Dear all,
I am trying to get stress strain plot for a box filled with polymer. Initially I used to compress the box to get required density, then minimize, equilibrate and then deform to get stress strain plot. The problem is the value of stress is not zero during the starting point of deformation. It is far high. I tried to vary the Tdamp and Pdamp values but still initial values are high at zero strain. I have attached the input script below… Anyone could help me out of this.
#deformation to intial structure
fix 2 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1
fix 1 all deform 1 x final 0 220 units box remap x
thermo 100
thermo_style custom step temp ke pe press
dump 4 all dcd 1000 dumpforxdeform.dcd
run 10000
unfix 1
unfix 2
write_restart systemafter.xchanged
fix 1 all npt temp 300 300 1 x 0 0 1 z 0 0 1 drag 1
fix 2 all deform 1 y final 0 220 units box remap x
thermo 100
thermo_style custom step temp ke pe press
dump 5 all dcd 1000 dumpforydeform.dcd
run 10000
unfix 1
unfix 2
write_restart systemafter.xychanged
fix 1 all npt temp 300 300 1 y 0 0 1 x 0 0 1 drag 1
fix 2 all deform 1 z final 0 220 units box remap x
thermo 100
thermo_style custom step temp ke pe press
dump 6 all dcd 500 dumpforzdeform.dcd
run 10000
unfix 1
unfix 2
write_restart systemafter.xyzchanged
minimization
dump 2 all dcd 1000 dump_for_min.dcd
thermo 100
thermo_style custom step pe lx ly lz press pxx pyy pzz
min_style cg
minimize 1e-25 0.0 400000 100000000000
print “MINIMIZATION DONE”
write_restart system_after.minimize
EQUILIBRATION
timestep 1.0
velocity all create 300 123475 mom yes rot no
fix 1 all npt temp 300 300 100 iso 0 0 1000 drag 1
Set thermo output
thermo 1000
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
dump 3 all dcd 1000 dumpforequil.dcd
Run for at least 10 picosecond (assuming 1 fs timestep)
run 100000
unfix 1
print “EQUILIBRIATION DONE”
write_restart systemafter.equil