[lammps-users] Configuration file.

I use lammps for both parallel and serial simulations. In the configuration file of parallel simulations, the atoms coordinates, are not at the same order as in the input file. Is that a problem in compilation ? If it is not, how can I , take the atoms at the correct order ?

the reason they are not in order is because of the fact that atoms are spatially distributed on different parallel machines. I think when you call dump, they get dumped machine by machine (by default). If you want your atoms to be in order, you could use some options (such as dump xyz). Please read dump and dump_modify commands sections of the manual.

From the dump doc page:

When LAMMPS is running in parallel, the atom information written to
dump files (typically one line per atom) may be written in an
indeterminate order. This is because data for a single snapshot is
collected from multiple processors. This is always the case for the
{atom}, {bond}, and {custom} styles. It is also the case for the
{xyz} style if the dump group is not {all}. It is not the case for
the {dcd} and {xtc} styles which always write atoms in sorted order.
So does the {xyz} style if the dump group is {all}.

Steve

I use lammps for both parallel and serial simulations. In the configuration file of parallel simulations, the atoms coordinates, are not at the same order as in the input file. Is that a problem in compilation ? If it is not, how can I , take the atoms at the correct order

Not at all. From the documentation (LAMMPS Molecular Dynamics Simulator):

"When LAMMPS is running in parallel, the atom information written to
dump files (typically one line per atom) may be written in an
indeterminate order. This is because data for a single snapshot is
collected from multiple processors."