[lammps-users] Reading in positions in text-files

Dear Mailinglist,

How does reading in a text-file with read_data work exactly? Consider a text file with the atomar positions as explained in (1). The header section will include boundaries of the form xlo xhi etc. Lets assume that we want to restore from this file a setup with lateral periodic boundary conditions (normal could be shrink-wrapped). Do the specified boundaries represent the periodic simulation box or the extremal positions of particles?

I’m wondering about this because I made an experiment as follows:
A lateral periodic crystalline substrate is relaxed to E->minimal and p_lateral->0. Afterwards this configuration is saved as restart_file and as text-file in the above format. Then a new run is started reading in the positions with both methods. Using the binary restart_file everything seems nice; using the text-file there are small oscillations in the lateral pressure.

What would be the recommened file format to read in saved configurations?

Best regards:

(1) http://lammps.sandia.gov/doc/read_data.html

In the data file, the xlo/xhi are the periodic boundaries. You might
get oscillations due to the data file being lower precision coords
than a binary restart file. You could alter restart2data.cpp (if that's
how you're creating it) to write out higher precision coords.


Hi Steve,

The coordinates were written out with %10.10f from a binary dump-file.

Best regards:

2007/12/6, Steve Plimpton < sjplimp@…24…>: