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Pytest fix
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Lines changed: 10 additions & 149 deletions

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‎alignn/examples/sample_data/config_example.json‎

Lines changed: 1 addition & 83 deletions
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{
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"version": "112bbedebdaecf59fb18e11c929080fb2f358246",
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"dataset": "user_data",
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"target": "target",
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"atom_features": "cgcnn",
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"neighbor_strategy": "k-nearest",
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"id_tag": "jid",
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"dtype": "float32",
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"random_seed": 123,
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"classification_threshold": null,
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"n_val": null,
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"n_test": null,
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"n_train": null,
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"train_ratio": 0.8,
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"val_ratio": 0.1,
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"test_ratio": 0.1,
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"target_multiplication_factor": null,
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"epochs": 3,
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"batch_size": 2,
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"weight_decay": 1e-05,
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"learning_rate": 0.001,
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"filename": "A",
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"warmup_steps": 2000,
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"criterion": "mse",
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"optimizer": "adamw",
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"scheduler": "onecycle",
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"pin_memory": false,
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"save_dataloader": false,
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"write_checkpoint": true,
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"write_predictions": true,
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"store_outputs": true,
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"progress": true,
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"log_tensorboard": false,
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"standard_scalar_and_pca": false,
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"use_canonize": true,
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"num_workers": 0,
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"cutoff": 8.0,
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"cutoff_extra": 3.0,
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"max_neighbors": 12,
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"keep_data_order": true,
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"normalize_graph_level_loss": false,
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"distributed": false,
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"data_parallel": false,
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"n_early_stopping": null,
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"output_dir": "temp",
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"use_lmdb": true,
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"model": {
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"name": "alignn_atomwise",
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"alignn_layers": 4,
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"gcn_layers": 4,
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"atom_input_features": 92,
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"edge_input_features": 80,
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"triplet_input_features": 40,
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"embedding_features": 64,
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"hidden_features": 256,
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"output_features": 1,
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"grad_multiplier": -1,
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"calculate_gradient": false,
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"atomwise_output_features": 0,
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"graphwise_weight": 1.0,
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"gradwise_weight": 1.0,
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"stresswise_weight": 0.0,
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"atomwise_weight": 0.0,
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"link": "identity",
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"zero_inflated": false,
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"classification": false,
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"force_mult_natoms": false,
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"energy_mult_natoms": false,
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"include_pos_deriv": false,
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"use_cutoff_function": false,
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"inner_cutoff": 3.0,
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"stress_multiplier": 1.0,
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"add_reverse_forces": true,
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"lg_on_fly": true,
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"batch_stress": true,
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"multiply_cutoff": false,
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"use_penalty": true,
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"extra_features": 0,
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"exponent": 5,
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"penalty_factor": 0.1,
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"penalty_threshold": 1.0
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}
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}
1+
{"version": "112bbedebdaecf59fb18e11c929080fb2f358246", "dataset": "user_data", "target": "target", "atom_features": "cgcnn", "neighbor_strategy": "k-nearest", "id_tag": "jid", "dtype": "float32", "random_seed": 123, "classification_threshold": null, "n_val": null, "n_test": null, "n_train": null, "train_ratio": 0.8, "val_ratio": 0.1, "test_ratio": 0.1, "target_multiplication_factor": null, "epochs": 3, "batch_size": 2, "weight_decay": 1e-05, "learning_rate": 0.001, "filename": "A", "warmup_steps": 2000, "criterion": "mse", "optimizer": "adamw", "scheduler": "onecycle", "pin_memory": false, "save_dataloader": false, "write_checkpoint": true, "write_predictions": true, "store_outputs": true, "progress": true, "log_tensorboard": false, "standard_scalar_and_pca": false, "use_canonize": true, "num_workers": 0, "cutoff": 8.0, "cutoff_extra": 3.0, "max_neighbors": 12, "keep_data_order": true, "normalize_graph_level_loss": false, "distributed": false, "data_parallel": false, "n_early_stopping": null, "output_dir": "temp", "use_lmdb": true, "model": {"name": "alignn_atomwise", "alignn_layers": 4, "gcn_layers": 4, "atom_input_features": 92, "edge_input_features": 80, "triplet_input_features": 40, "embedding_features": 64, "hidden_features": 256, "output_features": 1, "grad_multiplier": -1, "calculate_gradient": false, "atomwise_output_features": 0, "graphwise_weight": 1.0, "gradwise_weight": 1.0, "stresswise_weight": 0.0, "atomwise_weight": 0.0, "link": "identity", "zero_inflated": false, "classification": false, "force_mult_natoms": false, "energy_mult_natoms": false, "include_pos_deriv": false, "use_cutoff_function": false, "inner_cutoff": 3.0, "stress_multiplier": 1.0, "add_reverse_forces": true, "lg_on_fly": true, "batch_stress": true, "multiply_cutoff": false, "use_penalty": true, "extra_features": 0, "exponent": 5, "penalty_factor": 0.1, "penalty_threshold": 1.0}}

