OCP->FAIRChem + paper highlight list in docs (#772)

* adding new notebook for using fairchem models with NEBs without CatTSunami enumeration (#764) * adding new notebook for using fairchem models with NEBs * adding md tutorials * blocking code cells that arent needed or take too long * OCP->FAIRChem + paper list --------- Co-authored-by: Brook Wander <[email protected]> Co-authored-by: Muhammed Shuaibi <[email protected]>
FAIR-Chem · Jul 19, 2024 · f9ecf73 · f9ecf73
1 parent 9abc429
commit f9ecf73
Show file tree

Hide file tree

Showing 15 changed files with 334 additions and 25 deletions.
diff --git a/docs/core/fine-tuning/fine-tuning-oxides.md b/docs/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/docs/core/gotchas.md b/docs/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/docs/core/inference.md b/docs/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/docs/core/papers_using_models.md b/docs/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/docs/core/quickstart.md b/docs/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/docs/legacy_tutorials/OCP_Tutorial.md b/docs/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/')
 
 ```