Error: thermo.cpp:398

Hi,
I am facing this problem and cannot seem to find an appropriate solution. Can someone help me please.

Following is my log.lammps file.

LAMMPS (16 Feb 2016)
#… Initialization …
units metal
boundary p p p
atom_style atomic

#… Atom description …
region reg block 0.0 57.54 0.0 57.54 0.0 57.54
create_box 1 reg
Created orthogonal box = (0 0 0) to (57.54 57.54 57.54)
1 by 2 by 2 MPI processor grid
create_atoms 1 random 686 1234 NULL
Created 686 atoms
mass 1 22.99 #Na

#Dreiding potential information
pair_style lj/cut 15.0
pair_coeff * * 0.05161 3.24
#neighbor 1.0 bin
#neigh_modify every 1 delay 5 check yes

group Na type 1
686 atoms in group Na

#Equilibration
velocity all create 373.0 492825 dist gaussian

timestep 0.001
#thermo_style custom step temp press vol v_den pe etotal
#thermo_modify flush yes
thermo 1000

fix md all nvt temp 373.0 373.0 100

compute kin all ke
compute pot all pe

fix energy all ave/time 1 1 100 c_kin c_pot file ener.txt mode scalar
dump 1 all xyz 100 300_Na.xyz

run 50000
Neighbor list info …
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5 -> bins = 7 7 7
Memory usage per processor = 3.54874 Mbytes
Step Temp E_pair E_mol TotEng Press
0 373 1.654904e+09 0 1.654904e+09 5.567215e+10
ERROR: Lost atoms: original 686 current 663 (…/thermo.cpp:398)

Thanks.

Hi,
I am facing this problem and cannot seem to find an appropriate solution.
Can someone help me please.

this "lost atom" error message is one of the most frequently reported
(and answered) error in this mailing list.
you will have to significantly improve your solution finding skills,
if you cannot find a solution to address this.

as can be seen from your thermo output, by creating atoms at random
positions, you have atoms that are *extremely* close and thus have
very high potential energy. that will converted into kinetic energy
within a few steps, which will accelerate atoms so much, LAMMPS cannot
keep track of them, as they move from subdomain to subdomain.
there are different ways to "unoverlap" atoms in such a situation and
thus avoid the highly unphysical initial state for an MD.

happy solution hunting,

axel.