deploy: bcb3cf5

FAIR-Chem · May 17, 2024 · 44249a0 · 44249a0
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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
@@ -1,16 +1,16 @@
-2024-05-16 01:16:48 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
-2024-05-16 01:16:49 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-05-16 01:16:49 (INFO): amp: true
+2024-05-17 04:26:51 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-17 04:26:52 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-17 04:26:52 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-05-16-01-16-48
-  commit: 58f2726
+  checkpoint_dir: ./checkpoints/2024-05-17-04-26-40
+  commit: bcb3cf5
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-05-16-01-16-48
+  logs_dir: ./logs/tensorboard/2024-05-17-04-26-40
   print_every: 10
-  results_dir: ./results/2024-05-16-01-16-48
+  results_dir: ./results/2024-05-17-04-26-40
   seed: 0
-  timestamp_id: 2024-05-16-01-16-48
-  version: 0.1.dev1+g58f2726
+  timestamp_id: 2024-05-17-04-26-40
+  version: 1.0.0
 dataset:
   a2g_args:
     r_energy: false
@@ -121,23 +121,23 @@ test_dataset:
 trainer: ocp
 val_dataset: null
 
-2024-05-16 01:16:49 (INFO): Loading dataset: ase_db
-2024-05-16 01:16:49 (INFO): rank: 0: Sampler created...
-2024-05-16 01:16:49 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-16 01:16:49 (INFO): rank: 0: Sampler created...
-2024-05-16 01:16:49 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-16 01:16:49 (INFO): Loading model: gemnet_t
-2024-05-16 01:16:51 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-05-16 01:16:51 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-05-16 01:16:51 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-05-16 01:16:51 (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. 
-2024-05-16 01:16:51 (WARNING): Scale factor comment not found in model
-2024-05-16 01:16:51 (INFO): Predicting on test.
+2024-05-17 04:26:52 (INFO): Loading dataset: ase_db
+2024-05-17 04:26:52 (INFO): rank: 0: Sampler created...
+2024-05-17 04:26:52 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-17 04:26:52 (INFO): rank: 0: Sampler created...
+2024-05-17 04:26:52 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-17 04:26:52 (INFO): Loading model: gemnet_t
+2024-05-17 04:26:54 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-05-17 04:26:54 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-17 04:26:54 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-05-17 04:26:54 (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 04:26:54 (WARNING): Scale factor comment not found in model
+2024-05-17 04:26:54 (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,  3.32s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.17s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:06<00:00,  1.99s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.33s/it]
-2024-05-16 01:16:58 (INFO): Writing results to ./results/2024-05-16-01-16-48/ocp_predictions.npz
-2024-05-16 01:16:58 (INFO): Total time taken: 7.149884939193726
-Elapsed time = 13.2 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:04<00:08,  4.49s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:02,  2.95s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.11s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.50s/it]
+2024-05-17 04:27:02 (INFO): Writing results to ./results/2024-05-17-04-26-40/ocp_predictions.npz
+2024-05-17 04:27:02 (INFO): Total time taken: 7.6487016677856445
+Elapsed time = 13.7 seconds

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diff --git a/_images/df81306bc2df8846723f37101ee39d5e6ed7c601a8d3301743ed30d682d6fcb9.png b/_images/df81306bc2df8846723f37101ee39d5e6ed7c601a8d3301743ed30d682d6fcb9.png
diff --git a/_images/e034aa0bf50e94c9b8c21dfd38685144358e18df151b860989429ad3c691fad5.png b/_images/e034aa0bf50e94c9b8c21dfd38685144358e18df151b860989429ad3c691fad5.png
diff --git a/_images/e638e3dfce54d9f2628a94f1bb80dd5af14cd9a8bc9749d3b7d63401694e0023.png b/_images/e638e3dfce54d9f2628a94f1bb80dd5af14cd9a8bc9749d3b7d63401694e0023.png
diff --git a/_images/e8ef0f1cc7af5773559f7fbca167e0b01c0fd0f8135d77912f0ab06fff4fdb7d.png b/_images/e8ef0f1cc7af5773559f7fbca167e0b01c0fd0f8135d77912f0ab06fff4fdb7d.png
diff --git a/_sources/core/install.md b/_sources/core/install.md
@@ -4,7 +4,7 @@
 
 We do not have official conda recipes (yet!); in the meantime you can use the
 following environment yaml files for CPU [env.cpu.yml](https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/packages/env.cpu.yml)
-and GPU [env.gpu.yml](https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/packages/env.gpu.yml) to easily set up a
+or GPU [env.gpu.yml](https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/packages/env.gpu.yml) to easily set up a
 working environment and install `fairchem-core`.
 
