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* omat24 example * formatting fixed * remove unused parsed arguments * exists set to True for data download * exists set to True for data download * updated download script to move tar files into subdirectories * bug fixed in normalization of the energy * fixes on omat24 example * black formatting fixed * Update examples/omat24/train.py * formatting fixed --------- Co-authored-by: Massimiliano Lupo Pasini <[email protected]> Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,85 @@ | ||
| import argparse | ||
| import glob | ||
| import logging | ||
| import os | ||
| import shutil | ||
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| DOWNLOAD_LINKS = { | ||
| "train": { | ||
| "rattled-1000": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-1000.tar.gz", | ||
| "rattled-1000-subsampled": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-1000-subsampled.tar.gz", | ||
| "rattled-500": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-500.tar.gz", | ||
| "rattled-500-subsampled": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-500-subsampled.tar.gz", | ||
| "rattled-300": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-300.tar.gz", | ||
| "rattled-300-subsampled": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-300-subsampled.tar.gz", | ||
| "aimd-from-PBE-1000-npt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/aimd-from-PBE-1000-npt.tar.gz", | ||
| "aimd-from-PBE-1000-nvt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/aimd-from-PBE-1000-nvt.tar.gz", | ||
| "aimd-from-PBE-3000-npt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/aimd-from-PBE-3000-npt.tar.gz", | ||
| "aimd-from-PBE-3000-nvt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/aimd-from-PBE-3000-nvt.tar.gz", | ||
| "rattled-relax": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/train/rattled-relax.tar.gz", | ||
| }, | ||
| "val": { | ||
| "rattled-1000": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-1000.tar.gz", | ||
| "rattled-1000-subsampled": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-1000-subsampled.tar.gz", | ||
| "rattled-500": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-500.tar.gz", | ||
| "rattled-500-subsampled": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-500-subsampled.tar.gz", | ||
| "rattled-300": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-300.tar.gz", | ||
| "rattled-300-subsampled": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-300-subsampled.tar.gz", | ||
| "aimd-from-PBE-1000-npt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/aimd-from-PBE-1000-npt.tar.gz", | ||
| "aimd-from-PBE-1000-nvt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/aimd-from-PBE-1000-nvt.tar.gz", | ||
| "aimd-from-PBE-3000-npt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/aimd-from-PBE-3000-npt.tar.gz", | ||
| "aimd-from-PBE-3000-nvt": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/aimd-from-PBE-3000-nvt.tar.gz", | ||
| "rattled-relax": "wget https://dl.fbaipublicfiles.com/opencatalystproject/data/omat/241018/omat/val/rattled-relax.tar.gz", | ||
| }, | ||
| } | ||
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| assert ( | ||
| DOWNLOAD_LINKS["train"].keys() == DOWNLOAD_LINKS["val"].keys() | ||
| ), "data partition names in train do not match with equivalent names in val" | ||
| dataset_names = list(DOWNLOAD_LINKS["train"].keys()) | ||
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| def get_data(datadir, task, split): | ||
| os.makedirs(datadir, exist_ok=True) | ||
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| if (task == "train" or task == "val") and split is None: | ||
| raise NotImplementedError(f"{task} requires a split to be defined.") | ||
|
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| assert ( | ||
| split in DOWNLOAD_LINKS[task] | ||
| ), f'{task}/{split}" split not defined, please specify one of the following: {list(DOWNLOAD_LINKS[task].keys())}' | ||
| download_link = DOWNLOAD_LINKS[task][split] | ||
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| os.makedirs(os.path.join(datadir, task), exist_ok=True) | ||
