""" Creates LMDB files with extracted graph features from provided *.extxyz files for the S2EF task. """ import argparse import glob import multiprocessing as mp import os import pickle import random import sys import ase.io import lmdb import numpy as np import torch from tqdm import tqdm from ocpmodels.preprocessing import AtomsToGraphs def write_images_to_lmdb(mp_arg): a2g, db_path, samples, pid = mp_arg db = lmdb.open( db_path, map_size=1099511627776 * 2, subdir=False, meminit=False, map_async=True, ) pbar = tqdm( total=len(samples), position=pid, desc="Preprocessing data into LMDBs", ) idx = 0 for sample in samples: ml_relaxed = ase.io.read(sample, "-1") data_object = a2g.convert(ml_relaxed) sid, _ = os.path.splitext(os.path.basename(sample)) fid = -1 # add atom tags data_object.tags = torch.LongTensor(ml_relaxed.get_tags()) data_object.sid = int(sid) data_object.fid = fid txn = db.begin(write=True) txn.put( f"{idx}".encode("ascii"), pickle.dumps(data_object, protocol=-1), ) txn.commit() idx += 1 pbar.update(1) # Save count of objects in lmdb. txn = db.begin(write=True) txn.put("length".encode("ascii"), pickle.dumps(idx, protocol=-1)) txn.commit() db.sync() db.close() def main(args, split): systems = glob.glob(f"{eval(f'args.{split}')}/*.traj") systems_chunked = np.array_split(systems, args.num_workers) # Initialize feature extractor. a2g = AtomsToGraphs( max_neigh=50, radius=6, r_energy=False, r_forces=False, r_distances=False, r_fixed=True, r_edges=True, ) # Create output directory if it doesn't exist. out_path = f"{args.out_path}_{split}" os.makedirs(out_path, exist_ok=True) # Initialize lmdb paths db_paths = [ os.path.join(out_path, "data.%04d.lmdb" % i) for i in range(args.num_workers) ] pool = mp.Pool(args.num_workers) mp_args = [ ( a2g, db_paths[i], systems_chunked[i], i, ) for i in range(args.num_workers) ] list(pool.imap(write_images_to_lmdb, mp_args)) pool.close() if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument( "--id", required=True, help="Path to ID trajectories", ) parser.add_argument( "--ood-ads", required=True, help="Path to OOD-Ads trajectories", ) parser.add_argument( "--ood-cat", required=True, help="Path to OOD-Cat trajectories", ) parser.add_argument( "--ood-both", required=True, help="Path to OOD-Both trajectories", ) parser.add_argument( "--out-path", required=True, help="Directory to save extracted features. Will create if doesn't exist", ) parser.add_argument( "--num-workers", type=int, default=1, help="No. of feature-extracting processes.", ) args = parser.parse_args() for split in ["id", "ood_ads", "ood_cat", "ood_both"]: main(args, split)