Dear All, I have been trying to understand the basic mechanics of SiC oxidation I have read several papers that using ReaxFF MD. I’m totally new to MD anyhow I have managed to prepare a data file and LAMMPS script. My question is that after the simulation lammps output file shows different atoms arrangement (e.g. in data file carbon changed to si in output file). I double checked everything but I could not figure it out what is causing the problem. Input data and script are attached. Only small part of output file is attached due to the large file size.
Best regards
Garip
output_reduced.xyz (195 KB)
sic_h2o_o2.xyz (346 KB)
SiC_h2o_o2.lmp (1.23 KB)
LAMMPS has options to sort the output of a dump file. If it is is unsorted
it could be a confusing order to you, i.e. different when
you run in parallel with different numbers of procs.
The dump doc page says xyz files should be sorted by default. They also
will have the atom type in the first column. But you have the element in
the first column, which would require a dump_modify command, which
I don’t see in your input script. So how did you produce that output file?
I suggest you first try writing a native LAMMPS dump file with the atom
IDs. They you will see whether it is sorted or not and can verify that
atoms have not changed their type. Those files are unsorted by
default, but you can change that with dump_modfy sort.
Steve