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).