"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)

:line

NEMD simulations :h3

Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceding Howto section).

A shear strain can be applied to the simulation box at a desired
strain rate by using the "fix deform"_fix_deform.html command.  The
"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system.  Fix nvt/sllod uses "compute
temp/deform"_compute_temp_deform.html to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms.  The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.

NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems.  The latter can be tricky to do correctly.

As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
length.  However, "fix deform"_fix_deform.html can continuously strain
a box by an arbitrary amount.  As discussed in the "fix
deform"_fix_deform.html command, when the tilt value reaches a limit,
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space.  The strain rate can then continue to change as
before.  In a long NEMD simulation these box re-shaping events may
occur many times.

In a NEMD simulation, the "remap" option of "fix
deform"_fix_deform.html should be set to "remap v", since that is what
"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
profile consistent with the applied shear strain rate.

An alternative method for calculating viscosities is provided via the
"fix viscosity"_fix_viscosity.html command.

NEMD simulations can also be used to measure transport properties of a fluid
through a pore or channel. Simulations of steady-state flow can be performed
using the "fix flow/gauss"_fix_flow_gauss.html command.

:line

:link(Daivis-nemd)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
