units              real
atom_style         full
boundary           p p p
dimension          3

pair_style	lj/class2/coul/long 10 10
bond_style	class2
angle_style	class2
dihedral_style	class2
improper_style	class2
pair_modify	mix sixthpower tail yes
special_bonds	lj/coul 0.0 0.0 1.0

kspace_style   pppm 0.0001
# -----------------Potential definition-----------------
#read_restart 8000000npt300npt.restart
read_data  300knpt.data


compute 1peratom all pe/atom
compute pote all pe
compute pe22 all reduce sum c_1peratom
#compute COM all com
variable natoms equal "count(all)"
variable teng equal "c_pe22"
variable ecoh equal "v_teng/v_natoms"

# -----------------Integration-----------------
neighbor 3 bin
neigh_modify every 1 delay 0 check yes

delete_atoms overlap 0.1 all all

write_coeff polymer.coeff
# ----------------- Minimization-----------------

group pol type 1 2 3 4 5 6 7 8 9 10 11 12 13
group hbn type 14 15 16 17 

compute     inter pol group/group hbn pair yes kspace yes


# -----------------nvt---Run-----------------
timestep       0.5

#--------npt----------


##########2222222##########
reset_timestep     0
thermo_style custom step temp etotal edihed eimp press vol #v_st_total v_exx v_strx v_eyy v_stry v_ezz v_strz #c_p[*]
thermo 500


#dump 1 all custom 500 dump.shear.unwrap id type xsu ysu zsu vx vy vz
dump 22 all custom 500 dump.shear22 id type x y z vx vy vz


fix 1 all npt temp 300 300 50 y 1 1 1000 z 1 1 1000 drag 2  # #
fix 3 all deform 1 x erate 1e-5 units box remap x #
compute peratom all stress/atom NULL  #fix ##bond angle dihedral improper  #

compute newT all temp 						
compute press1 all pressure newT
fix            gr_gr all ave/time 20 20 400 c_inter file gro_grop1.dat

##############################################

variable ily equal ly
variable Ly equal ${ily}
variable ilx equal lx
variable Lx equal ${ilx}
variable ilz equal lz
variable Lz equal ${ilz}

############################################

variable  exy equal xy/v_Ly
variable  exz equal xz/v_Lz
variable  eyz equal yz/v_Lz
variable exx equal (lx-v_Lx)/v_Lx
variable eyy equal (ly-v_Ly)/v_Ly
variable ezz equal (lz-v_Lz)/v_Lz

#########################################

compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] c_peratom[4] c_peratom[5] c_peratom[6]
variable st_total equal -(c_p[1]+c_p[2]+c_p[3])/3/vol#*101.325e-3

#########################################

variable strx equal -c_p[1]/vol#*101.325e-3
variable stry equal -c_p[2]/vol#*101.325e-3
variable strz equal -c_p[3]/vol#*101.325e-3
variable strxy equal -c_p[4]/vol#*101.325e-3
variable strxz equal -c_p[5]/vol#*101.325e-3
variable stryz equal -c_p[6]/vol#*101.325e-3

compute o2 all chunk/atom bin/1d y center 0.05 units reduced
fix             wholesystem all ave/chunk 20 20 400 o2 vx vy vz file density.dat

#fix 5 all ave/time 50 20 1000 f_3[1] file strain_ave2.dat
#fix 4 all ave/time 20 20 400 v_st_total v_exx v_strx file stress_ave2.dat
# v_strxy v_exy v_exz v_strxz v_stryz v_eyz v_strx  v_exx v_stry v_eyy v_strz v_ezz file stress_ave2.dat
#etotal edihed eimp press c_press1 
#v_exx v_strx v_eyy v_stry v_ezz v_strz #c_p[*]


thermo_style custom step temp c_press1[1] pxx v_strx c_press1[2] pyy v_stry c_press1[3] pzz v_strz &
				c_press1[4] pxy v_strxy c_press1[5] pxz v_strxz c_press1[6] pyz v_stryz &
				v_st_total press

thermo 500

run 250000
undump    	22

unfix 		1
unfix		 3
 unfix 		wholesystem
unfix         4


write_restart	*npt3003.restart

write_data     3003k.data