deploy: ef5cbbe

_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt

@@ -1,17 +1,17 @@
-2024-05-10 22:54:58 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-10 23:14:35 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
 /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(
-2024-05-10 22:55:00 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-05-10 22:55:00 (INFO): amp: true
+2024-05-10 23:14:37 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-10 23:14:37 (INFO): amp: true
 cmd:
-  checkpoint_dir: fine-tuning/checkpoints/2024-05-10-22-56-00-ft-oxides
-  commit: 7a0ae57
+  checkpoint_dir: fine-tuning/checkpoints/2024-05-10-23-15-12-ft-oxides
+  commit: ef5cbbe
   identifier: ft-oxides
-  logs_dir: fine-tuning/logs/tensorboard/2024-05-10-22-56-00-ft-oxides
+  logs_dir: fine-tuning/logs/tensorboard/2024-05-10-23-15-12-ft-oxides
   print_every: 10
-  results_dir: fine-tuning/results/2024-05-10-22-56-00-ft-oxides
+  results_dir: fine-tuning/results/2024-05-10-23-15-12-ft-oxides
   seed: 0
-  timestamp_id: 2024-05-10-22-56-00-ft-oxides
+  timestamp_id: 2024-05-10-23-15-12-ft-oxides
 dataset:
   a2g_args:
     r_energy: true
@@ -142,34 +142,34 @@ val_dataset:
     r_forces: true
   src: val.db
 
-2024-05-10 22:55:00 (INFO): Loading dataset: ase_db
-2024-05-10 22:55:00 (INFO): rank: 0: Sampler created...
-2024-05-10 22:55:00 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-10 22:55:00 (INFO): rank: 0: Sampler created...
-2024-05-10 22:55:00 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-10 22:55:00 (INFO): rank: 0: Sampler created...
-2024-05-10 22:55:00 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-10 22:55:00 (INFO): Loading model: gemnet_oc
-2024-05-10 22:55:00 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
-2024-05-10 22:55:03 (INFO): Loaded GemNetOC with 38864438 parameters.
-2024-05-10 22:55:03 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-05-10 22:55:03 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
-2024-05-10 22:55:03 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gnoc_oc22_oc20_all_s2ef.pt
-2024-05-10 22:55:03 (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. 
+2024-05-10 23:14:37 (INFO): Loading dataset: ase_db
+2024-05-10 23:14:37 (INFO): rank: 0: Sampler created...
+2024-05-10 23:14:37 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-10 23:14:37 (INFO): rank: 0: Sampler created...
+2024-05-10 23:14:37 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-10 23:14:37 (INFO): rank: 0: Sampler created...
+2024-05-10 23:14:37 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-10 23:14:37 (INFO): Loading model: gemnet_oc
+2024-05-10 23:14:37 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
+2024-05-10 23:14:40 (INFO): Loaded GemNetOC with 38864438 parameters.
+2024-05-10 23:14:40 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-10 23:14:40 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
+2024-05-10 23:14:40 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gnoc_oc22_oc20_all_s2ef.pt
+2024-05-10 23:14:40 (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. 
 /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(
-2024-05-10 22:55:27 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 6.77e+00, forcesx_mae: 4.11e-02, forcesy_mae: 3.63e-02, forcesz_mae: 5.26e-02, forces_mae: 4.33e-02, forces_cosine_similarity: 8.24e-02, forces_magnitude_error: 7.42e-02, loss: 6.86e+00, lr: 5.00e-04, epoch: 1.69e-01, step: 1.00e+01
-2024-05-10 22:55:28 (INFO): Evaluating on val.
+2024-05-10 23:15:03 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 6.77e+00, forcesx_mae: 4.11e-02, forcesy_mae: 3.63e-02, forcesz_mae: 5.26e-02, forces_mae: 4.33e-02, forces_cosine_similarity: 8.24e-02, forces_magnitude_error: 7.42e-02, loss: 6.86e+00, lr: 5.00e-04, epoch: 1.69e-01, step: 1.00e+01
+2024-05-10 23:15:04 (INFO): Evaluating on val.
 device 0:   0%|          | 0/2 [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)
-device 0:  50%|█████     | 1/2 [00:04<00:04,  4.91s/it]device 0: 100%|██████████| 2/2 [00:07<00:00,  3.71s/it]device 0: 100%|██████████| 2/2 [00:07<00:00,  3.93s/it]
-2024-05-10 22:55:36 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 8.7334, forcesx_mae: 0.0231, forcesy_mae: 0.0188, forcesz_mae: 0.0198, forces_mae: 0.0206, forces_cosine_similarity: -0.0317, forces_magnitude_error: 0.0290, loss: 8.6591, epoch: 0.1695
+device 0:  50%|█████     | 1/2 [00:04<00:04,  4.79s/it]device 0: 100%|██████████| 2/2 [00:07<00:00,  3.65s/it]device 0: 100%|██████████| 2/2 [00:07<00:00,  3.88s/it]
+2024-05-10 23:15:11 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 8.7333, forcesx_mae: 0.0231, forcesy_mae: 0.0188, forcesz_mae: 0.0198, forces_mae: 0.0206, forces_cosine_similarity: -0.0317, forces_magnitude_error: 0.0290, loss: 8.6590, epoch: 0.1695
 Traceback (most recent call last):
   File "/home/runner/work/fairchem/fairchem/src/fairchem/../../main.py", line 8, in <module>
     main()

