Extract Trajectory Frame to Data File

Take a later entry from a LAMMPS trajectory and save it as a data file.

import os
from pathlib import Path

from pylimer_tools_cpp import DataFileWriter, UniverseSequence

if not os.path.exists("generated_structures"):
    os.makedirs("generated_structures")

For large trajectories, frames are loaded on-demand Load a LAMMPS dump trajectory file (replace with your file)

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()
file_path = str(_fixtures_dir)
sequence = UniverseSequence()
sequence.initialize_from_dump_file(
    initial_data_file=os.path.join(file_path, "big_dump_file_data.out"),
    dump_file=os.path.join(file_path, "big_dump_file.lammpstrj"),
)
# Get the last frame, for example
final_universe = sequence.at_index(len(sequence) - 1)

# Write as data file
writer = DataFileWriter(final_universe)
writer.config_include_angles(True)
writer.write_to_file("generated_structures/final_configuration.data")