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