# ----------------- Init Section -----------------

include "system.in.init"


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

read_data "combine.data"

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

include "system.in.settings"


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

# The lines above define the system you want to simulate.
# What you do next is up to you.
# Typically a user would minimianisoe and equilibrate
# the system using commands similar to the following:
#  ----   examples   ----
#
#  -- minimianisoe --
# minimianisoe 1.0e-5 1.0e-7 1000 10000
# (Note: Some fixes, for example "shake", interfere with the minimianisoe command,
#        You can use the "unfix" command to disable them before minimianisoation.)
#  -- declare time step for normal MD --
# timestep 1.0
#  -- run at constant pressure (Nose-Hoover)--
# fix   fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
#  -- ALTERNATELY, run at constant volume (Nose-Hoover) --
# fix   fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
#  -- ALTERNATELY, run at constant volume using Langevin dynamics. --
#  -- (This is good for sparse CG polymers in implicit solvent.)   --
# fix fxLAN all langevin 300.0 300.0 5000 48279
# fix fxNVE all nve  #(<--needed by fix langevin)
#  -- Now, finally run the simulation --
# run   50000
#  ---- (end of examples) ----
timestep 1.0
group mof type 1:6
group pol subtract all mof
group metal id 259
group mobile subtract all mof

neigh_modify every 1 delay 0 check yes 
thermo_style   custom step temp density press etotal lx ly lz
thermo 10000

dump my_dump all atom 10000 dump.lammpstrj
fix rigidMof mof rigid single
fix freeze mof setforce 0.0 0.0 0.0 
velocity mof set 0 0 0 

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 5000
unfix 1
fix 1 all npt temp 300 300 100 z 592 592 1000 dilate mobile
run 5000
unfix 1

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 10000
unfix 1
fix 1 all npt temp 300 300 100 z 17764 17764 1000 dilate mobile
run 5000
unfix 1

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 10000
unfix 1
fix 1 all npt temp 300 300 100 z 29607 29607 1000 dilate mobile
run 5000
unfix 1

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 10000
unfix 1
fix 1 all npt temp 300 300 100 z 14803 14803 1000 dilate mobile
run 5000
unfix 1

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 10000
unfix 1
fix 1 all npt temp 300 300 100 z 2960 2960 1000 dilate mobile
run 5000
unfix 1

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 10000
unfix 1
fix 1 all npt temp 300 300 100 z 296 296 1000 dilate mobile
run 5000
unfix 1

fix 1 all nvt temp 600 600 100
run 5000
unfix 1
fix 1 all nvt temp 300 300 100
run 10000
unfix 1
fix 1 all npt temp 300 300 100 z 0.98 0.98 1000 dilate mobile
run 800000
unfix 1
write_data mmm.data

fix 1 all nvt temp 300 300 100

variable a loop 300
label loop
run 10000
write_data eq_${a}.data
next a
jump SELF loop
write_data final.data