deploy: 3edcf80

FAIR-Chem · Apr 17, 2024 · 7b61d4f · 7b61d4f
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ac0276eee55fc00b9e2e0b7128308701
+config: efa2b153c9e066cd129008874a6226a9
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt b/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt
diff --git a/_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt b/_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt
@@ -1,17 +1,17 @@
-2024-04-16 23:01:59 (INFO): Project root: /home/runner/work/ocp/ocp
+2024-04-17 16:33:33 (INFO): Project root: /home/runner/work/ocp/ocp
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/cuda/amp/grad_scaler.py:126: UserWarning: torch.cuda.amp.GradScaler is enabled, but CUDA is not available.  Disabling.
   warnings.warn(
-2024-04-16 23:02:01 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-04-16 23:02:01 (INFO): amp: true
+2024-04-17 16:33:35 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-04-17 16:33:35 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-04-16-23-02-24
-  commit: 46df531
+  checkpoint_dir: ./checkpoints/2024-04-17-16-34-08
+  commit: 3edcf80
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-04-16-23-02-24
+  logs_dir: ./logs/tensorboard/2024-04-17-16-34-08
   print_every: 10
-  results_dir: ./results/2024-04-16-23-02-24
+  results_dir: ./results/2024-04-17-16-34-08
   seed: 0
-  timestamp_id: 2024-04-16-23-02-24
+  timestamp_id: 2024-04-17-16-34-08
 dataset:
   a2g_args:
     r_energy: false
@@ -36,7 +36,6 @@ eval_metrics:
     - magnitude_error
     misc:
     - energy_forces_within_threshold
-  primary_metric: forces_mae
 gpus: 0
 logger: tensorboard
 loss_fns:
@@ -122,29 +121,29 @@ test_dataset:
 trainer: ocp
 val_dataset: null
 
-2024-04-16 23:02:01 (INFO): Loading dataset: ase_db
-2024-04-16 23:02:01 (INFO): rank: 0: Sampler created...
-2024-04-16 23:02:01 (INFO): Batch balancing is disabled for single GPU training.
-2024-04-16 23:02:01 (INFO): rank: 0: Sampler created...
-2024-04-16 23:02:01 (INFO): Batch balancing is disabled for single GPU training.
-2024-04-16 23:02:01 (INFO): Loading model: gemnet_t
-2024-04-16 23:02:03 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-04-16 23:02:03 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-04-16 23:02:03 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-04-16 23:02:03 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. 
-2024-04-16 23:02:03 (WARNING): Scale factor comment not found in model
-2024-04-16 23:02:03 (INFO): Predicting on test.
+2024-04-17 16:33:35 (INFO): Loading dataset: ase_db
+2024-04-17 16:33:35 (INFO): rank: 0: Sampler created...
+2024-04-17 16:33:35 (INFO): Batch balancing is disabled for single GPU training.
+2024-04-17 16:33:35 (INFO): rank: 0: Sampler created...
+2024-04-17 16:33:35 (INFO): Batch balancing is disabled for single GPU training.
+2024-04-17 16:33:35 (INFO): Loading model: gemnet_t
+2024-04-17 16:33:37 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-04-17 16:33:37 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-04-17 16:33:37 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-04-17 16:33:37 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. 
+2024-04-17 16:33:37 (WARNING): Scale factor comment not found in model
+2024-04-17 16:33:37 (INFO): Predicting on test.
 device 0:   0%|                                           | 0/3 [00:00<?, ?it/s]/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/amp/autocast_mode.py:250: UserWarning: User provided device_type of 'cuda', but CUDA is not available. Disabling
   warnings.warn(
-device 0:  33%|███████████▋                       | 1/3 [00:04<00:08,  4.11s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:08<00:04,  4.25s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  2.93s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.28s/it]
+device 0:  33%|███████████▋                       | 1/3 [00:04<00:08,  4.34s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:07<00:03,  3.88s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.01s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.30s/it]
 /home/runner/work/ocp/ocp/ocpmodels/trainers/ocp_trainer.py:510: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
   predictions[key] = np.array(predictions[key])
 /home/runner/work/ocp/ocp/ocpmodels/trainers/base_trainer.py:840: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
   np.array(gather_results[k])[idx]
-2024-04-16 23:02:13 (INFO): Writing results to ./results/2024-04-16-23-02-24/ocp_predictions.npz
-2024-04-16 23:02:13 (INFO): Total time taken: 10.010130405426025
-Elapsed time = 16.4 seconds
+2024-04-17 16:33:47 (INFO): Writing results to ./results/2024-04-17-16-34-08/ocp_predictions.npz
+2024-04-17 16:33:47 (INFO): Total time taken: 10.054125785827637
+Elapsed time = 16.5 seconds

