[lammps-users] Question about lammps bonding.

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1

Does the order in which the bonds is listed in the lammps data file affect
the outcome?

For example, for a very small polymer, atom 1 is bonded to atom 3, atom 2
to atom 3...etc.

1 3
2 3
3 6 (listing of bonds)
4 6
5 6

would lammps read the below listing of bonds and do the same thing as the
above listing of bonds?

3 1
3 2 (same listing of bonds just in different order)
3 6
4 6
5 6

Because, I notice if I switch 1 3 for 3 1, I get different coordinates.
Also, if I put in the first list it says "1 = MaxBonds/Atom," but if I put
in the second list it says "3 = MaxBonds/Atom"

3 1
3 2 (this one also gives me different coordinates from the others)
3 6
6 4
6 5

So does the order of bond listings matter, and if I say 3 1 instead of like
1 3 will it make something that is not the polymer I want it to make?

Thank you,

Alexandru Bacanu,

Undergraduate, University of North Carolina at Chapel Hill

2

No, the order shouldn't matter. See: http://lammps.sandia.gov/doc/read_data.html, specifically the section on Bonds. If that doesn't help, you might try sending your input.

Paul

3

I assume you are listing the 2 atoms in the bond below, and not
getting confused by the first numbers on the bond lines, which is
just a counter and the bond types. There should be
no difference if you list a bond as 1-3 vs 3-1. The bond might
get assigned to atom 1 vs atom 3 (changing the bonds per atom)
but that doesn't matter. There also might be a slight
difference over long times between 2 runs setup this way due to
numeric round-off,
but that's it.

Steve