How to load LAMMPS data file with chemfiles.py

[Roy-Kid]

I use python to load the chemfiles/tests-data, for example lammps-data/solvated.lmp. But it raises an error that ChemfilesError: can not find a format associated with the '.lmp' extension. In the supported formats page, the extension of lammps data is false. Could you please tell me how to load lammps data? I want to extract topology info.

[Luthaf]

Since there is no standard for extension for LAMMPS data files, you'll need to specify the format explicitly when opening the file:

from chemfiles import Trajectory

trajectory = Trajectory("lammps-data/solvated.lmp", "r", format="LAMMPS Data")
frame = trajectory.read()

# depending on what's inside the data file, you might want to guess the bonds using a distance-based algorithm
# frame.guess_bonds()

topology = frame.topology

(you can always specify a format, and it will override the guess based on file extension, for example Trajectory("solvated.mol", "r", format="XYZ") will try to read the file as an XYZ file)