src/01_batch_data.py

import os
import math

input_dir = "input_data"        
output_dir = "batches"           
batch_size = 1000                
os.makedirs(output_dir, exist_ok=True)

all_files = sorted([
    os.path.join(input_dir, f)
    for f in os.listdir(input_dir)
    if f.endswith(".xyz")
])

n_batches = math.ceil(len(all_files) / batch_size)

for i in range(n_batches):
    batch_files = all_files[i*batch_size : (i+1)*batch_size]
    with open(f"{output_dir}/batch_{i:03d}.txt", "w") as f:
        f.write("\n".join(batch_files))