|
|
| 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) |
|
|
