"Domain too large for neighbor bins" error but no significant change of domain

LAMMPS LAMMPS Beginners
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1

Dear Sir,

I am trying to simulate gliding between hydroxylapatite and titanium oxide. I am using version of LAMMPS 24 Dec 2020 in workstation. Because I am newcomer, it is impossible to upload input file. I will provide my input information below.

Here is initial information of system.
units metal
dimension 3
boundary p p s
atom_style full

The atomic model includes 2650 atoms which are belonged to 7 types (1-Ca, 2-P, 3-O, 4-O, 5-H, 6-Ti, 7-O). Potential parameters are following:
pair_style hybrid/overlay lj/class2 9.6 coul/wolf 0.2 9.6 buck 12 lj/cut 6.0

pair_coeff	1	1	lj/class2	0.010403121	3.55
pair_coeff	1	2	lj/class2	0.010538514	4.15596616
pair_coeff	1	3	lj/class2	0.000119856	3.525443145
pair_coeff	1	4	lj/class2	0.000444298	3.685565322
pair_coeff	1	5	lj/class2	7.69584E-07	3.163151757
pair_coeff	2	2	lj/class2	0.010836584	4.5
pair_coeff	2	4	lj/class2	0.000401311	4.221196028
pair_coeff	2	5	lj/class2	6.94919E-07	4.009185222
pair_coeff	3	3	lj/class2	0.002384049	3.5
pair_coeff	3	4	lj/class2	0.001690174	3.665276256
pair_coeff	3	5	lj/class2	3.06057E-05	3.118640711
pair_coeff	4	4	lj/class2	0.003467707	3.8
pair_coeff	5	5	lj/class2	0.000563502	1.098

pair_coeff	6	7	buck		16957.7		0.194		12.593
pair_coeff	6	6	buck		31120.4		0.154		5.247
pair_coeff	7	7	buck		11782.8		0.234		30.222

pair_coeff	1	6	lj/cut		0.014018	3.296483
pair_coeff	2	6	lj/cut		0.013449	3.809286
pair_coeff	3	6	lj/cut		0.007655	3.357039
pair_coeff	4	6	lj/cut		0.007655	3.357039
pair_coeff	5	6	lj/cut		0.006566	30047523
pair_coeff	1	7	lj/cut		0.029760	3.451346
pair_coeff	2	7	lj/cut		0.029868	3.889502
pair_coeff	3	7	lj/cut		0.015000	3.500000
pair_coeff	4	7	lj/cut		0.015000	3.500000
pair_coeff	5	7	lj/cut		0.010959	3.263471

pair_coeff	*	*	coul/wolf

In first stage of simulation, system is minimized using cg algorithm. Then, gliding process is performed with NVE ensemble method using following commands.
#MINIMIZE
minimize 1.0e-4 1.0e-6 100 1000
min_style cg

#GLIDING
reset_timestep 0
timestep 0.0001
velocity all create 300 12345 mom yes rot yes dist gaussian

#FIX_COMMANDS
fix 1 all nve
fix 2 1 addforce 0 0 -0.00261
fix 3 3 setforce 0 0 0
fix 4 all temp/rescale 1 300 300 0.02 1
fix 5 1 move linear 1 0 0

#THERMAL
thermo 1 
thermo_style custom step lx ly lz pxx pyy pzz pxy pxz pyz pe ke etotal press vol density temp

run 1.0E7

In this stage, simulation just performed only 29 steps then error “Domain too large for neighbor bins” is reported like in this image.

image
image1103Ă—739 36 KB

Could you give me some instruction to solve this problem?
Thank you.

2

Hello sir,
May I ask your error: “Domain too large for neighbor bins” is the problem solved? I have encountered the same problem now, if you have a good solution, can you tell me? Thank you very much.
Jackie

3

Dear Long_zhou,

I have solve this problem (in my cases)
There are 2 reasons that I usually meet.

  1. Neighbor bins are small. Modify bin size using neigh_modify command is work well in this case.
  2. Initial geometry is too bad (when I ask in this topic). In this situation, we could check atomic coordinations from the input.

Thank you and Best regards.

1 Like
4

Sincere gratitude for your reply and help, the problem I have encountered has been resolved.

Jackie