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FAIR-Chem · Jul 19, 2024 · 6544e84 · 6544e84
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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: 3e16fc85e4d09f60ba66e881fe15276a
+config: 21ab98e528573f73f1b5d8a9a8dc8e52
 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
@@ -1,16 +1,16 @@
-2024-07-14 21:59:31 (INFO): Running in non-distributed local mode
-2024-07-14 21:59:31 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
-2024-07-14 21:59:32 (INFO): amp: true
+2024-07-19 20:42:08 (INFO): Running in non-distributed local mode
+2024-07-19 20:42:08 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-07-19 20:42:10 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-07-14-22-00-32
-  commit: c2f8928
+  checkpoint_dir: ./checkpoints/2024-07-19-20-41-36
+  commit: f9ecf73
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-07-14-22-00-32
+  logs_dir: ./logs/tensorboard/2024-07-19-20-41-36
   print_every: 10
-  results_dir: ./results/2024-07-14-22-00-32
+  results_dir: ./results/2024-07-19-20-41-36
   seed: 0
-  timestamp_id: 2024-07-14-22-00-32
-  version: 0.1.dev1+gc2f8928
+  timestamp_id: 2024-07-19-20-41-36
+  version: 0.1.dev1+gf9ecf73
 dataset: {}
 evaluation_metrics:
   metrics:
@@ -113,20 +113,20 @@ test_dataset:
 trainer: ocp
 val_dataset: {}
 
-2024-07-14 21:59:32 (INFO): rank: 0: Sampler created...
-2024-07-14 21:59:32 (INFO): Batch balancing is disabled for single GPU training.
-2024-07-14 21:59:32 (INFO): Loading model: gemnet_t
-2024-07-14 21:59:34 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-07-14 21:59:34 (WARNING): log_summary for Tensorboard not supported
-2024-07-14 21:59:34 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-07-14 21:59:34 (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. 
-2024-07-14 21:59:34 (WARNING): Scale factor comment not found in model
-2024-07-14 21:59:34 (INFO): Predicting on test.
+2024-07-19 20:42:10 (INFO): rank: 0: Sampler created...
+2024-07-19 20:42:10 (INFO): Batch balancing is disabled for single GPU training.
+2024-07-19 20:42:10 (INFO): Loading model: gemnet_t
+2024-07-19 20:42:11 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-07-19 20:42:11 (WARNING): log_summary for Tensorboard not supported
+2024-07-19 20:42:12 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gndt_oc22_all_s2ef.pt
+2024-07-19 20:42:12 (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. 
+2024-07-19 20:42:12 (WARNING): Scale factor comment not found in model
+2024-07-19 20:42:12 (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)
-device 0:  33%|███████████▋                       | 1/3 [00:03<00:06,  3.13s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.02s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:08<00:00,  2.97s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.01s/it]
-2024-07-14 21:59:43 (INFO): Writing results to ./results/2024-07-14-22-00-32/ocp_predictions.npz
-2024-07-14 21:59:43 (INFO): Total time taken: 9.158892154693604
-Elapsed time = 15.3 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:03<00:07,  3.55s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.23s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.27s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.30s/it]
+2024-07-19 20:42:22 (INFO): Writing results to ./results/2024-07-19-20-41-36/ocp_predictions.npz
+2024-07-19 20:42:22 (INFO): Total time taken: 10.0305335521698
+Elapsed time = 16.3 seconds

