Hello everyone:
Last week , I ran NVT simulation for 144 atoms using a single processor . I ran for 100,000 timesteps, the simulation ran fine. I found a reasonable damping parameter.Currently I am running a NPT simulation for the same number of atoms. NPT conditions =300k and pressure =0bars, pdamp =0.1. I initially ran for 100,000 timesteps on 1 processor, however the job was terminated at 32000 steps. The error message I received is stated below
“lmp_Star:14566 terminated with signal 11 at PC=536a51 SP=7fbfffd190. Backtrace”
I lowered the pdamp value to 0.09, now the error message is “Domain too large for neighbor bins”. I am not too sure how to fix this problem. I used the default skin distance of 2.0 provided by lammps for the neighbor command. Can anyone assist me with this problem?
Format of Output file
units metal
boundary p p p
atom_style charge
pair_style hybrid/overlay buck 10.0 sw coul/long 10.0
kspace_style ewald 8.0
read_data data3.hamid
orthogonal box = (0 0 0) to (16.74 14.78 22.77)
1 by 1 by 1 processor grid
144 atoms
pair_coeff 1 1 buck 4369.01 0.29 0.0 5.5
pair_coeff 1 8 buck 4369.01 0.29 0.0 5.5
pair_coeff 2 2 buck 1171.52 0.29 0.0 5.5
pair_coeff 3 3 buck 452.5051 0.29 0.0 5.5
pair_coeff 6 6 buck 452.5051 0.29 0.0 5.5
pair_coeff 3 6 buck 452.5051 0.29 0.0 5.5
pair_coeff 7 7 buck 21.228 0.35 0.0 5.5
pair_coeff 8 8 buck 4369.01 0.29 0.0 5.5
pair_coeff 1 2 buck 1382.4811 0.29 0.0 5.5
pair_coeff 2 8 buck 1382.4811 0.29 0.0 5.5
pair_coeff 1 3 buck 3557.62 0.29 0.0 5.5
pair_coeff 1 6 buck 3557.62 0.29 0.0 5.5
pair_coeff 3 8 buck 3557.62 0.29 0.0 5.5
pair_coeff 6 8 buck 3557.62 0.29 0.0 5.5
pair_coeff 2 7 buck 430.6566 0.29 0.0 5.5
pair_coeff 2 3 buck 1848.7174 0.29 0.0 5.5
pair_coeff 6 7 buck 248.6324 0.29 0.0 5.5
pair_coeff 3 7 buck 248.6324 0.29 0.0 5.5
pair_coeff * * coul/long
pair_coeff * * sw SiOOO.sw NULL Si O NULL NULL NULL NULL NULL
neighbor 2.0 bin
neigh_modify delay 5
equilibrate
min_style cg
thermo 5
thermo_style custom step lx ly lz
minimize 1.0e-4 1.0e-6 120 1000
Ewald initialization …
G vector = 0.103808
vectors: actual 1d max = 0 -2147483648 -2147483648
Memory usage per processor = 3.51844e+13 Mbytes
Step Lx Ly Lz
0 16.74 14.78 22.77
5 16.74 14.78 22.77
7 16.74 14.78 22.77
Loop time of 0.0248649 on 1 procs for 7 steps with 144 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4099.54952324 -4231.36772167 -4231.51619502
Force two-norm initial, final = 127.971 33.0275
Force max component initial, final = 21.5803 5.74964
Final line search alpha, max atom move = 0.00013569 0.000780168
Iterations, force evaluations = 7 21
Pair time () = 0.0240731 (96.8156)
Kspce time () = 5.17368e-05 (0.208072)
Neigh time () = 0 (0)
Comm time () = 0.000520468 (2.09318)
Outpt time () = 1.00136e-05 (0.0402719)
Other time () = 0.00020957 (0.842834)
Nlocal: 144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2099 ave 2099 max 2099 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 12900 ave 12900 max 12900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 25800 ave 25800 max 25800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25800
Ave neighs/atom = 179.167
Neighbor list builds = 0
Dangerous builds = 0
300-NPT
velocity all create 300.0 5812775
fix 1 all npt 300.0 300.0 0.001 xyz 0.0 0.0 1.0 drag 1.0
fix 1 all npt 300 300 0.001 aniso 0.0 0.0 0.0 0.0 0.0 0.0 0.09
thermo 200
thermo_style custom step temp etotal press
thermo_modify flush yes
timestep 0.0001
run 100000
Ewald initialization …
G vector = 0.103808
vectors: actual 1d max = 0 -2147483648 -2147483648
Memory usage per processor = 3.51844e+13 Mbytes
Step Temp TotEng Press
7 300 -4225.9709 -9845.3832
200 305.31236 -4219.7988 8593.4767
400 296.33348 -4279.1396 -3136.6414
600 300.67251 -4308.4551 -9233.2729
800 299.01002 -4284.7804 4482.8603
1000 299.83777 -4269.7065 11694.432
1200 297.47747 -4299.2658 -3965.9411
1400 301.44018 -4301.9263 -293.11076
1600 298.91999 -4313.6304 -2490.9204
1800 301.88908 -4314.859 -3598.6121
2000 298.77294 -4308.8824 1856.1262
2200 308.06267 -4325.8125 -2941.8701
2400 0.082293505 -4413.0225 87622.221
2600 0.090123374 -4452.2817 -10144.745
2800 0.091723152 -4319.5728 -11660.254
3000 2.7249169 -4504.5926 -81281.119
3200 1.4441016e-05 -4321.3052 20736.807
3400 0.00019945601 -4212.1929 98612.497
3600 0.0032489983 -4466.7367 -55776.185
3800 0.56453887 -4596.3082 -51099.127
4000 0.012043746 -4037.4378 97998.002
4200 0.035817182 -4002.4483 136178.7
4400 0.16948562 -4243.8126 -31846.715
4600 1.6603359 -4342.3423 -113296.47
4800 233.75893 -4264.4707 -2686.2819
5000 421.0063 -4169.8963 106552.81
5200 44373.533 -5356.1305 -73249.315
ERROR: Domain too large for neighbor bins
Shanique Murray