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import argparse |
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import bz2 |
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import json |
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from pathlib import Path |
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from tqdm.auto import tqdm |
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from ase import Atoms |
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from ase.calculators.singlepoint import SinglePointCalculator |
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from ase.io import write, read |
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from pymatgen.core import Structure |
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def parse_args(): |
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parser = argparse.ArgumentParser() |
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parser.add_argument("--src_path", type=str, required=True) |
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parser.add_argument("--dst_dir", type=str, required=True) |
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return parser.parse_args() |
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def main(src_path: Path | str, dst_dir: Path | str): |
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"""Extracts the structures from a bz2 compressed json file and writes them to an extended xyz file.""" |
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if isinstance(src_path, str): |
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src_path = Path(src_path) |
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if isinstance(dst_dir, str): |
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dst_dir = Path(dst_dir) |
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dst_dir.mkdir(exist_ok=True, parents=True) |
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with bz2.open(src_path, "rb") as f: |
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data = json.load(f) |
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assert isinstance(data, dict) |
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for alex_id, u in tqdm(data.items(), desc="Extracting structures"): |
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for calc_id, v in enumerate(u): |
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for ionic_step, w in enumerate(v["steps"]): |
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atoms = Structure.from_dict(w["structure"]).to_ase_atoms() |
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results = { |
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"energy": w["energy"], |
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"forces": w["forces"], |
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"stress": w["stress"], |
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} |
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atoms.calc = SinglePointCalculator(atoms=atoms, **results) |
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atoms.info = { |
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"alex_id": alex_id, |
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"calc_id": calc_id, |
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"ionic_step": ionic_step, |
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} |
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traj_file = dst_dir / f"{atoms.get_chemical_formula()}.traj" |
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exist = False |
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if traj_file.exists(): |
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traj = read(traj_file, index=":") |
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for frame in traj: |
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assert isinstance(frame, Atoms) |
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if frame.info == atoms.info: |
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exist = True |
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break |
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if not exist: |
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write( |
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traj_file, |
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atoms, |
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append=True, |
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) |
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if __name__ == "__main__": |
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args = parse_args() |
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main(args.src_path, args.dst_dir) |
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