[lammps-users] Question about boundary command

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1

To whom it may concern:

I'm trying to run lammps on a non-periodic system. The in the input file, I define:

# AIREBO diamond test
units metal
atom_style atomic
boundary s s s

read_data data.xyz

I define a boundary in the input "data.xyz":

....
1003908 atoms

1 atom types

-100 2345.5368250000 xlo xhi
-100 140.0000000000 ylo yhi
-100 1206.4611480000 zlo zhi
....

I did CG relaxation on the system and output xyz in .bin format.
Then I checked the first output and found the xhi, yhi, and zhi are
2291.105300 4.291778 1146.45561 respectively. I understand these are the shrink-wrap box size found by lammps.

However, I found some atoms are shifted at the very first step. For example, in the input "data.xyz", I have an atom shown as below:

5079 1 2269.7992000000 0.0000000000 1.2301024836

and in the output file, the corresponding atom has xyz:
-19.8857 4.2917777947 1.2301024836

I don't understand how this will happen.

I thought the non-periodic option won't make the atoms shift over a box length. Anyone can give me a hint why this happens and point me to a way to avoid this?

Thanks a lot in advance.

Sincerely,

2

When you say it moved a long ways, do you mean after
one step of minimization, or after the entire minimization
process? You are correct that the atom did not move
thru the periodic box, but just a long distance.

You should be able to dump multiple snapshots during
a minimization and via viz, see where things move to.

Steve

3

Thank you Steve.

The problem happens at the very first step or ZEROth step. None of atoms actually moved.

I'm expecting the identical positions of each atom recorded in the output. Contrary to what I expect, some atoms are translated over a box size as if it is periodic.

This is what puzzles me.

Is there any other thing I might miss?

4

Send me you rinput script and data file - I'll take a look.

Steve

5

Oh, sorry about this. I guess I made a mistake. When I transfer the data files I manually moved those atoms in my post-processing script.

Really sorry about this. Thank you anyway.