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