Merge pull request #83 from usnistgov/develop

Develop

README.md

@@ -130,7 +130,9 @@ These scripts automatically download datasets from [Databases in jarvis-tools](h
 Using pre-trained models
 -------------------------
 
-All the trained models are distributed on [figshare](https://figshare.com/projects/ALIGNN_models/126478) and this [pretrained.py script](https://github.com/usnistgov/alignn/blob/develop/alignn/pretrained.py) can be applied to use them. These models can be used to directly make predictions.
+All the trained models are distributed on [Figshare](https://figshare.com/projects/ALIGNN_models/126478.
+
+The [pretrained.py script](https://github.com/usnistgov/alignn/blob/develop/alignn/pretrained.py) can be applied to use them. These models can be used to directly make predictions.
 
 A brief help section (`-h`) is shown using:
 

alignn/__init__.py

@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2022.11.06"
+__version__ = "2023.01.08"

alignn/examples/sample_data_ff/mlearn_data/Cu/config.json

@@ -0,0 +1,64 @@
+{
+    "version": "112bbedebdaecf59fb18e11c929080fb2f358246",
+    "dataset": "user_data",
+    "target": "target",
+    "atom_features": "cgcnn",
+    "neighbor_strategy": "k-nearest",
+    "id_tag": "jid",
+    "random_seed": 123,
+    "classification_threshold": null,
+    "n_val": 31,
+    "n_test": 31,
+    "n_train": 262,
+    "train_ratio": 0.9,
+    "val_ratio": 0.05,
+    "test_ratio": 0.05,
+    "target_multiplication_factor": null,
+    "epochs": 50,
+    "batch_size": 5,
+    "weight_decay": 1e-05,
+    "learning_rate": 0.001,
+    "filename": "sample",
+    "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": false,
+    "num_workers": 0,
+    "cutoff": 8.0,
+    "max_neighbors": 12,
+    "keep_data_order": true,
+    "normalize_graph_level_loss": false,
+    "distributed": false,
+    "n_early_stopping": null,
+    "output_dir": "./",
+    "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": true,
+        "atomwise_output_features": 3,
+        "graphwise_weight": 1.0,
+        "gradwise_weight": 10.0,
+        "stresswise_weight": 0.0,
+        "atomwise_weight": 0.0,
+        "link": "identity",
+        "zero_inflated": false,
+        "classification": false
+    }
+}

alignn/examples/sample_data_ff/mlearn_data/Ge/config.json

@@ -0,0 +1,64 @@
+{
+    "version": "112bbedebdaecf59fb18e11c929080fb2f358246",
+    "dataset": "user_data",
+    "target": "target",
+    "atom_features": "cgcnn",
+    "neighbor_strategy": "k-nearest",
+    "id_tag": "jid",
+    "random_seed": 123,
+    "classification_threshold": null,
+    "n_val": 25,
+    "n_test": 25,
+    "n_train": 228,
+    "train_ratio": 0.9,
+    "val_ratio": 0.05,
+    "test_ratio": 0.05,
+    "target_multiplication_factor": null,
+    "epochs": 50,
+    "batch_size": 5,
+    "weight_decay": 1e-05,
+    "learning_rate": 0.001,
+    "filename": "sample",
+    "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": false,
+    "num_workers": 0,
+    "cutoff": 8.0,
+    "max_neighbors": 12,
+    "keep_data_order": true,
+    "normalize_graph_level_loss": false,
+    "distributed": false,
+    "n_early_stopping": null,
+    "output_dir": "./",
+    "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": true,
+        "atomwise_output_features": 3,
+        "graphwise_weight": 1.0,
+        "gradwise_weight": 10.0,
+        "stresswise_weight": 0.0,
+        "atomwise_weight": 0.0,
+        "link": "identity",
+        "zero_inflated": false,
+        "classification": false
+    }
+}

