in.lammps.lj

#########################################################################################
#											#
# Generate dynamics of Lennard-Jones system of 108 particles using Tensorflow DNN	#
#											#
# Lennard-Jones potential is for ficticious strongly-coupled Nobel element		#
# in the liquid state at T=1000 K, rho = 5.314 g/cc (atomic mass = 100 g/mol)		#
#											#
# DNN potential corresponds approx to LJ potential of:					#
# epsilon = 1 kcal/mol, sigma = 4.5 angstroms, cutoff is 2.5*sigma			#
#											#
# Initial state is fcc lattice melted over 100 ps					#
# For equilibration: Noose-Hoover thermostat with NVT					#
# For production: NVE dynamics / 1 fs timestep / output every 10 steps / 1e6 steps	#
#											#
# @2017, Jon Belof and Will Lowe 							#
#											#
#########################################################################################

# set the thermodynamic conditions
variable	temperature		equal	1000.	# in K

# initial lattice parameter (sets the density)
variable	lattice_parameter	equal	5.	# in angstroms

# number of primitive cells in x, y, z
variable	nx			equal	3
variable	ny			equal	3
variable	nz			equal	3

# output frequency
variable	traj_equil_freq		equal	1
variable	traj_prod_freq		equal	1
variable	thermo_freq		equal	1

# "real" units: mass = g/mol, distance = angstroms, time = fs, energy = kcal/mol, pressure = atm
units		real

# fully periodic
boundary	p p p
atom_style	atomic
atom_modify     sort 0 0.0

# energy conserving timestep
timestep	1.

# set the initial lattice spacing and orientation
# z aligned with 001
lattice         fcc ${lattice_parameter} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

# replicate the primitive cell
region          box prism 0 ${nx} 0 ${ny} 0 ${nz} 0 0 0

# populate the simulation box
create_box      1 box
create_atoms    1 box

# mass = 100 g/mol
mass 1 100.

# neighbor list
neighbor        2.0 bin
neigh_modify	every 1 delay 10 check yes

# output observables
thermo_style	custom step time vol density temp press etotal ke pe
thermo		${thermo_freq}
thermo_modify	flush yes

# write trajectory of equilibration
dump		equil_dump all custom ${traj_equil_freq} lj.equil.lammpstrj x y z vx vy vz fx fy fz

# thermo/barostat to our desired state
velocity	all create ${temperature} 12345 dist gaussian
velocity	all zero linear
fix             dyn_equil all nvt temp ${temperature} ${temperature} 100.

# set callback interface to retrieve forces from our trained DNN
fix		dyn_DNN all external pf/callback 1 1

# equilibrate
run		100000

# set NVE dynamics
undump		equil_dump
unfix		dyn_equil
reset_timestep	0
fix             dyn_prod all nve

# write production trajectory
dump		prod_dump all custom ${traj_prod_freq} lj.lammpstrj x y z vx vy vz fx fy fz

# production dynamics
run		1000000