process_cif.py

import os
from tqdm import tqdm
from ase.io import read, write
from pymatgen.io.cif import CifParser
from multiprocessing import Pool, cpu_count
import warnings

warnings.filterwarnings("ignore")

# Define your input and output folders
input_folder = "/users/PAS2490/marcusshen/cmame/Data/CSD_non_disordered/CSD_non_disordered/"
output_folder_ase = "/users/PAS2490/marcusshen/cmame/Data/CSD_non_disordered/CSD_non_disordered/cleaned_ase/"
output_folder_pymatgen = "/users/PAS2490/marcusshen/cmame/Data/CSD_non_disordered/CSD_non_disordered/cleaned_pymatgen/"

# Create output directories if they do not exist
os.makedirs(output_folder_ase, exist_ok=True)
os.makedirs(output_folder_pymatgen, exist_ok=True)

# Get the list of CIF files in the input folder
cif_files = [f for f in os.listdir(input_folder) if f.endswith(".cif")]

def process_file(file_name):
    input_path = os.path.join(input_folder, file_name)
    ase_output_path = os.path.join(output_folder_ase, file_name)
    pymatgen_output_path = os.path.join(output_folder_pymatgen, file_name)

    try:
        # Step 1: Use ASE to clean the structure and save to output folder
        structure = read(input_path)
        write(ase_output_path, structure)

        # Step 2: Use Pymatgen to further clean and save the structure
        parser = CifParser(ase_output_path)
        structure_pymatgen = parser.get_structures()[0]  # Extract the first structure
        structure_pymatgen.to(filename=pymatgen_output_path)
    except Exception as e:
        return f"Error processing file {file_name}: {e}"
    return f"Successfully processed {file_name}"

if __name__ == "__main__":
    # Use a Pool to process files in parallel
    num_workers = cpu_count()  # Use all available CPUs
    with Pool(processes=num_workers) as pool:
        # Use tqdm for a progress bar
        results = list(tqdm(pool.imap(process_file, cif_files), total=len(cif_files), desc="Processing CIF files"))
    
    # Print results
    for result in results:
        if "Error" in result:
            print(result)