errors in a naive example

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1

Hi all:

I heard the best way to learn is to practice. As my first run, I do a methane molecule, only harmonic bond is considered. However, I got an error like:
ERROR: Atom sorting has bin size = 0.0.
I find some information on this error in doc@…2508… as well as by google. However, I can not understand. Please be patient to go through my input files and give me some advice on why this error would occur and how can I fix it. Many thanks!

my input files:
########## in.CH4 ###########
units metal
boundary f f f
atom_style full
bond_style harmonic
read_data data.CH4
fix 1 all nve
thermo 10
timestep 1.0
run 100

########## data.CH4 ###########

5 atoms
4 bonds
2 atom types
1 bond types

0 500 xlo xhi
0 500 ylo yhi
0 500 zlo zhi

Masses

1 12.0000
2 1.0080

Atoms

1 1 1 0.1 100 100 100
2 1 2 0.2 100.019804 100.498181 100.961302
3 1 2 0.3 100.969898 100.439106 100.199047
4 1 2 0.4 100.236513 100.719141 100.774359
5 1 2 0.5 100.753123 100.778237 100.012120

Bond Coeffs

1 0.28 1.087

Bonds

1 1 1 2
2 1 1 3
3 1 1 4
4 1 1 5

2

Hi all:

I heard the best way to learn is to practice. As my first run, I do a
methane molecule, only harmonic bond is considered. However, I got an error
like:
ERROR: Atom sorting has bin size = 0.0.
I find some information on this error in [email protected]... as well as by google.
However, I can not understand. Please be patient to go through my input
files and give me some advice on why this error would occur and how can I
fix it. Many thanks!

your input is "too naiive", i.e. it leaves out non-bonded interactions, which
are associated with a cutoff, which in turn is required to determine the
bin size that is used when sorting atoms.

you can set this binsize manually via atom_modify,
or just define a reasonable pair_style (and cutoff).

cheers,
    axel.