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FAIR-Chem · May 15, 2024 · 7a76d24 · 7a76d24
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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 @@
-2024-05-14 21:21:35 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-15 00:20:17 (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(
-2024-05-14 21:21:36 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-05-14 21:21:36 (INFO): amp: true
+2024-05-15 00:20:19 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-15 00:20:19 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-05-14-21-22-08
-  commit: bcae55c
+  checkpoint_dir: ./checkpoints/2024-05-15-00-21-20
+  commit: 27d812e
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-05-14-21-22-08
+  logs_dir: ./logs/tensorboard/2024-05-15-00-21-20
   print_every: 10
-  results_dir: ./results/2024-05-14-21-22-08
+  results_dir: ./results/2024-05-15-00-21-20
   seed: 0
-  timestamp_id: 2024-05-14-21-22-08
+  timestamp_id: 2024-05-15-00-21-20
 dataset:
   a2g_args:
     r_energy: false
@@ -122,25 +122,25 @@ test_dataset:
 trainer: ocp
 val_dataset: null
 
-2024-05-14 21:21:36 (INFO): Loading dataset: ase_db
-2024-05-14 21:21:36 (INFO): rank: 0: Sampler created...
-2024-05-14 21:21:36 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-14 21:21:36 (INFO): rank: 0: Sampler created...
-2024-05-14 21:21:36 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-14 21:21:36 (INFO): Loading model: gemnet_t
-2024-05-14 21:21:38 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-05-14 21:21:38 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-05-14 21:21:38 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-05-14 21:21:38 (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. 
-2024-05-14 21:21:38 (WARNING): Scale factor comment not found in model
-2024-05-14 21:21:38 (INFO): Predicting on test.
+2024-05-15 00:20:19 (INFO): Loading dataset: ase_db
+2024-05-15 00:20:19 (INFO): rank: 0: Sampler created...
+2024-05-15 00:20:19 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-15 00:20:19 (INFO): rank: 0: Sampler created...
+2024-05-15 00:20:19 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-15 00:20:19 (INFO): Loading model: gemnet_t
+2024-05-15 00:20:21 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-05-15 00:20:21 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-15 00:20:21 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-05-15 00:20:21 (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. 
+2024-05-15 00:20:21 (WARNING): Scale factor comment not found in model
+2024-05-15 00:20:21 (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<00:06,  3.11s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:04<00:02,  2.38s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.39s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.47s/it]
-2024-05-14 21:21:46 (INFO): Writing results to ./results/2024-05-14-21-22-08/ocp_predictions.npz
-2024-05-14 21:21:46 (INFO): Total time taken: 7.559128284454346
-Elapsed time = 14.1 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:03<00:06,  3.09s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:05<00:02,  2.91s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.44s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.59s/it]
+2024-05-15 00:20:29 (INFO): Writing results to ./results/2024-05-15-00-21-20/ocp_predictions.npz
+2024-05-15 00:20:29 (INFO): Total time taken: 7.931819200515747
+Elapsed time = 14.3 seconds

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diff --git a/_images/9f1083631e62c45cf0caa4eb5365ce94edf347e6a01de6d13bde591eeeacfb30.png b/_images/9f1083631e62c45cf0caa4eb5365ce94edf347e6a01de6d13bde591eeeacfb30.png
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diff --git a/_sources/autoapi/cattsunami/index.rst b/_sources/autoapi/cattsunami/index.rst
@@ -3,6 +3,14 @@
 
 .. py:module:: cattsunami
 
+.. autoapi-nested-parse::
+
+   Copyright (c) Meta, Inc. and its affiliates.
+
+   This source code is licensed under the MIT license found in the
+   LICENSE file in the root directory of this source tree.
+
+
 
 Subpackages
 -----------
@@ -14,3 +22,10 @@ Subpackages
    databases/index.rst
 
 
+Package Contents
+----------------
+
+.. py:data:: __version__
+
+   
+
diff --git a/_sources/autoapi/data/oc/index.rst b/_sources/autoapi/data/oc/index.rst
@@ -3,6 +3,14 @@
 