diff --git a/_images/1109562e7d207b01d4bbaec75065a7373c812846544444edb8782cf62a3bbac7.png b/_images/1109562e7d207b01d4bbaec75065a7373c812846544444edb8782cf62a3bbac7.png
diff --git a/_images/1c00a60ec6825804ceaf2cd92498f6edea6a10e85281888a20b9794ce2c728e1.png b/_images/1c00a60ec6825804ceaf2cd92498f6edea6a10e85281888a20b9794ce2c728e1.png
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diff --git a/_images/adb891328fabd0a89c888b81b387960f8a0bbbd4cd66ed19728fc7893d09b3bd.png b/_images/adb891328fabd0a89c888b81b387960f8a0bbbd4cd66ed19728fc7893d09b3bd.png
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diff --git a/_images/dcdc99549323297e5dd30a0baf29747f2425e39a3d3be78b205c036848adc458.png b/_images/dcdc99549323297e5dd30a0baf29747f2425e39a3d3be78b205c036848adc458.png
diff --git a/_images/dff1fbc3de1f6dc1e221f96257bc74db5d1a0965e76810d25d53f2c0c1315fb3.png b/_images/dff1fbc3de1f6dc1e221f96257bc74db5d1a0965e76810d25d53f2c0c1315fb3.png
diff --git a/_images/fa083ce0dec8caded35818ff6f33dfc5cad86df966ad654d7615cb13df4d5c2e.png b/_images/fa083ce0dec8caded35818ff6f33dfc5cad86df966ad654d7615cb13df4d5c2e.png
diff --git a/_sources/core/fine-tuning/fine-tuning-oxides.md b/_sources/core/fine-tuning/fine-tuning-oxides.md
@@ -208,8 +208,8 @@ yml = generate_yml_config(checkpoint_path, 'config.yml',
                            'dataset', 'test_dataset', 'val_dataset'],
                    update={'gpus': 1,
                            'task.dataset': 'ase_db',
-                           'optim.eval_every': 1,
-                           'optim.max_epochs': 4,
+                           'optim.eval_every': 10,
+                           'optim.max_epochs': 1,
                            'optim.batch_size': 4,
                             'logger':'tensorboard', # don't use wandb!
                            # Train data

diff --git a/_sources/index.md b/_sources/index.md
@@ -4,7 +4,7 @@
 [![codecov](https://codecov.io/gh/Open-Catalyst-Project/ocp/graph/badge.svg?token=M606LH5LK6)](https://codecov.io/gh/Open-Catalyst-Project/ocp)
 
 `ocp` is the [Open Catalyst Project](https://opencatalystproject.org/)'s
-library of state-of-the-art machine learning algorithms for catalysis.
+library of state-of-the-art machine learning algorithms for chemistry. We've used it for catalysis and direct air capture (MOF) applications, and we hope it's useful for your projects too!
 
 <div align="left">
     <img src="https://user-images.githubusercontent.com/1156489/170388229-642c6619-dece-4c88-85ef-b46f4d5f1031.gif">

diff --git a/_sources/tutorials/advanced/fine-tuning-in-python.md b/_sources/tutorials/advanced/fine-tuning-in-python.md
@@ -80,8 +80,8 @@ yml = generate_yml_config(checkpoint_path, 'config.yml',
                            'dataset', 'test_dataset', 'val_dataset'],
                    update={'gpus': 1,
                            'task.dataset': 'ase_db',
-                           'optim.eval_every': 1,
-                           'optim.max_epochs': 4,
+                           'optim.eval_every': 10,
+                           'optim.max_epochs': 1,
                            'optim.batch_size': 4,
                            'logger': 'tensorboard', # don't use wandb unless you already are logged in 
                            # Train data

diff --git a/_static/basic.css b/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/_static/doctools.js b/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/_static/graphviz.css b/_static/graphviz.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- graphviz extension.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/_static/language_data.js b/_static/language_data.js
@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer