About error: Too many neighbor bins

Dear All

I got this error : ERROR on proc 0: Too many neighbor bins (src/nbin_standard.cpp:184)

And also I found the volume extremely expands

error message is like below:

Total # of neighbors = 86940
Ave neighs/atom = 14.49
Neighbor list builds = 100
Dangerous builds = 100
System init for write_data ...
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 1000
  Time step     : 0.001
Per MPI rank memory allocation (min/avg/max) = 2.928 | 2.952 | 3.294 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
    1000         7000   -326.61347            0    5101.4078    7670.1367    861066.14 
2000 3485.5920030450051854 0.43327922033638888166 36.963613110313822574
3000 3507.9648037165675305 0.44720983046468404387 61.488036597323116439
4000 3509.8791934372584365 0.45249004284686034083 100.16406584557960002
5000 3536.8047788657240744 0.4568187591803601344 161.16134695125921894
6000 3469.9650775442855775 0.44834846569073799616 257.0265162327562507
7000 3447.3664440617676519 0.44553281857982057756 406.91774065922635373
8000 3552.7601927747955415 0.4591537592853532912 640.53718002872938087
9000 3501.92497748386495 0.45258388714695807487 1003.2774788280752318
10000 3493.8862738989341779 0.45154497633662299405 1564.4585278641854984
11000 3517.4110125855900151 0.45458528066849163141 2431.5788338047673278
ERROR on proc 0: Too many neighbor bins (src/nbin_standard.cpp:184)
Last command: run 500000
ERROR on proc 1: Too many neighbor bins (src/nbin_standard.cpp:184)
Last command: run 500000

My input is like this

units metal
boundary p p p



atom_modify map yes


read_data SiO2.data   # Unit cell of SiO2
replicate 5 5 8
pair_style vashishta
pair_coeff * * SiO2.vashishta Si O


fix myprint all print 1000 "$(step) $(temp) $(etotal/atoms) $(lx/3)" file e.dat

min_style cg
minimize 1e-9 1e-3 100 100
write_data SiO2_after_min.data

velocity all create 7000 123456
fix mynpt all  npt temp 3500 3500 0.01 iso 0 0 0.1
run 1000

velocity all create 7000 123456
fix mynpt all  npt temp 3500 3500 0.01 iso 0 0 0.1
run 500000

write_data SiO2_after_min.data

I checked input structure and potential and they looks fine.

How can I revised this?

Best regards

The reason the box expands (which likely causes the error) is that you use a barostat set to 0 pressure, when you’re starting configuration has a pressure of ~7670. Is there a reason you use 0 pressure instead of something like atmospheric pressure?

1 Like

Please note that you have a lot of “dangerous builds” that is not a good sign. You probably need to change your neighbor list settings to compute it more frequently.

Have you checked with the melting and - more importantly - boiling point of your material?
If your system is heated beyond the boiling point, then it will expand a lot.
Also please check how well the potential parameters are supposed to model your compound at this temperature, and what melting and boiling point are for the potential (which may not be exactly the same as in experiments, after all this is just a model). Also, some manybody potential parameters can only be applied to solids or only to liquids.

I would first run with fix nvt and let the system equilibrate for temperature first before also equilibrating for pressure.

But if your system is supposed to evaporate, then I would just define the target volume and density and use fix nvt. For gas there is not much of a point of using fix npt.

1 Like

Thanks for your comments.
Now I running by changing the pressure condition . :slight_smile:

Thanks for your kind comments. :smile:
you are right.

So. I first run the stabilization by nve and nvt.

as you mentioned I need to do first make thermal equilibrium of the system.