Inquiry on Discrepancy between Data File and Dump File at Initial Timestep

Dear Dr. Axel Kohlmeyer and LAMMPS Users,

Hello Dr. Kohlmeyer. Thank you for your advice. I was curious if I could ask a question regarding how the interatomic pairwise and bond potentials are applied at zero timestep.

The initial portion of my script looks as the following where the polymer chains described in the external data file are allowed to relax by allowing the volume of the simulation box to fluctuate via fix press/Berendsen.

units lj
atom_style full
neighbor 0.36 bin
neigh_modify delay 2
pair_style lj/cut 1.122462

bond_style fene
special_bonds lj 0.0 1.0 1.0

read_data DataFile

pair_coeff * * 1.0 1.0 1.122462
bond_coeff * 30.0 1.5 1.0 1.0
pair_modify shift yes
timestep 0.010

reset_timestep 0
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

I have 3 fixes applied at the same time on my system but I did not see any issues in terms of relaxation of the polymer chains.

My DataFile contains information on the side length of the simulation box as 22.7956. However, when I run the above script, my first dump file outputted 0 timestep states that my simulation box length is 34.6598.

I would greatly appreciate if you could provide me with an advice on why there is a discrepancy between the side length read by the initial data file and the box length specified in my first dump file at 0 timestep. Should not these length be equal since both files are in its initial state?

Even if the pairwise and bond style along with the fix command was applied at time zero, the box should not immediately inflate this much.

Thank you so much for your time.

Sincerely,

Masato Koizumi

Dear Dr. Axel Kohlmeyer and LAMMPS Users,

Hello Dr. Kohlmeyer. Thank you for your advice. I was curious if I could ask
a question regarding how the interatomic pairwise and bond potentials are
applied at zero timestep.

The initial portion of my script looks as the following where the polymer
chains described in the external data file are allowed to relax by allowing
the volume of the simulation box to fluctuate via fix press/Berendsen.

units lj
atom_style full
neighbor 0.36 bin
neigh_modify delay 2
pair_style lj/cut 1.122462

bond_style fene
special_bonds lj 0.0 1.0 1.0

read_data DataFile

pair_coeff * * 1.0 1.0 1.122462
bond_coeff * 30.0 1.5 1.0 1.0
pair_modify shift yes
timestep 0.010

reset_timestep 0
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

I have 3 fixes applied at the same time on my system but I did not see any
issues in terms of relaxation of the polymer chains.

My DataFile contains information on the side length of the simulation box as
22.7956. However, when I run the above script, my first dump file outputted
0 timestep states that my simulation box length is 34.6598.

1) What happens if you replace "run 100000" with
run 0
write_data NEW_FILE.data

What is size of the box in the "Boundaries" section of NEW_FILE.data ?

2) What happens if you remove (or comment out) the line containing
"fix 2 all press/berendsen iso 0.0 0.0 10.0"?

3) If that helps, then try replacing that line with a different
barostat like fix nph
https://lammps.sandia.gov/doc/fix_nh.html

Good luck

Andrew