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).
