deploy: 59cf718

.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: ac9e52e0f6ce67401b12e91af06590f6
+config: b5d0ff58eedd87b93894b95d734e1b60
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt

@@ -0,0 +1,143 @@
+2024-05-17 16:46:54 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-17 16:46:55 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-17 16:46:55 (INFO): amp: true
+cmd:
+  checkpoint_dir: ./checkpoints/2024-05-17-16-46-56
+  commit: 59cf718
+  identifier: ''
+  logs_dir: ./logs/tensorboard/2024-05-17-16-46-56
+  print_every: 10
+  results_dir: ./results/2024-05-17-16-46-56
+  seed: 0
+  timestamp_id: 2024-05-17-16-46-56
+  version: 0.1.dev1+g59cf718
+dataset:
+  a2g_args:
+    r_energy: false
+    r_forces: false
+  format: ase_db
+  key_mapping:
+    force: forces
+    y: energy
+  select_args:
+    selection: natoms>5,xc=PBE
+  src: data.db
+eval_metrics:
+  metrics:
+    energy:
+    - mae
+    forces:
+    - forcesx_mae
+    - forcesy_mae
+    - forcesz_mae
+    - mae
+    - cosine_similarity
+    - magnitude_error
+    misc:
+    - energy_forces_within_threshold
+  primary_metric: forces_mae
+gpus: 0
+logger: tensorboard
+loss_fns:
+- energy:
+    coefficient: 1
+    fn: mae
+- forces:
+    coefficient: 1
+    fn: l2mae
+model: gemnet_t
+model_attributes:
+  activation: silu
+  cbf:
+    name: spherical_harmonics
+  cutoff: 6.0
+  direct_forces: true
+  emb_size_atom: 512
+  emb_size_bil_trip: 64
+  emb_size_cbf: 16
+  emb_size_edge: 512
+  emb_size_rbf: 16
+  emb_size_trip: 64
+  envelope:
+    exponent: 5
+    name: polynomial
+  extensive: true
+  max_neighbors: 50
+  num_after_skip: 2
+  num_atom: 3
+  num_before_skip: 1
+  num_blocks: 3
+  num_concat: 1
+  num_radial: 128
+  num_spherical: 7
+  otf_graph: true
+  output_init: HeOrthogonal
+  rbf:
+    name: gaussian
+  regress_forces: true
+noddp: false
+optim:
+  batch_size: 16
+  clip_grad_norm: 10
+  ema_decay: 0.999
+  energy_coefficient: 1
+  eval_batch_size: 16
+  eval_every: 5000
+  force_coefficient: 1
+  loss_energy: mae
+  loss_force: atomwisel2
+  lr_gamma: 0.8
+  lr_initial: 0.0005
+  lr_milestones:
+  - 64000
+  - 96000
+  - 128000
+  - 160000
+  - 192000
+  max_epochs: 80
+  num_workers: 2
+  optimizer: AdamW
+  optimizer_params:
+    amsgrad: true
+  warmup_steps: -1
+outputs:
+  energy:
+    level: system
+  forces:
+    eval_on_free_atoms: true
+    level: atom
+    train_on_free_atoms: false
+slurm: {}
+task:
+  dataset: ase_db
+  prediction_dtype: float32
+test_dataset:
+  a2g_args:
+    r_energy: false
+    r_forces: false
+  select_args:
+    selection: natoms>5,xc=PBE
+  src: data.db
+trainer: ocp
+val_dataset: null
+
+2024-05-17 16:46:55 (INFO): Loading dataset: ase_db
+2024-05-17 16:46:56 (INFO): rank: 0: Sampler created...
+2024-05-17 16:46:56 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-17 16:46:56 (INFO): rank: 0: Sampler created...
+2024-05-17 16:46:56 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-17 16:46:56 (INFO): Loading model: gemnet_t
+2024-05-17 16:46:57 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-05-17 16:46:57 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-17 16:46:58 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-05-17 16:46:58 (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. 
+2024-05-17 16:46:58 (WARNING): Scale factor comment not found in model
+2024-05-17 16:46:58 (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 [00:04<00:09,  4.89s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.18s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.10s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.57s/it]
+2024-05-17 16:47:05 (INFO): Writing results to ./results/2024-05-17-16-46-56/ocp_predictions.npz
+2024-05-17 16:47:05 (INFO): Total time taken: 7.855764865875244
+Elapsed time = 13.9 seconds

_sources/core/install.md

@@ -1,13 +1,12 @@
 # Installation
+
+To install `fairchem-core` you will need to setup the `fairchem-core` environment (using [conda](#Conda) or [pip](#PyPi)) and then either install `fairchem-core` package [directly](#Install-fairchem-core) or install [development version](#Development-install) from our git repository.
 
-To install `fairchem-core` you will need to setup the `fairchem-core` environment (using [conda](#Conda) or [pip](#PyPi))
-and then either install `fairchem-core` package [directly](#Install-fairchem-core) or install a [development version](#Development-install) from our git repository.
-
-## Environment
+## Environment 
 
 You can install the environment using either conda or pip
 
-### Conda
+### Conda 
 
 We do not have official conda recipes (yet!); in the meantime you can use the
 following environment yaml files to setup on CPU or GPU. If conda is too slow for you, please consider using [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html)
@@ -60,8 +59,9 @@ pip install fairchem-{package-to-install}
 