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diff --git a/_images/be62301e07594b3378c727532f052de9b51cd1de9c835cc644571ba8714ac17c.png b/_images/be62301e07594b3378c727532f052de9b51cd1de9c835cc644571ba8714ac17c.png
diff --git a/_images/f508405455676bf2a7ab2b64f3133d6a31c7e2bed12b4e68b1bae30fb759e03b.png b/_images/f508405455676bf2a7ab2b64f3133d6a31c7e2bed12b4e68b1bae30fb759e03b.png
diff --git a/_sources/core/fine-tuning/fine-tuning-oxides.md b/_sources/core/fine-tuning/fine-tuning-oxides.md
@@ -29,7 +29,7 @@ We get this checkpoint here.
 ```{code-cell} ipython3
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 ```
 
 The data we need is provided in `supporting-information.json`. That file is embedded in the supporting information for the article, and is provided here in the tutorial. We load this data and explore it a little. The json file provides a dictionary with the structure:

diff --git a/_sources/core/gotchas.md b/_sources/core/gotchas.md
@@ -45,7 +45,7 @@ The problem here is that no neighbors are found for the single atom which causes
 ```{code-cell} ipython3
 from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 from fairchem.core.models.model_registry import model_name_to_local_file
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 calc = OCPCalculator(checkpoint_path=checkpoint_path)
 ```
 
@@ -79,7 +79,7 @@ add_adsorbate(slab, 'O', height=1.2, position='fcc')
 from fairchem.core.models.model_registry import model_name_to_local_file
 
 # OC20 model - trained on adsorption energies
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EF-OC20-All', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EF-OC20-All', local_cache='/tmp/fairchem_checkpoints/')
 
 with contextlib.redirect_stdout(StringIO()) as _:
     calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=False)
@@ -92,7 +92,7 @@ slab.get_potential_energy()
 
 ```{code-cell} ipython3
 # An OC22 checkpoint - trained on total energy
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 
 with contextlib.redirect_stdout(StringIO()) as _:
     calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=False)
@@ -105,7 +105,7 @@ slab.get_potential_energy()
 
 ```{code-cell} ipython3
 # This eSCN model is trained on adsorption energies
-checkpoint_path = model_name_to_local_file('eSCN-L4-M2-Lay12-S2EF-OC20-2M', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('eSCN-L4-M2-Lay12-S2EF-OC20-2M', local_cache='/tmp/fairchem_checkpoints/')
 
 with contextlib.redirect_stdout(StringIO()) as _:
     calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=False)
@@ -158,7 +158,7 @@ from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 from fairchem.core.models.model_registry import model_name_to_local_file
 import os
 
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 
 calc = OCPCalculator(checkpoint_path=checkpoint_path)
 ```
@@ -184,7 +184,7 @@ from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 from fairchem.core.models.model_registry import model_name_to_local_file
 import os
 
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 calc = OCPCalculator(checkpoint_path=checkpoint_path)
 ```
 
@@ -209,7 +209,7 @@ from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 from fairchem.core.models.model_registry import model_name_to_local_file
 import os
 
-checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/fairchem_checkpoints/')
 
 calc = OCPCalculator(checkpoint_path=checkpoint_path)
 ```
@@ -231,7 +231,7 @@ This happens because a random selection of is made to sample edges, and a differ
 from fairchem.core.models.model_registry import model_name_to_local_file
 from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 
-checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/fairchem_checkpoints/')
 calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=True)
 
 from ase.build import fcc111, add_adsorbate
@@ -258,7 +258,7 @@ In DFT, the forces on all the atoms should sum to zero; otherwise, there is a ne
 
 ```{code-cell} ipython3
 from fairchem.core.models.model_registry import model_name_to_local_file
-checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/fairchem_checkpoints/')
 
 from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=True)

diff --git a/_sources/core/inference.md b/_sources/core/inference.md
@@ -70,7 +70,7 @@ print(available_pretrained_models)
 ```{code-cell} ipython3
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('GemNet-dT-S2EFS-OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-dT-S2EFS-OC22', local_cache='/tmp/fairchem_checkpoints/')
 checkpoint_path
 
 ```

diff --git a/_sources/core/papers_using_models.md b/_sources/core/papers_using_models.md
@@ -1,5 +1,47 @@
-# Studies that have leveraged OCP models
+# Studies leveraging pre-trained or fine-tuned FAIR-Chem models
+
+Many papers have now used FAIR-Chem models to accelerate screening and discovery efforts and enable new computational chemistry simulations. We highlight some here just to give an idea of the breadth of possibilities and how they have been used. Feel free to reach out (or submit PRs) if you want them included!
+
+## Accelerating computational catalysis
+
+```{bibliography}
+:style: plain
+:filter: category == "accelerating catalysis"
+```
+
+## Transfer/fine-tuning strategies for FAIR-Chem pre-trained checkpoints
+
+```{bibliography}
+:style: plain
+:filter: category == "transfer strategies"
+```
+
+## Transfer/fine-tuning applications for FAIR-Chem pre-trained checkpoints
+
+```{bibliography}
+:style: plain
+:filter: category == "transfer applications"
+```
+
+## Catalyst discovery or optimization
+
+```{bibliography}
+:style: plain
+:filter: category == "catalyst discovery"
+```
+
+## Uncertainty quantification
+
+```{bibliography}
+:style: plain
+:filter: category == "uncertainty"
+```
+
+## Properties beyond energies and forces
+
+```{bibliography}
+:style: plain
+:filter: category == "other properties"
+```
 
-Many papers have now used the latest OCP models to accelerate screening and discovery efforts and enable new computational chemistry simulations! 
-We highlight some here just to give an idea of the breadth of possibilities and how they have been used. Feel free to reach out (or submit PRs with links to your papers if you want them included)!
 
diff --git a/_sources/core/quickstart.md b/_sources/core/quickstart.md
@@ -26,7 +26,7 @@ print(available_pretrained_models)
 
