# ----------------------------- Initialization Section --------------------

include system.in.init


# ----------------------------- Atom Definition Section -------------------

read_data system.data


# ----------------------------- Settings Section --------------------------

include system.in.settings


# ----------------------------- Run Section -------------------------------



# Optional: Improve efficiency by omitting the calcuation of interactions 
# between immobile atoms. (Note: This is not optional under NPT conditions.)
neigh_modify exclude group Cgraphene Cgraphene

# Only the Cgraphene atoms are immobile.
group mobile subtract all Cgraphene



# -- minimization protocol --

# Unfortunately you can not use the LAMMPS "minimize" command on this system
# because there is no way to immobilize the carbon graphene & nanotube atoms
# during minimization.  Instead, we can use langevin dynamics with a large 
# damping parameter and a small timestep.

print "--------- beginning minimization (using fix langevin) ---------"

timestep        0.1
fix fxlan mobile langevin 1.0 1.0 100.0 48279
fix fxnve mobile nve   # <-- needed by fix langevin (see lammps documentation)
thermo          100
run 2500

unfix fxlan
unfix fxnve

# -- simulation protocol --

print "--------- beginning simulation (using fix nvt) ---------"

timestep        1.0
dump            1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz

thermo_style    custom step temp pe etotal press vol epair #ebond eangle edihed
thermo          500  # time interval for printing out "thermo" data


# Integrate the equations of motion:
fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0

# The next two lines recalculate the temperature 
# using only the mobile degrees of freedom:

compute tempMobile mobile temp
fix_modify fxMoveStuff temp tempMobile

restart         5000000   restart_nvt
run		10000000

write_restart  system_after_nvt.rst