‎alignn/examples/sample_data_ff/config_example_atomwise.json‎

Lines changed: 1 addition & 58 deletions
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@@ -1,58 +1 @@
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{
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"version": "112bbedebdaecf59fb18e11c929080fb2f358246",
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"dataset": "user_data",
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"target": "target",
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"atom_features": "cgcnn",
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"neighbor_strategy": "radius_graph",
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"id_tag": "jid",
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"dtype": "float32",
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"random_seed": 123,
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"classification_threshold": null,
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"n_val": null,
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"n_test": null,
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"n_train": null,
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"train_ratio": 0.8,
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"val_ratio": 0.1,
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"test_ratio": 0.1,
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"target_multiplication_factor": null,
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"epochs": 3,
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"batch_size": 2,
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"weight_decay": 1e-05,
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"learning_rate": 0.001,
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"filename": "B",
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"warmup_steps": 2000,
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"criterion": "l1",
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"optimizer": "adamw",
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"scheduler": "onecycle",
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"pin_memory": false,
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"save_dataloader": false,
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"write_checkpoint": true,
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"write_predictions": true,
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"store_outputs": false,
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"progress": true,
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"log_tensorboard": false,
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"standard_scalar_and_pca": false,
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"use_canonize": true,
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"num_workers": 0,
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"cutoff": 4.0,
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"max_neighbors": 12,
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"keep_data_order": true,
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"distributed": false,
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"use_lmdb": true,
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"model": {
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"name": "alignn_atomwise",
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"atom_input_features": 92,
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"calculate_gradient": true,
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"atomwise_output_features": 0,
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"alignn_layers": 1,
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"gcn_layers": 1,
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"hidden_features": 64,
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"output_features": 1,
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"graphwise_weight": 0.85,
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"gradwise_weight": 0.05,
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"atomwise_weight": 0.0,
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"use_cutoff_function": false,
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"stresswise_weight": 0.05,
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"add_reverse_forces": true
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}
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}
1+
{"version": "112bbedebdaecf59fb18e11c929080fb2f358246", "dataset": "user_data", "target": "target", "atom_features": "cgcnn", "neighbor_strategy": "radius_graph", "id_tag": "jid", "dtype": "float32", "random_seed": 123, "classification_threshold": null, "n_val": null, "n_test": null, "n_train": null, "train_ratio": 0.8, "val_ratio": 0.1, "test_ratio": 0.1, "target_multiplication_factor": null, "epochs": 3, "batch_size": 2, "weight_decay": 1e-05, "learning_rate": 0.001, "filename": "B", "warmup_steps": 2000, "criterion": "l1", "optimizer": "adamw", "scheduler": "onecycle", "pin_memory": false, "save_dataloader": false, "write_checkpoint": true, "write_predictions": true, "store_outputs": false, "progress": true, "log_tensorboard": false, "standard_scalar_and_pca": false, "use_canonize": true, "num_workers": 0, "cutoff": 4.0, "max_neighbors": 12, "keep_data_order": true, "distributed": false, "use_lmdb": true, "model": {"name": "alignn_atomwise", "atom_input_features": 92, "calculate_gradient": true, "atomwise_output_features": 0, "alignn_layers": 1, "gcn_layers": 1, "hidden_features": 64, "output_features": 1, "graphwise_weight": 0.85, "gradwise_weight": 0.05, "atomwise_weight": 0.0, "use_cutoff_function": false, "stresswise_weight": 0.05, "add_reverse_forces": true}}

‎alignn/tests/test_eprop.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -86,7 +86,7 @@ def test_alignn_train_regression():
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tmp["filename"] = "AA"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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local_rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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)
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@@ -109,7 +109,7 @@ def test_alignn_train_regression_multi_out():
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tmp["filename"] = "BB"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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local_rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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)
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@@ -130,7 +130,7 @@ def test_alignn_train_classification():
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tmp["filename"] = "A"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0,
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local_rank=0,
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world_size=world_size,
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root_dir=root_dir,
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config_name=config,
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tmp["filename"] = "B"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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local_rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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)
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cmd = "rm *.pt *.csv *.json *range"
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os.system(cmd)

‎alignn/tests/test_prop.py‎

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@@ -100,7 +100,7 @@ def test_alignn_train_regression():
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tmp["filename"] = "AA"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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local_rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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)
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@@ -123,7 +123,7 @@ def test_alignn_train_regression_multi_out():
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tmp["filename"] = "BB"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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local_rank=0, world_size=world_size, root_dir=root_dir, config_name=config
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)
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@@ -144,7 +144,7 @@ def test_alignn_train_classification():
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tmp["filename"] = "A"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0,
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local_rank=0,
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world_size=world_size,
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root_dir=root_dir,
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config_name=config,
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tmp["filename"] = "B"
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dumpjson(data=tmp, filename=config)
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train_for_folder(
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rank=0, world_size=world_size, root_dir=root_dir, config_name=config
172+
local_rank=0, world_size=world_size, root_dir=root_dir, config_name=config
173173
)
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cmd = "rm *.pt *.csv *.json *range"
175175
os.system(cmd)

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