#This file is for using lammps to optimize PS-PMMA structure
clear
units real
#Initialization

#what about using atom_syle angle or molecular
atom_style full  
#By default, atomic (non-molecular) problems do not allocate maps. For molecular problems, the option default is map = array. By default, a "first" group is not defined. By default, sorting is enabled with a frequency of 1000 and a binsize of 0.0, which means the neighbor cutoff will be used to set the bin size
atom_modify map hash

#Define the force field parameters, do not know if needed for ms generated structure file while use a cvff force field

pair_style lj/cut/coul/cut 10

#still cant find related thing with cvff.
angle_style harmonic
bond_style harmonic
dihedral_style harmonic
improper_style cvff

#Data reading
read_data ps100pmma50.lammps05

#Setting
#Force field coeff given in input file
#Neighbor info
neighbor 2.0 bin

#Minimization
min_style cg
minimize 1.0e-4 1.0e-6 1000 5000

#Setting MD run
timestep 1.0
thermo_style custom step pe ke etotal enthalp vol press temp 

#Equilibrium
#npt
fix 1 all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0
run 200000
unfix 1
#calculate rdf
fix 1 all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0
compute myRDF all rdf 50
fix 2 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector
thermo 10
log log_PS_PMMA
dump 1 all custom 10 dump_PS_PMMA  position id type vx vy vz 
run 20000
unfix 1
unfix 2
write_restart restart_PS_PMMA_relaxed