ERROR occurs when the in file step is adjusted to 1fs

LAMMPS LAMMPS Beginners
1

ERROR: Domain too large for neighbor bins (src/nbin_standard.cpp:133)
Last command: run 100000, how should I solve this problem, please
My in file code

Model basic Settings

units metal
boundary p p p # Initial periodic boundary condition
atom_style atomic
neighbor 2.0 bin

Simulation step size 1 fs

timestep 1

Read the data file

read_data layerni3.data

Force field setup

pair_style lj/cut 6.0
pair_coeff 1 1 0.0224 3.893 # Bi-Bi
pair_coeff 1 2 0.0182 3.938 # Bi-Te
pair_coeff 2 2 0.0172 3.982 # Te-Te
pair_coeff 1 3 0.104 3.0875 # Bi-Ni
pair_coeff 2 3 0.097 3.132 # Te-Ni
pair_coeff 3 3 0.52 2.282 # Ni-Ni

Calculate the temperature

compute ke1 all ke/atom
variable kb equal 8.625e-5
variable temp1 atom c_ke1/1.5/${kb}

Thermodynamic quantity output

thermo 1000
thermo_style custom step temp pxx pyy pzz press vol

Temperature initialization

velocity all create 300 898758 mom yes rot yes dist gaussian

Energy minimization

min_style cg
minimize 1.0e-6 1.0e-8 10000 100000

Relaxation under NPT ensemble

thermo 2000
thermo_style custom step temp pe ke etotal vol pxx pyy pzz press
fix 1 all npt temp 300 300 0.5 iso 0.0 0.0 0.5
dump 1 all custom 10000 npt.xyz id type x y z
run 100000
unfix 1
undump 1
reset_timestep 0
write_data Gp.data

2

Did you look at the error message page ? For that particular error message:

The domain has become extremely large so that neighbor bins cannot be used. Most likely, one or more atoms have been blown out of the simulation box to a great distance.

On the side note, why are you using a cut-off of 6 Angstroms? Is it a normal value for your type of model?

3

Thank you for your answer. I don’t know how to modify it. Do you have any suggestions

4

That this line:

Your question suggests that you should spend some time learning the basics of LAMMPS. This will save you time and headaches in the future.

5

You have been already reminded once, now for the second time: you are not quoting your input file correctly. Please study and follow the forum guidelines so that your quoted input is properly readable. The better your information is readable and the more consistent and complete it is, the better your chances to get actual help. If we first have to play “20 questions” with you, you are massively reducing the chance that somebody will be interested to help you. If not this time, then the next time and beyond.

More issues and missing context:

  • you do not provide the LAMMPS version you are using, are not saying which platform you are running on and it would be extremely helpful to see your input and the output before the error message.
  • have you visualized your trajectory? that often provides good hints for what is happening
  • what do you mean by “when the file step is ajusted to 1fs”?
  • what kind of system do you simulate. It looks like an alloy. Is it a bulk system? Wouldn’t it be better to use EAM instead of lj/cut?