Extract Trajectory Frame to Data File

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

import os

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)

file_path = os.path.join(
    os.getcwd(),
    "../..",
    "tests/pylimer_tools/fixtures/",
)
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")