 .. py:module:: data.oc
 
+.. autoapi-nested-parse::
+
+   Copyright (c) Meta, Inc. and its affiliates.
+
+   This source code is licensed under the MIT license found in the
+   LICENSE file in the root directory of this source tree.
+
+
 
 Subpackages
 -----------
@@ -25,3 +33,10 @@ Submodules
    structure_generator/index.rst
 
 
+Package Contents
+----------------
+
+.. py:data:: __version__
+
+   
+
diff --git a/_sources/autoapi/ocpapi/index.rst b/_sources/autoapi/ocpapi/index.rst
@@ -3,6 +3,14 @@
 
 .. py:module:: ocpapi
 
+.. autoapi-nested-parse::
+
+   Copyright (c) Meta, Inc. and its affiliates.
+
+   This source code is licensed under the MIT license found in the
+   LICENSE file in the root directory of this source tree.
+
+
 
 Subpackages
 -----------
@@ -75,10 +83,15 @@ Attributes
 
 .. autoapisummary::
 
+   ocpapi.__version__
    ocpapi.NO_LIMIT
    ocpapi.NoLimitType
 
 
+.. py:data:: __version__
+
+   
+
 .. py:class:: Client(host: str = 'open-catalyst-api.metademolab.com', scheme: str = 'https')
 
 

diff --git a/_sources/core/ocpapi.md b/_sources/core/ocpapi.md
@@ -103,6 +103,9 @@ A finite set of bulk materials and adsorbates can be referenced by ID throughout
 2. Use the low-level client that ships with this library:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 from fairchem.demo.ocpapi import Client
 
 client = Client()
@@ -137,6 +140,9 @@ results = await find_adsorbate_binding_sites(
 Run relaxations only for slabs with Miller Indices in the input set:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 from fairchem.demo.ocpapi import find_adsorbate_binding_sites, keep_slabs_with_miller_indices
 
 results = await find_adsorbate_binding_sites(
@@ -155,13 +161,19 @@ print(results)
 Assuming `results` was generated with the `find_adsorbate_binding_sites` method used above, it is an `AdsorbateBindingSites` object. This can be saved to file with:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 with open("results.json", "w") as f:
     f.write(results.to_json())
 ```
 
 Similarly, results can be read back from file to an `AdsorbateBindingSites` object with:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 from fairchem.demo.ocpapi import AdsorbateBindingSites
 
 with open("results.json", "r") as f:
@@ -175,6 +187,9 @@ Relaxation results can be viewed in a web UI. For example, https://open-catalyst
 Extending the examples above, the URLs to visualize the results of relaxations on each Pt surface can be obtained with:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 print([
     slab.ui_url
     for slab in results.slabs
@@ -192,6 +207,9 @@ The API currently supports two models:
 A specific model type can be requested with:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 from fairchem.demo.ocpapi import find_adsorbate_binding_sites
 
 results = await find_adsorbate_binding_sites(
@@ -220,6 +238,9 @@ Two classes have support for generating [ase.Atoms](https://wiki.fysik.dtu.dk/as
 For example, the following would generate an `ase.Atoms` object for the first relaxed adsorbate configuration on the first slab generated for *OH binding on Pt:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 from fairchem.demo.ocpapi import find_adsorbate_binding_sites
 
 results = await find_adsorbate_binding_sites(
@@ -237,6 +258,9 @@ print(ase_atoms)
 From an `ase.Atoms` object (see previous section), is is possible to [write to other structure formats](https://wiki.fysik.dtu.dk/ase/ase/io/io.html#ase.io.write). Extending the example above, the `ase_atoms` object could be written to a [VASP POSCAR file](https://www.vasp.at/wiki/index.php/POSCAR) with:
 