 ## Development install
 
-If you plan to make contributions you will need to fork and clone (for windows user please see next section) the repo,
-set up the environment, and install fairchem-core from source in editable mode with dev dependencies,
+If you plan to make contributions you will need to fork and clone (for windows user please see next section) the repo, set up the environment, and install from source.
+`fairchem-core` in editable mode with dev
+dependencies,
 ```bash
 git clone https://github.com/FAIR-Chem/fairchem.git
 cd fairchem

_sources/index.md

@@ -1,5 +1,4 @@
-
-<h2 align="center"> <code>fairchem</code> by FAIR Chemistry </h2>
+<h1 align="center"> <code>fairchem</code> by FAIR Chemistry </h1>
 
 <p align="center">
   <img width="559" height="200" src="https://github.com/FAIR-Chem/fairchem/assets/45150244/5872c21c-8f39-41af-b703-af9817f0affe"?
@@ -12,8 +11,6 @@
 
 </h4>
 
-#### FAIR-Chem overview
-
 `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:
@@ -25,7 +22,7 @@ We re-organized and rebranded the repository in 2024 (previously the `fairchem`
 general usability of these models beyond catalysis, including things like direct air capture.
 ```
 
-#### Datasets in `fairchem`:
+### 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
@@ -36,7 +33,7 @@ tasks, data, and metrics, please read the documentations and respective papers:
  - [OC20Dense](core/datasets/oc20dense)
  - [OC20NEB](core/datasets/oc20neb)
 
-#### Projects and models built on `fairchem`:
+### 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)]
@@ -56,15 +53,15 @@ Older model implementations that are no longer supported:
 - SpinConv [[`arXiv`](https://arxiv.org/abs/2106.09575)] [[`code`](https://github.com/FAIR-Chem/fairchem/blob/e7a8745eb307e8a681a1aa9d30c36e8c41e9457e/ocpmodels/models/spinconv.py)]
 - ForceNet [[`arXiv`](https://arxiv.org/abs/2103.01436)] [[`code`](https://github.com/FAIR-Chem/fairchem/blob/e7a8745eb307e8a681a1aa9d30c36e8c41e9457e/ocpmodels/models/forcenet.py)]
 
-### Discussion
+## Discussion
 
 For all non-codebase related questions and to keep up-to-date with the latest OCP
 announcements, please join the [discussion board](https://discuss.opencatalystproject.org/).
 
 All code-related questions and issues should be posted directly on our
 [issues page](https://github.com/FAIR-Chem/fairchem/issues).
 
-### Acknowledgements
+## Acknowledgements
 
 - This codebase was initially forked from [CGCNN](https://github.com/txie-93/cgcnn)
 by [Tian Xie](http://txie.me), but has undergone significant changes since.
@@ -73,11 +70,11 @@ by [Tian Xie](http://txie.me), but has undergone significant changes since.
 - It was then developed as the OCP repo, and includes many contributions from the community and collaborators.
 - Much of the documentation was developed for various papers or as part of a comprehensive tutorial for the 2023 ACS Fall Chemistry conference.
 
-### License
+## License
 
 `fairchem` is released under the [MIT](https://github.com/FAIR-Chem/fairchem/blob/main/LICENSE.md) license.
 
-### Citing `fairchem`
+## Citing `fairchem`
 
 If you use this codebase in your work, please consider citing:
 

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

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>adsorbml.2023_neurips_challenge.challenge_eval</title>
+    <title>adsorbml.2023_neurips_challenge.challenge_eval &#8212; FAIR Chemistry Documentation</title>
 
 
 
@@ -146,8 +146,14 @@
 
 
 
+
+
+
+
+
+    <img src="../../../../_static/logo.png" class="logo__image only-light" alt="FAIR Chemistry Documentation - Home"/>
+    <script>document.write(`<img src="../../../../_static/logo.png" class="logo__image only-dark" alt="FAIR Chemistry Documentation - Home"/>`);</script>
 
-    <p class="title logo__title"></p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -167,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    FAIR-Chem overview
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/dense_eval/index.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>adsorbml.scripts.dense_eval</title>
+    <title>adsorbml.scripts.dense_eval &#8212; FAIR Chemistry Documentation</title>
 
 
 
@@ -146,8 +146,14 @@
 
 
 
+
+
+
+
+
+    <img src="../../../../_static/logo.png" class="logo__image only-light" alt="FAIR Chemistry Documentation - Home"/>
+    <script>document.write(`<img src="../../../../_static/logo.png" class="logo__image only-dark" alt="FAIR Chemistry Documentation - Home"/>`);</script>
 
-    <p class="title logo__title"></p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -167,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    FAIR-Chem overview
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/process_mlrs/index.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>adsorbml.scripts.process_mlrs</title>
+    <title>adsorbml.scripts.process_mlrs &#8212; FAIR Chemistry Documentation</title>
 
 
 
@@ -146,8 +146,14 @@
 
 
 
+
+
+
+
+
+    <img src="../../../../_static/logo.png" class="logo__image only-light" alt="FAIR Chemistry Documentation - Home"/>
+    <script>document.write(`<img src="../../../../_static/logo.png" class="logo__image only-dark" alt="FAIR Chemistry Documentation - Home"/>`);</script>
 
-    <p class="title logo__title"></p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -167,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    FAIR-Chem overview
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>

autoapi/adsorbml/scripts/utils/index.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>adsorbml.scripts.utils</title>
+    <title>adsorbml.scripts.utils &#8212; FAIR Chemistry Documentation</title>
 
 
 
@@ -146,8 +146,14 @@
 
 
 
+
+
+
+
+
+    <img src="../../../../_static/logo.png" class="logo__image only-light" alt="FAIR Chemistry Documentation - Home"/>
+    <script>document.write(`<img src="../../../../_static/logo.png" class="logo__image only-dark" alt="FAIR Chemistry Documentation - Home"/>`);</script>
 
-    <p class="title logo__title"></p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -167,7 +173,7 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../../../index.html">
-                    FAIR-Chem overview
+                    Datasets in fairchem:
                 </a>
             </li>
         </ul>