README

The input script in.GD is an example simulation using Gaussian dynamics (GD).
The simulation is of a simple 2d Lennard-Jones fluid flowing through a pipe.
For details see online LAMMPS documentation and
Strong and Eaves, J. Phys. Chem. Lett. 7(10) 2016, p. 1907.

Note that the run times and box size are chosen to allow a fast example run.
They are not adequate for a real simulation.

The script has the following parts:
1) initialize variables
    These can be modified to customize the simulation. Note that if the
    pipe dimensions L or d are changed, the geometry should be checked
    by visualizing the coordinates in all.init.lammpstrj.

2) create box

3) set up potential

4) create atoms

5) set up profile-unbiased thermostat (PUT)
    see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
    By default, this uses boxes which contain on average 8 molecules.

6) equilibrate without GD

7) initialize the center-of-mass velocity and run to achieve steady-state
    The system is initialized with a uniform velocity profile, which
    relaxes over the course of the simulation.

8) collect data
    The data is output in several files:
    GD.out contains the force that GD applies, and the flux in the x- and
        y- directions. The output Jx should be equal to the value of
        J set in section 1, which is 0.1 by default.
    x_profiles contains the velocity, density, and pressure profiles in
        the x-direction. The pressure profile is given by
        (-1/2V)*(c_spa[1] + c_spa[2]), where V is the volume of a
        slice. The pressure profile is computed with IK1, see
        Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627.
        Note that to compare with the pump method, or to
        compute a pressure drop, you must correct this pressure
        profile as described in Strong 2016 above.
    Vy_profile is the velocity profile inside the pipe along the
        y-direction, u_x(y).