_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt

@@ -1,17 +1,17 @@
-2024-05-10 22:57:42 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-10 23:17:10 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
 /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(
-2024-05-10 22:57:43 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-05-10 22:57:43 (INFO): amp: true
+2024-05-10 23:17:11 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-10 23:17:11 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-05-10-22-58-08
-  commit: 7a0ae57
+  checkpoint_dir: ./checkpoints/2024-05-10-23-17-20
+  commit: ef5cbbe
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-05-10-22-58-08
+  logs_dir: ./logs/tensorboard/2024-05-10-23-17-20
   print_every: 10
-  results_dir: ./results/2024-05-10-22-58-08
+  results_dir: ./results/2024-05-10-23-17-20
   seed: 0
-  timestamp_id: 2024-05-10-22-58-08
+  timestamp_id: 2024-05-10-23-17-20
 dataset:
   a2g_args:
     r_energy: false
@@ -121,25 +121,25 @@ test_dataset:
 trainer: ocp
 val_dataset: null
 
-2024-05-10 22:57:43 (INFO): Loading dataset: ase_db
-2024-05-10 22:57:43 (INFO): rank: 0: Sampler created...
-2024-05-10 22:57:43 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-10 22:57:43 (INFO): rank: 0: Sampler created...
-2024-05-10 22:57:43 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-10 22:57:43 (INFO): Loading model: gemnet_t
-2024-05-10 22:57:45 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-05-10 22:57:45 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-05-10 22:57:46 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-05-10 22:57:46 (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. 
-2024-05-10 22:57:46 (WARNING): Scale factor comment not found in model
-2024-05-10 22:57:46 (INFO): Predicting on test.
+2024-05-10 23:17:11 (INFO): Loading dataset: ase_db
+2024-05-10 23:17:11 (INFO): rank: 0: Sampler created...
+2024-05-10 23:17:11 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-10 23:17:11 (INFO): rank: 0: Sampler created...
+2024-05-10 23:17:11 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-10 23:17:11 (INFO): Loading model: gemnet_t
+2024-05-10 23:17:13 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-05-10 23:17:13 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-10 23:17:13 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-05-10 23:17:13 (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. 
+2024-05-10 23:17:13 (WARNING): Scale factor comment not found in model
+2024-05-10 23:17:13 (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 [00:03<00:07,  3.63s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:02,  2.97s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.04s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.09s/it]
-2024-05-10 22:57:55 (INFO): Writing results to ./results/2024-05-10-22-58-08/ocp_predictions.npz
-2024-05-10 22:57:55 (INFO): Total time taken: 9.435298919677734
-Elapsed time = 16.0 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:03<00:07,  3.59s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.01s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:08<00:00,  2.83s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:08<00:00,  2.94s/it]
+2024-05-10 23:17:22 (INFO): Writing results to ./results/2024-05-10-23-17-20/ocp_predictions.npz
+2024-05-10 23:17:22 (INFO): Total time taken: 8.971215963363647
+Elapsed time = 15.2 seconds