 ```{code-cell} ipython3
 from fairchem.core.models.model_registry import model_name_to_local_file
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 checkpoint_path
 ```
 

diff --git a/_sources/legacy_tutorials/OCP_Tutorial.md b/_sources/legacy_tutorials/OCP_Tutorial.md
@@ -1388,7 +1388,7 @@ relax_dataset = "data/is2re/val_20/data.lmdb"
 
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('GemNet-dT-S2EF-OC20-All', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-dT-S2EF-OC20-All', local_cache='/tmp/fairchem_checkpoints/')
 
 ```
 
@@ -2021,7 +2021,7 @@ For this tutorial we download one of our earlier model checkpoints: GemNet-T
 
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('GemNet-dT-S2EF-OC20-All', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-dT-S2EF-OC20-All', local_cache='/tmp/fairchem_checkpoints/')
 
 ```
 

diff --git a/_sources/tutorials/NRR/NRR_example.md b/_sources/tutorials/NRR/NRR_example.md
@@ -34,12 +34,17 @@ import os
 from glob import glob
 import pandas as pd
 from fairchem.data.oc.utils import DetectTrajAnomaly
+
+# Set random seed to ensure adsorbate enumeration yields a valid candidate
+# If using a larger number of random samples this wouldn't be necessary
+import numpy as np
+np.random.seed(22)
 ```
 
 ```{code-cell} ipython3
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/fairchem_checkpoints/')
 checkpoint_path
 ```
 

diff --git a/_sources/tutorials/OCP-introduction.md b/_sources/tutorials/OCP-introduction.md
@@ -60,7 +60,7 @@ The different models have different compute requirements. If you find your kerne
 ```{code-cell}
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/fairchem_checkpoints/')
 ```
 
 Next we load the checkpoint. The output is somewhat verbose, but it can be informative for debugging purposes.

diff --git a/_sources/tutorials/adsorbml_walkthrough.md b/_sources/tutorials/adsorbml_walkthrough.md
@@ -75,7 +75,7 @@ from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 from fairchem.core.models.model_registry import model_name_to_local_file
 import os
 
-checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('EquiformerV2-31M-S2EF-OC20-All+MD', local_cache='/tmp/fairchem_checkpoints/')
 
 os.makedirs(f"data/{bulk}_{adsorbate}", exist_ok=True)
 

diff --git a/_sources/tutorials/advanced/embeddings.md b/_sources/tutorials/advanced/embeddings.md
@@ -58,7 +58,7 @@ from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 from fairchem.core.models.model_registry import model_name_to_local_file
 
 import os
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 
 calc = OCPCalculator(checkpoint_path=checkpoint_path)
 ```

diff --git a/_sources/tutorials/advanced/fine-tuning-in-python.md b/_sources/tutorials/advanced/fine-tuning-in-python.md
@@ -51,7 +51,7 @@ root.addHandler(handler_err)
 ```{code-cell} ipython3
 from fairchem.core.models.model_registry import model_name_to_local_file
 
-checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
+checkpoint_path = model_name_to_local_file('GemNet-OC-S2EFS-OC20+OC22', local_cache='/tmp/fairchem_checkpoints/')
 from fairchem.core.common.relaxation.ase_utils import OCPCalculator
 calc = OCPCalculator(checkpoint_path=checkpoint_path, trainer='forces', cpu=False)
 ```