update

preprocess.py

@@ -1,10 +1,4 @@
-# # %%
-# from datasets import load_dataset
 
-# dataset = load_dataset("atomind/alexandria", name='1D', streaming=True)
-
-# print(dataset)
-# # %%
 import argparse
 import bz2
 import json
@@ -14,7 +8,7 @@ from tqdm.auto import tqdm
 
 from ase import Atoms
 from ase.calculators.singlepoint import SinglePointCalculator
-from ase.io import write, read
+from ase.io import write, iread
 from pymatgen.core import Structure
 
 
@@ -41,7 +35,7 @@ def main(src_path: Path | str, dst_dir: Path | str):
 
     assert isinstance(data, dict)
 
-    for alex_id, u in tqdm(data.items(), desc="Extracting structures"):
+    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()
@@ -59,12 +53,14 @@ def main(src_path: Path | str, dst_dir: Path | str):
                     "calc_id": calc_id,
                     "ionic_step": ionic_step,
                 }
+                
+                elements = sorted(set(atoms.get_chemical_symbols()))
 
-                traj_file = dst_dir / f"{atoms.get_chemical_formula()}.traj"
+                traj_file = dst_dir / f"{'-'.join(elements)}.extxyz"
 
                 exist = False
                 if traj_file.exists():
-                    traj = read(traj_file, index=":")
+                    traj = iread(traj_file, index=":")
                     for frame in traj:
                         assert isinstance(frame, Atoms)
                         if frame.info == atoms.info: