units              lj
atom_style         full
neighbor           0.36 bin
neigh_modify       delay 2

pair_style         lj/cut 2.5

bond_style         fene
special_bonds    lj  0.0 1.0 1.0
read_restart 10000_Load_Unload_Restart_File.restart

pair_coeff         * * 1.0 1.0 2.5
bond_coeff        * 30.0 1.5 1.0 1.0
pair_modify        shift yes

timestep        0.010
reset_timestep 10000


fix   1 all langevin 1.0 1.0 2.0 542305
# fix   2 all press/berendsen iso 0.0 0.0 10.0
fix   3 all nve
thermo     1000
thermo_style custom step temp pe etotal epair pxx pyy pzz lx ly lz
# run 100000

# unfix 2

# Store final simulation box length for strain calculation
variable tmp equal "lx"
variable L0 equal ${tmp}
print "Initial Length, L0: ${L0}"


# Perform Deformation
# reset_timestep 0

variable Tp equal "200"
variable A equal "2*(1/v_Tp)*v_L0"

variable Y1 equal "0.99*sin(2*PI*(1/v_Tp)*step*dt)"
variable Y2 equal "0.99*sin(2*PI*(1/v_Tp)*step*dt - PI)"

variable displace equal "(0.5*v_L0)*(1 + (2/PI)*asin(sin((2*PI*(1/v_Tp)*step*dt) - (PI/2))))"
variable rate equal "v_A*(floor(v_Y1) + (-floor(v_Y2)))"

fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v

compute p all pressure thermo_temp
fix 5 all ave/time 4 25 100 c_p[1] c_p[2] c_p[3] c_p[4] c_p[5] c_p[6] file press.1

# Output stress strain data to file entitled Stress_Strain_Periodic_20K.txt
variable strain equal "(lx - v_L0)/v_L0"
variable p1 equal "v_strain"
variable p2 equal "-pxx"
variable p3 equal "-pyy"
variable p4 equal "-pzz"

fix Deformation1 all print 1000 "${p1} ${p2} ${p3} ${p4}" file Stress_Strain_Periodic_20K.txt screen no
dump    1 all custom 1000 *_Monomer_Coordinates id type x y z ix iy iz

restart 1000 *_Strain_Rate_Periodic_200K.restart
run    20000