# PREREQUISITES:
#
#      You must use moltemplate.sh (& packmol?) to create 3 files:
#        system.data  system.in.init  system.in.settings
#
# See "README_setup.sh" for instructions how to use moltemplate.sh
# Note: This input script file only covers equilibration of the system.
#
# ------------------------------- Initialization Section --------------------

include    "system.in.init"
boundary        p p p

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

read_data  "system.data"

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

include    "system.in.settings"

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

# Output:
thermo          100
thermo_style custom step etotal evdwl ke pe temp press vol density &
                c_myMSD[1] c_myMSD[2] c_myMSD[3] c_myMSD[4] cpu
dump 1 all custom 100 traj.lammpstrj &
id type x y z c_q[1] c_q[2] c_q[3] c_q[4] &
c_shape[1] c_shape[2] c_shape[3] &
angmomx angmomy angmomz


# -- minimization protocol --

minimize 1.0e-4 1.0e-6 100000 400000

# dynamics (NPT conditions)
timestep        10.0
fix             2 all npt/asphere temp 300. 300. 1000. iso 1. 1. 10000.
fix_modify      2 press press_trasl
run             5000

# dynamics (NVT conditions)
unfix 2
fix             2 all nvt/asphere temp 300. 300. 1000.
run             10000