pymatgen.io.lammps.outputs module¶
This module implements classes and methods for processing LAMMPS output files (log and dump).
-
class
LammpsDump
(timestep, natoms, box, data)[source]¶ Bases:
monty.json.MSONable
Object for representing dump data for a single snapshot.
Base constructor.
- Parameters
timestep (int) – Current timestep.
natoms (int) – Total number of atoms in the box.
box (LammpsBox) – Simulation box.
data (pd.DataFrame) – Dumped atomic data.
-
parse_lammps_dumps
(file_pattern)[source]¶ Generator that parses dump file(s).
- Parameters
file_pattern (str) – Filename to parse. The timestep wildcard (e.g., dump.atom.’*’) is supported and the files are parsed in the sequence of timestep.
- Yields
LammpsDump for each available snapshot.
-
parse_lammps_log
(filename='log.lammps')[source]¶ Parses log file with focus on thermo data. Both one and multi line formats are supported. Any incomplete runs (no “Loop time” marker) will not be parsed.
Notes
SHAKE stats printed with thermo data are not supported yet. They are ignored in multi line format, while they may cause issues with dataframe parsing in one line format.
- Parameters
filename (str) – Filename to parse.
- Returns
[pd.DataFrame] containing thermo data for each completed run.