Dump File Reader

The DumpFileReader processes LAMMPS trajectory files. Is has a practical interface to read frames from a trajectory file and access them as Universe objects in the UniverseSequence class.

Trajectory contains 1 frames
Dump file contains 3 frames

import os
from pathlib import Path

from pylimer_tools_cpp import DumpFileReader, UniverseSequence

# Load trajectory data
sequence = 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()
file_path = str(_fixtures_dir)
sequence.initialize_from_dump_file(
    initial_data_file=os.path.join(file_path, "lammps_data_file_small.out"),
    dump_file=os.path.join(file_path, "lammps_dump_small.lammpstrj"),
)

print(f"Trajectory contains {len(sequence)} frames")

# Access specific frames
first_frame = sequence.at_index(0)
last_frame = sequence.at_index(len(sequence) - 1)  # Last frame

dump_file_reader = DumpFileReader(
    os.path.join(file_path, "lammps_dump_small_3step.lammpstrj")
)
print(f"Dump file contains {dump_file_reader.get_length()} frames")