[lammps-users] Non-bonded interaction using pair_style list

Hi,
I am trying to introduce non-bonded harmonic interaction within a monoatomic system containing N particles. I created the list file as specified in the documentation containing all pairs of atoms(=N^2) with parameters K=10 and r_0=1 for all pairs. However, when I am running the simulation, all forces are evaluated as NaN in the first timestep. This is the case even when I try to carry out a minimization of a random initial configuration. I got the same result when I changed the interaction from ‘harmonic’ to ‘lj126’. Can anyone suggest what is going wrong here? The relevant part of input script is as follows:

region simbox block -4.7 4.7 -4.7 4.7 -4.7 4.7
create_box 2 simbox
create_atoms 1 random 500 2213 simbox
group atype type 1
mass * 1.0
pair_style list list.dat 10.0
pair_coeff * *
velocity all create 2 86452 dist gaussian
variable dt equal 0.001
minimize 1.0e-4 1.0e-6 1000 1000

There is not enough information here to say for certain, but likely you are doing something wrong. Most likely your list.dat file is not correct.

What is your LAMMPS version?

Also, your quoted input must be incomplete. When I try to use it, there is an error about a missing atom map (which is easily fixable, but again underlines that you didn’t provide sufficient information). But with that fixed and a list file of my own using the parameters given, it works without a problem for me (see quoted output below).

Axel.

./lmp -in in.list LAMMPS (8 Apr 2021) using 1 OpenMP thread(s) per MPI task Created orthogonal box = (-4.7000000 -4.7000000 -4.7000000) to (4.7000000 4.7000000 4.7000000) 1 by 1 by 1 MPI processor grid Created 500 atoms create_atoms CPU = 0.001 seconds 500 atoms in group atype Read 124750 (124750/0/0) interacting pairs from list.dat WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) ERROR: Pair style list requires an atom map (src/USER-MISC/pair_list.cpp:372) Last command: minimize 1.0e-4 1.0e-6 1000 1000 libgcov profiling error:/home/akohlmey/compile/lammps/build-test/CMakeFiles/lammps.dir/home/akohlmey/compile/lammps/src/USER-OMP/fix_qeq_reax_omp.cpp.gcda:overwriting an existing profile data with a different timestamp libgcov profiling error:/home/akohlmey/compile/lammps/build-test/CMakeFiles/lammps.dir/home/akohlmey/compile/lammps/src/USER-REAXC/fix_qeq_reax.cpp.gcda:overwriting an existing profile data with a different timestamp [akohlmey@silence build-test] vim in.list
[akohlmey@silence build-test]$ ./lmp -in in.list
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
Created orthogonal box = (-4.7000000 -4.7000000 -4.7000000) to (4.7000000 4.7000000 4.7000000)
1 by 1 by 1 MPI processor grid
Created 500 atoms
create_atoms CPU = 0.001 seconds
500 atoms in group atype
Read 124750 (124750/0/0) interacting pairs from list.dat
WARNING: Using ‘neigh_modify every 1 delay 0 check yes’ setting during minimization (src/min.cpp:188)
Setting up cg style minimization …
Unit style : lj
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 13.81 | 13.81 | 13.81 Mbytes
Step Temp E_pair E_mol TotEng Press
0 2 91373.665 0 91376.659 -37223.765
55 2 2.7360778 0 5.7300778 1.1441384
Loop time of 1.498 on 1 procs for 55 steps with 500 atoms

99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
91373.6646599166 2.7362847693611 2.736077822657
Force two-norm initial, final = 890801.60 135.92910
Force max component initial, final = 43266.408 11.083299
Final line search alpha, max atom move = 0.0013733340 0.015221071
Iterations, force evaluations = 55 79

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total