My code is below. Please help me fix it, thanks!
units real
atom_style full
boundary p p p
timestep 1
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
pair_style lj/cut/coul/long 12.0
read_data 4-5-4.data extra/bond/per/atom 4 extra/angle/per/atom 7 extra/special/per/atom 30
kspace_style pppm 1.0e-4
special_bonds lj/coul 0.0 0.0 0.5
minimize 1e-4 1e-6 1000 10000
velocity all create 298.0 3489
fix 111 all npt temp 298.0 298.0 100.0 iso 0.0 0.0 100.0
thermo 200
thermo_style custom step temp press
run 20000
unfix 111
reset_timestep 0
compute ymin0 all reduce min y
compute ymax0 all reduce max y
variable ly0 equal c_ymax0 - c_ymin0
group AP molecule 1
group mix subtract all AP
variable y_thick equal 8.0
variable ybot_region equal c_ymin0 + ${y_thick}
variable ytop_region equal c_ymax0 - ${y_thick}
region bottom block INF INF {c_ymin0} {ybot_region} INF INF units box
region top block INF INF {ytop_region} {c_ymax0} INF INF units box
group bottom region bottom
group up region top
group mid subtract all bottom up
compute Nbot bottom count
compute Ntop up count
fix 100 bottom nve
fix 101 bottom addforce 0.0 -0.01/c_Nbot 0.0
fix_modify 101 virial yes
fix 200 up nve
fix 201 up addforce 0.0 0.01/c_Ntop 0.0
fix_modify 201 virial yes
fix 300 mid nvt temp 298.0 298.0 100.0
compute myPress all pressure NULL pair bond angle dihedral improper kspace
variable pyy equal c_myPress[2]
compute ymin all reduce min y
compute ymax all reduce max y
variable L equal c_ymax - c_ymin
variable strain equal (v_L - v_ly0)/v_ly0
variable stress_GPa equal -v_pyy * 0.000101325
thermo 1000
thermo_style custom step temp v_strain v_stress_GPa
dump 2 all cfg 10000 dump.tensile.*.cfg mass type xs ys zs id
dump_modify 2 sort id
fix 1000 all print 1000 “{step} {strain} ${stress_GPa}” file stress_strain.txt screen no
run 500000