alignn/examples/sample_data_ff/mlearn_data/Li/config.json

@@ -0,0 +1,64 @@
+{
+    "version": "112bbedebdaecf59fb18e11c929080fb2f358246",
+    "dataset": "user_data",
+    "target": "target",
+    "atom_features": "cgcnn",
+    "neighbor_strategy": "k-nearest",
+    "id_tag": "jid",
+    "random_seed": 123,
+    "classification_threshold": null,
+    "n_val": 29,
+    "n_test": 29,
+    "n_train": 241,
+    "train_ratio": 0.9,
+    "val_ratio": 0.05,
+    "test_ratio": 0.05,
+    "target_multiplication_factor": null,
+    "epochs": 50,
+    "batch_size": 5,
+    "weight_decay": 1e-05,
+    "learning_rate": 0.001,
+    "filename": "sample",
+    "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": false,
+    "num_workers": 0,
+    "cutoff": 8.0,
+    "max_neighbors": 12,
+    "keep_data_order": true,
+    "normalize_graph_level_loss": false,
+    "distributed": false,
+    "n_early_stopping": null,
+    "output_dir": "./",
+    "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": true,
+        "atomwise_output_features": 3,
+        "graphwise_weight": 1.0,
+        "gradwise_weight": 10.0,
+        "stresswise_weight": 0.0,
+        "atomwise_weight": 0.0,
+        "link": "identity",
+        "zero_inflated": false,
+        "classification": false
+    }
+}

alignn/examples/sample_data_ff/mlearn_data/Mo/config.json

@@ -0,0 +1,64 @@
+{
+    "version": "112bbedebdaecf59fb18e11c929080fb2f358246",
+    "dataset": "user_data",
+    "target": "target",
+    "atom_features": "cgcnn",
+    "neighbor_strategy": "k-nearest",
+    "id_tag": "jid",
+    "random_seed": 123,
+    "classification_threshold": null,
+    "n_val": 23,
+    "n_test": 23,
+    "n_train": 194,
+    "train_ratio": 0.9,
+    "val_ratio": 0.05,
+    "test_ratio": 0.05,
+    "target_multiplication_factor": null,
+    "epochs": 50,
+    "batch_size": 5,
+    "weight_decay": 1e-05,
+    "learning_rate": 0.001,
+    "filename": "sample",
+    "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": false,
+    "num_workers": 0,
+    "cutoff": 8.0,
+    "max_neighbors": 12,
+    "keep_data_order": true,
+    "normalize_graph_level_loss": false,
+    "distributed": false,
+    "n_early_stopping": null,
+    "output_dir": "./",
+    "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": true,
+        "atomwise_output_features": 3,
+        "graphwise_weight": 1.0,
+        "gradwise_weight": 10.0,
+        "stresswise_weight": 0.0,
+        "atomwise_weight": 0.0,
+        "link": "identity",
+        "zero_inflated": false,
+        "classification": false
+    }
+}

alignn/examples/sample_data_ff/mlearn_data/Ni/config.json

@@ -0,0 +1,64 @@
+{
+    "version": "112bbedebdaecf59fb18e11c929080fb2f358246",
+    "dataset": "user_data",
+    "target": "target",
+    "atom_features": "cgcnn",
+    "neighbor_strategy": "k-nearest",
+    "id_tag": "jid",
+    "random_seed": 123,
+    "classification_threshold": null,
+    "n_val": 31,
+    "n_test": 31,
+    "n_train": 263,
+    "train_ratio": 0.9,
+    "val_ratio": 0.05,
+    "test_ratio": 0.05,
+    "target_multiplication_factor": null,
+    "epochs": 50,
+    "batch_size": 5,
+    "weight_decay": 1e-05,
+    "learning_rate": 0.001,
+    "filename": "sample",
+    "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": false,
+    "num_workers": 0,
+    "cutoff": 8.0,
+    "max_neighbors": 12,
+    "keep_data_order": true,
+    "normalize_graph_level_loss": false,
+    "distributed": false,
+    "n_early_stopping": null,
+    "output_dir": "./",
+    "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": true,
+        "atomwise_output_features": 3,
+        "graphwise_weight": 1.0,
+        "gradwise_weight": 10.0,
+        "stresswise_weight": 0.0,
+        "atomwise_weight": 0.0,
+        "link": "identity",
+        "zero_inflated": false,
+        "classification": false
+    }
+}