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| os.system(f"wget {download_link} -P {datadir}") | ||
| filename = os.path.join(datadir, os.path.basename(download_link)) | ||
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| # Move the directory | ||
| new_filename = os.path.join(datadir, task, os.path.basename(download_link)) | ||
| shutil.move(filename, new_filename) | ||
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| logging.info("Extracting contents...") | ||
| os.system(f"tar -xvf {new_filename} -C {os.path.join(datadir, task)}") | ||
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| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument( | ||
| "--data-path", | ||
| type=str, | ||
| default="./dataset", | ||
| help="Specify path to save datasets. Defaults to './dataset'", | ||
| ) | ||
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| args, _ = parser.parse_known_args() | ||
|
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| for task in ["train", "val"]: | ||
| for split in dataset_names: | ||
| get_data( | ||
| datadir=args.data_path, | ||
| task=task, | ||
| split=split, | ||
| ) |
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| @@ -0,0 +1 @@ | ||
| fairchem-core |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,58 @@ | ||
| { | ||
| "Verbosity": { | ||
| "level": 2 | ||
| }, | ||
| "NeuralNetwork": { | ||
| "Architecture": { | ||
| "model_type": "EGNN", | ||
| "equivariance": true, | ||
| "radius": 5.0, | ||
| "max_neighbours": 100000, | ||
| "num_gaussians": 50, | ||
| "envelope_exponent": 5, | ||
| "int_emb_size": 64, | ||
| "basis_emb_size": 8, | ||
| "out_emb_size": 128, | ||
| "num_after_skip": 2, | ||
| "num_before_skip": 1, | ||
| "num_radial": 6, | ||
| "num_spherical": 7, | ||
| "num_filters": 126, | ||
| "edge_features": ["length"], | ||
| "hidden_dim": 50, | ||
| "num_conv_layers": 3, | ||
| "output_heads": { | ||
| "graph":{ | ||
| "num_sharedlayers": 2, | ||
| "dim_sharedlayers": 50, | ||
| "num_headlayers": 2, | ||
| "dim_headlayers": [50,25] | ||
| } | ||
| }, | ||
| "task_weights": [1.0] | ||
| }, | ||
| "Variables_of_interest": { | ||
| "input_node_features": [0, 1, 2, 3], | ||
| "output_names": ["energy"], | ||
| "output_index": [0], | ||
| "output_dim": [1], | ||
| "type": ["graph"] | ||
| }, | ||
| "Training": { | ||
| "num_epoch": 50, | ||
| "perc_train": 0.8, | ||
| "loss_function_type": "mae", | ||
| "batch_size": 32, | ||
| "continue": 0, | ||
| "Optimizer": { | ||
| "type": "AdamW", | ||
| "learning_rate": 1e-3 | ||
| } | ||
| } | ||
| }, | ||
| "Visualization": { | ||
| "plot_init_solution": true, | ||
| "plot_hist_solution": false, | ||
| "create_plots": true | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| { | ||
| "Verbosity": { | ||
| "level": 2 | ||
| }, | ||
| "NeuralNetwork": { | ||
| "Architecture": { | ||
| "model_type": "EGNN", | ||
| "equivariance": true, | ||
| "radius": 5.0, | ||
| "max_neighbours": 100000, | ||
| "num_gaussians": 50, | ||
| "envelope_exponent": 5, | ||
| "int_emb_size": 64, | ||
| "basis_emb_size": 8, | ||
| "out_emb_size": 128, | ||
| "num_after_skip": 2, | ||
| "num_before_skip": 1, | ||
| "num_radial": 6, | ||
| "num_spherical": 7, | ||
| "num_filters": 126, | ||
| "edge_features": ["length"], | ||
| "hidden_dim": 50, | ||
| "num_conv_layers": 3, | ||
| "output_heads": { | ||
| "node": { | ||
| "num_headlayers": 2, | ||
| "dim_headlayers": [200,200], | ||
| "type": "mlp" | ||
| } | ||
| }, | ||
| "task_weights": [1.0] | ||
| }, | ||
| "Variables_of_interest": { | ||
| "input_node_features": [0, 1, 2, 3], | ||
| "output_names": ["forces"], | ||
| "output_index": [2], | ||
| "output_dim": [3], | ||
| "type": ["node"] | ||
| }, | ||
| "Training": { | ||
| "num_epoch": 50, | ||
| "EarlyStopping": true, | ||
| "perc_train": 0.9, | ||
| "loss_function_type": "mae", | ||
| "batch_size": 32, | ||
| "continue": 0, | ||
| "Optimizer": { | ||
| "type": "AdamW", | ||
| "learning_rate": 1e-3 | ||
| } | ||
| } | ||
| }, | ||
| "Visualization": { | ||
| "plot_init_solution": true, | ||
| "plot_hist_solution": false, | ||
| "create_plots": true | ||
| } | ||
| } |
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