This directory has 4 scripts that compute the viscosity (eta) of a Lennard-Jones fluid using 4 different methods. See the discussion in Section 6.21 of the manual for an overview of the methods and pointers to doc pages for the commands which implement them. Citations for the various methods can also be found in the manaul.

These scripts are provided for illustration purposes. No guarantee is made that the systems are fully equilibrated or that the runs are long enough to generate good statistics and highly accurate results.

These are the 4 methods for compute viscosity. The first 3 are non-equilibrium methods; the last is an equilibrium method.

in.wall = move a wall to shear the fluid between two walls in.nemd = use fix deform and fix nvt/sllod to perform a NEMD shear simulation in.mp = use fix viscosity and the Muller-Plathe method in.gk = use the Green-Kubo method

All the systems have around 800 atoms. The NEMD methods run for short times; the G-K system needs to run longer to generate good statistics.

The scripts were all run on a single processor. They all run in a minute or so and produce the accompanying log files and profile files (for velocity or momemtum flux).

The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut = 2.5 sigma. This system should have a shear viscosity of about 1.0.

Here is how to extract viscosity from the log file output for each method.

The NEMD methods use the formula eta = - dM / Velocity-gradient, where dM = momentum flux in the y-direction, and Vel gradient = dVelX / dY = the change in x-velocity over a distance dY in the y-direction.

(1) in.wall.2d

mom flux = pxy dVelX = Srate = 2.7 dY = Y box length = 41.99

eta = 0.946 = running average output as last log file column

(2) in.nemd.2d

mom flux = pxy dVelX = velocity of top box edge = Srate = 2.7 dY = Y box length = 36.51

eta = 1.18 = running average output as last log file column

(3) in.mp.2d

mom flux = dMom in Y / 2 / Area-perp-to-Y / dTime dMom = -1370.2 from log file, tallied by MP

factor of 2 since system is periodic and dMom goes 2 ways
Area for 2d = lx
dTime = elapsed time in tau for accumulating dMom

dVelX = 4th column of log output, from fix ave/spatial dY = 1/2 of Y box length

eta = 1.09 = running average output as last log file column

(4) in.gk.2d

eta is computed directly within the script, by performing a time integration of the formula discussed in Section 6.21 of the manual, analagous to the formula for thermal conductivity given on the compute heat/flux doc page - the resulting value prints at the end of the run and is in the log file

eta = 1.07