Data File Reader

The DataFileParser handles LAMMPS data files containing complete system definitions. The UniverseSequence provides a convenient way to have these data files read into the Universe objects.

import os
from pathlib import Path

from pylimer_tools_cpp import UniverseSequence


def _find_fixtures_dir() -> Path:
    for cur in (
        [Path(__file__).resolve().parent] if "__file__" in globals() else []
    ) + [Path.cwd()]:
        for p in [cur] + list(cur.parents):
            candidate = p / "tests" / "pylimer_tools" / "fixtures"
            if candidate.is_dir():
                return candidate
    return Path("tests/pylimer_tools/fixtures").resolve()


_fixtures_dir = _find_fixtures_dir()
base_structure_path = str(_fixtures_dir / "structure")

# Load a single data file
data_file = os.path.join(
    base_structure_path,
    "melt_83_a_100.structure.out",
)
one_universe_seq = UniverseSequence()
one_universe_seq.initialize_from_data_sequence([data_file])
universe = one_universe_seq.at_index(0)

# Load multiple data files as a sequence
sequence = UniverseSequence()
sequence.initialize_from_data_sequence(
    [
        os.path.join(
            base_structure_path,
            "3d-diamond-lattice_10x10x10_a_3_d_0.85_imperfect.structure.out",
        ),
        os.path.join(
            base_structure_path,
            "3d-diamond-lattice_10x10x10_a_3_d_0.85_v_0.V-fixed.structure.out",
        ),
    ]
)
for universe in sequence:
    print(f"Loaded universe with {universe.get_nr_of_atoms()} atoms")

Loaded universe with 56000 atoms
Loaded universe with 56000 atoms

Please note that the hybrid and tdpd atom styles are not fully supported.

If your data files don’t hint the atom style in the line that starts with “Atom”, you should specify it manually, see read() and set_data_file_atom_style().