8.2.6. NEMD simulations
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 command. The fix nvt/sllod 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 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 command.
A recent (2017) book by (Daivis and Todd) 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 can continuously strain a box by an arbitrary amount. As discussed in the fix deform 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 should be set to “remap v”, since that is what fix nvt/sllod 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 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 command.
(Daivis and Todd) Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).