# -- Init Section --

include system.in.init
boundary p p f

# -- Atom Definition Section --

read_data system.data

# -- Settings Section --

include system.in.settings

# -- Run Section --


timestep        0.0025
dump            1 all custom 200 traj.lammpstrj id mol type x y z ix iy iz

thermo_style    custom step temp pe etotal
thermo          100  # time interval for printing out "thermo" data

# ---- Set up the physical environment ----

# Add gravity:
fix fxGrav gMobile gravity 0.05 vector 0 0 -1 

# Create a "ground" surface.
# This is a repulsive "wall" which particles can bounce off of:

fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0


# ---- Evolve the system: ----

# Evolve the (mobile) atoms using ordinary Newton's laws (NVE)

fix fxNVE  gMobile nve


#  IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE:
#fix fxLan  gMobile langevin 0.001 0.001 10000.0 48279
#  To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve"
#  (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
#  This was not tested.

# OPTIONAL:
# For efficient simulation in parallel, try using "fix balance":
# (This will adjust the spatial decomposition as the distribution of
#  particles changes over time.)
# http://lammps.sandia.gov/doc/fix_balance.html
# fix fxBalance gMobile balance 1000 1.1 shift 1000 xy 20 1.1
# Alternatiely, try this:
#fix fxBalance gMobile balance 1000 1.2 rcb


# OPTIONAL: Improve efficiency by omitting the calcuation of interactions 
# between immobile atoms:

neigh_modify exclude group gImmobile gImmobile


restart         50000  restart_nvt

run		200000

write_data  system_after_nvt.data