# 3x3 array of liquid-crystal molecules
# long-range Coulombics via PPPM, NPH
# init temperature with middle layer hot (400K), top/bottom layer cool (300K)
# thermostat each layer at 400K or 300K via rescale fixes
# temperature initially drops as system equilibrates
# if compile LAMMPS with diagnostic_temp_molecules.f, LAMMPS will print-out
#   temperature of layers as simulation runs

units		real
neighbor	2.0 1 20 0 1

coulomb style	pppm 10.0 1.0E-4
nonbond style	lj/cutoff 10.0 0
mixing style	arithmetic

read data	data.lc.big

# bottom layer = molecules 1-9
# middle layer = molecules 10-18
# top layer = molecules 19-27

create group	molecules 10 18
create temp	uniform 400.0 4762
create group	molecules 1 9
create temp	uniform 300.0 598287
create group	molecules 19 27
create temp	uniform 300.0 33785

press control	nose/hoover xyz 1.0 1.0 0.0001

# fix middle layer at 400K, other 2 layers are remainder at 300K

fix style	1 rescale 400.0 400.0 10 10.0 0.5
fix style	2 rescale 300.0 300.0 10 10.0 0.5
assign fix	1 molecule 10
assign fix	1 molecule 11
assign fix	1 molecule 12
assign fix	1 molecule 13
assign fix	1 molecule 14
assign fix	1 molecule 15
assign fix	1 molecule 16
assign fix	1 molecule 17
assign fix	1 molecule 18
assign fix	2 remainder

timestep	1.0
thermo flag	50

# compute temp of molecules 10-18 and other = all the rest

diagnostic	temp_molecules 10 none 2 10 18

run		100