_sources/index.md

@@ -1,35 +1,37 @@
-# `fairchem` repository for atomistic AI/ML models in chemistry
+<h1 align="center"> <code>fairchem</code> by FAIR Chemistry </h1>
 
-![tests](https://github.com/FAIR-Chem/fairchem/actions/workflows/test.yml/badge.svg?branch=main)
-[![codecov](https://codecov.io/gh/FAIR-Chem/fairchem/badge.svg)](https://codecov.io/gh/FAIR-Chem/fairchem)
-
-`fairchem` is the FAIR Chemistry team's library of state-of-the-art machine learning algorithms for chemistry and materials. Collaborative projects that contribute or use the models and approaches in this repo:
-* [Open Catalyst Project (OCP)](https://opencatalystproject.org/)
-* [Open Direct Air Capture (OpenDAC)](https://open-dac.github.io/)
+<p align="center">
+  <img width="559" height="200" src="https://github.com/FAIR-Chem/fairchem/assets/45150244/d3abd756-cb96-40eb-b3a8-976939a2f0d8"?
+</p>
 
-We re-organized and rebranded the repository in 2024 (previously the `ocp` repo) to reflect the increasingly general usability of these models beyond catalysis, including things like direct air capture.
+<h4 align="center">
 
+![tests](https://github.com/FAIR-Chem/fairchem/actions/workflows/test.yml/badge.svg?branch=main)
+[![Static Badge](https://img.shields.io/badge/python-3.9%2B-blue)](https://www.python.org/downloads/)
 
-<div align="left">
-    <img src="https://user-images.githubusercontent.com/1156489/170388229-642c6619-dece-4c88-85ef-b46f4d5f1031.gif">
-</div>
+</h4>
 
-## [fairchem](https://fair-chem.github.io/fairchem/)
-Full documentation, released data/checkpoints, and tutorials are now available.
+`fairchem` is the [FAIR](https://ai.meta.com/research/) Chemistry's centralized repository of all its data, models, demos, and application efforts
+for materials science and quantum chemistry. Collaborative projects that contribute or use the models and approaches in
+this repo:
+* [Open Catalyst Project (OCP)](https://opencatalystproject.org/)
+* [Open Direct Air Capture (OpenDAC)](https://open-dac.github.io/)
 
-- [Installation](core/install)
-- [Pretrained model checkpoints](core/model_checkpoints)
-- [FAQ](core/model_faq)
+:::{note}
+We re-organized and rebranded the repository in 2024 (previously the `fairchem` repo) to reflect the increasingly
+general usability of these models beyond catalysis, including things like direct air capture.
+:::
 
-`ocp` provides training and evaluation code for tasks and models that take arbitrary
+### Datasets in `fairchem`:
+`fairchem` provides training and evaluation code for tasks and models that take arbitrary
 chemical structures as input to predict energies / forces / positions / stresses,
 and can be used as a base scaffold for research projects. For an overview of
 tasks, data, and metrics, please read the documentations and respective papers:
  - [OC20](core/datasets/oc20)
  - [OC22](core/datasets/oc22)
  - [ODAC23](core/datasets/odac)
 
-Projects and models built on `ocp`:
+### Projects and models built on `fairchem`:
 
 - SchNet [[`arXiv`](https://arxiv.org/abs/1706.08566)] [[`code`](https://github.com/FAIR-Chem/fairchem/blob/main/src/fairchem/core/models/schnet.py)]
 - DimeNet++ [[`arXiv`](https://arxiv.org/abs/2011.14115)] [[`code`](https://github.com/FAIR-Chem/fairchem/blob/main/src/fairchem/core/models/dimenet_plus_plus.py)]

autoapi/adsorbml/2023_neurips_challenge/challenge_eval/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/dense_eval/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/process_mlrs/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/utils/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/write_top_k_vasp/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/core/_cli/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/core/common/data_parallel/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/core/common/distutils/index.html

@@ -173,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    fairchem repository for atomistic AI/ML models in chemistry
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>