#3D lubricant fene
units		metal
#units		lj
dimension	3
boundary	s s s

atom_style  atomic
atom_style bond
bond_style fene

pair_style hybrid lj/cut 2.5 tersoff table linear 50 

read_data data3.txt

special_bonds lj 0.00000 1.0 1.0

bond_coeff 1 30.0 4.5 1.0 0.12


mass 1 430.0000
mass 2 69.0000
mass 3 85.0	  
mass 4 12.0

neighbor 2.0 nsq

fix 1 all nve
fix 2 all langevin 300.0 300.0 1 904297

pair_coeff 3 4 ebbb.table entry1 
pair_coeff 2 4 ebbb.table entry1 
pair_coeff 1 4 bbbb.table entry2 
pair_coeff 2 3 ebeb.table entry3 
pair_coeff 2 2 ebeb.table entry3
pair_coeff 3 3 ebeb.table entry3

pair_coeff 4 4 c.tersoff c c c
pair_coeff 1 1 1.0 1.0 2.7
pair_coeff 1 2 1.0 1.0 2.7
pair_coeff 1 3 1.0 1.0 2.7

timestep 0.00012

#min_style cg
minimize 1e-6 1e-6 1000 1000

group polymer molecule >= 1

compute gyration polymer gyration #/molecule
compute msdd polymer msd/molecule

fix 4 polymer ave/time 10000 1 10000 c_gyration file gyra.txt #mode vector

compute mycom all com
fix 5 all ave/time 10000 1 10000 c_mycom file com.txt mode vector

compute presss polymer stress/atom
compute pressss all stress/atom pair bond

thermo_style custom step temp c_gyration c_msdd[18][4] atoms pxx pyy pzz pxy pe ke dt 

dump 1 all xyz 10000 position.xyz
dump 2 all atom 10000 lammp.xyz
dump 3 all custom 10000 mp.xyz c_presss[1]c_presss[2] c_presss[3]
dump 4 all custom 10000 sa.xyz c_pressss[1]c_pressss[2] c_pressss[3]
dump 5 all custom 10000 ta.xyz vx vy vz fx fy fz


thermo 10000
run 50000000