 ```{code-cell} ipython3
+---
+tags: ["skip-execution"]
+---
 from ase.io import write
 
 write("POSCAR", ase_atoms, "vasp")

diff --git a/autoapi/cattsunami/index.html b/autoapi/cattsunami/index.html
@@ -614,6 +614,10 @@ <h2> Contents </h2>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#subpackages">Subpackages</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#package-contents">Package Contents</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cattsunami.__version__"><code class="docutils literal notranslate"><span class="pre">__version__</span></code></a></li>
+</ul>
+</li>
 </ul>
             </nav>
         </div>
@@ -627,6 +631,9 @@ <h2> Contents </h2>
 
   <section id="module-cattsunami">
 <span id="cattsunami"></span><h1><a class="reference internal" href="#module-cattsunami" title="cattsunami"><code class="xref py py-mod docutils literal notranslate"><span class="pre">cattsunami</span></code></a><a class="headerlink" href="#module-cattsunami" title="Link to this heading">#</a></h1>
+<p>Copyright (c) Meta, Inc. and its affiliates.</p>
+<p>This source code is licensed under the MIT license found in the
+LICENSE file in the root directory of this source tree.</p>
 <section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this heading">#</a></h2>
 <div class="toctree-wrapper compound">
@@ -640,6 +647,14 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l1"><a class="reference internal" href="databases/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">cattsunami.databases</span></code></a></li>
 </ul>
 </div>
+</section>
+<section id="package-contents">
+<h2>Package Contents<a class="headerlink" href="#package-contents" title="Link to this heading">#</a></h2>
+<dl class="py data">
+<dt class="sig sig-object py" id="cattsunami.__version__">
+<span class="sig-prename descclassname"><span class="pre">cattsunami.</span></span><span class="sig-name descname"><span class="pre">__version__</span></span><a class="headerlink" href="#cattsunami.__version__" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
 </section>
 </section>
 
@@ -708,6 +723,10 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#subpackages">Subpackages</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#package-contents">Package Contents</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cattsunami.__version__"><code class="docutils literal notranslate"><span class="pre">__version__</span></code></a></li>
+</ul>
+</li>
 </ul>
   </nav></div>
 

diff --git a/autoapi/data/oc/index.html b/autoapi/data/oc/index.html
@@ -615,6 +615,10 @@ <h2> Contents </h2>
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#subpackages">Subpackages</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submodules">Submodules</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#package-contents">Package Contents</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#data.oc.__version__"><code class="docutils literal notranslate"><span class="pre">__version__</span></code></a></li>
+</ul>
+</li>
 </ul>
             </nav>
         </div>
@@ -628,6 +632,9 @@ <h2> Contents </h2>
 
   <section id="module-data.oc">
 <span id="data-oc"></span><h1><a class="reference internal" href="#module-data.oc" title="data.oc"><code class="xref py py-mod docutils literal notranslate"><span class="pre">data.oc</span></code></a><a class="headerlink" href="#module-data.oc" title="Link to this heading">#</a></h1>
+<p>Copyright (c) Meta, Inc. and its affiliates.</p>
+<p>This source code is licensed under the MIT license found in the
+LICENSE file in the root directory of this source tree.</p>
 <section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this heading">#</a></h2>
 <div class="toctree-wrapper compound">
@@ -661,6 +668,14 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li class="toctree-l1"><a class="reference internal" href="structure_generator/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">data.oc.structure_generator</span></code></a></li>
 </ul>
 </div>
+</section>
+<section id="package-contents">
+<h2>Package Contents<a class="headerlink" href="#package-contents" title="Link to this heading">#</a></h2>
+<dl class="py data">
+<dt class="sig sig-object py" id="data.oc.__version__">
+<span class="sig-prename descclassname"><span class="pre">data.oc.</span></span><span class="sig-name descname"><span class="pre">__version__</span></span><a class="headerlink" href="#data.oc.__version__" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
 </section>
 </section>
 
@@ -730,6 +745,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#subpackages">Subpackages</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submodules">Submodules</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#package-contents">Package Contents</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#data.oc.__version__"><code class="docutils literal notranslate"><span class="pre">__version__</span></code></a></li>
+</ul>
+</li>
 </ul>
   </nav></div>