
ax.set_xlabel("Correlation Time (fs)")
ax.set_ylabel("Viscosity (Pa s)")