Lammps

Marcin Wojdyr edited this page Dec 28, 2010 · 6 revisions

LAMMPS log files contain both text and numeric data. The format of data from MD run can be customized by LAMMPS command thermo_style, e.g.:

thermo_style  custom  step c_gbT press pxx pyy pzz pxy pxz pyz v_dx v_dy pe etotal c_lsurfT

Each block of data from MD run has a header, e.g.:

Step gbT Press Pxx Pyy Pzz Pxy Pxz Pyz dx dy PotEng TotEng lsurfT

If the file starts with "LAMMPS (" string, fityk recognizes that this is LAMMPS log files, and implicitly uses last-line-header option when reading the file. That's the only LAMMPS-specific feature of fityk. This should be enough to parse most of the log files.

The data is NOT displayed correctly if the style of thermodynamic data (thermo_style) is changed between MD runs.

(let me know if there are other cases not handled properly - Marcin Wojdyr)

All the columns can be read from the command line:

$ fityk /tmp/log.D53-0-x2y25.gz:1:2..::

or from GUI, using Data > Load File dialog.

img/lammps2.png img/lammps3.png