 1. Create an environment to install *fairchem*
@@ -39,7 +39,7 @@ You can also install `pytorch` and `torch_geometric` dependencies from PyPI to s
 
 3. Install `fairchem-core` from PyPi
    ```bash
-   pip install -i fairchem-core
+   pip install fairchem-core
    ```
 
 
@@ -57,12 +57,12 @@ If you plan to make contributions you will need to clone (for windows user pleas
 `fairchem-core` in editable mode with dev
 dependencies,
 ```bash
-pip install -e pip install packages/fairchem-core[dev]
+pip install -e packages/fairchem-core[dev]
 ```
 
 And similarly for any other namespace package:
 ```bash
-pip install packages/fairchem-{package-to-install}
+pip install -e packages/fairchem-{package-to-install}
 ```
 
 ### Cloning and installing the git repository on windows

diff --git a/core/fine-tuning/fine-tuning-oxides.html b/core/fine-tuning/fine-tuning-oxides.html
@@ -826,7 +826,7 @@ <h1>Fine tuning a model<a class="headerlink" href="#fine-tuning-a-model" title="
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time 67.7 seconds.
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time 68.0 seconds.
 </pre></div>
 </div>
 <img alt="../../_images/779c250f6bf7aaa03eef896ef1541e648ebf742911fe25095bde7b712d7234d4.png" src="../../_images/779c250f6bf7aaa03eef896ef1541e648ebf742911fe25095bde7b712d7234d4.png" />
@@ -1189,7 +1189,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 <span class="expanded">Hide code cell output</span>
 </summary>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time = 205.3 seconds
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Elapsed time = 207.5 seconds
 </pre></div>
 </div>
 </div>
@@ -1205,7 +1205,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&#39;fine-tuning/checkpoints/2024-05-16-01-10-24-ft-oxides&#39;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&#39;fine-tuning/checkpoints/2024-05-17-04-22-24-ft-oxides&#39;
 </pre></div>
 </div>
 </div>
@@ -1264,7 +1264,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/86e50dd50fffa230849cbbdbf675714ecf18b7c5dff2366634cbed1af1e6552d.png" src="../../_images/86e50dd50fffa230849cbbdbf675714ecf18b7c5dff2366634cbed1af1e6552d.png" />
+<img alt="../../_images/e638e3dfce54d9f2628a94f1bb80dd5af14cd9a8bc9749d3b7d63401694e0023.png" src="../../_images/e638e3dfce54d9f2628a94f1bb80dd5af14cd9a8bc9749d3b7d63401694e0023.png" />
 </div>
 </div>
 <div class="cell docutils container">
@@ -1275,7 +1275,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>New MAE = 0.197 eV/atom
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>New MAE = 0.275 eV/atom
 </pre></div>
 </div>
 </div>
@@ -1294,7 +1294,7 @@ <h2>Running the training job<a class="headerlink" href="#running-the-training-jo
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/6903f584d9ae5d999aa5c9e320b8a21966af012bc13951da7d1ef126c2190c2a.png" src="../../_images/6903f584d9ae5d999aa5c9e320b8a21966af012bc13951da7d1ef126c2190c2a.png" />
+<img alt="../../_images/b0529f8dcd95c7828d264993233e6c09c5d313f219ed172352360334f07adeb3.png" src="../../_images/b0529f8dcd95c7828d264993233e6c09c5d313f219ed172352360334f07adeb3.png" />
 </div>
 </div>
 <p>It is possible to continue refining the fit. The simple things to do are to use more epochs of training. Eventually the MAE will stabilize, and then it may be necessary to adjust other optimization parameters like the learning rate (usually you decrease it).</p>

diff --git a/core/gotchas.html b/core/gotchas.html
@@ -979,7 +979,7 @@ <h1>I get wildly different energies from the different models<a class="headerlin
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.6612038612365723
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.6753945350646973
 </pre></div>
 </div>
 </div>
@@ -1484,7 +1484,7 @@ <h1>To tag or not?<a class="headerlink" href="#to-tag-or-not" title="Link to thi
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>-0.42973777651786804
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>-0.42973756790161133
 </pre></div>
 </div>
 </div>
@@ -1531,17 +1531,17 @@ <h1>Stochastic simulation results<a class="headerlink" href="#stochastic-simulat
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.2139862060546875 1.839998376996492e-06
-1.213987112045288
-1.2139861583709717
-1.2139852046966553
-1.2139906883239746
-1.213986873626709
-1.213986873626709
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1.2139867305755616 1.1039578345098711e-06
+1.2139878273010254
 1.2139852046966553
-1.2139854431152344
+1.2139878273010254
+1.2139878273010254
 1.2139852046966553
-1.2139832973480225
+1.2139873504638672
+1.2139861583709717
+1.2139880657196045
+1.2139861583709717
+1.2139856815338135
 </pre></div>
 </div>
 </div>
@@ -1579,7 +1579,7 @@ <h1>The forces don’t sum to zero<a class="headerlink" href="#the-forces-don-t-
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([ 0.00848202,  0.01409356, -0.0588274 ], dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([ 0.0084798 ,  0.01409972, -0.05882883], dtype=float32)
 </pre></div>
 </div>
 </div>
@@ -1592,7 +1592,7 @@ <h1>The forces don’t sum to zero<a class="headerlink" href="#the-forces-don-t-
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([-3.213063e-08, -2.514571e-08,  0.000000e+00], dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([9.1735274e-08, 6.3213520e-08, 1.1920929e-07], dtype=float32)
 </pre></div>
 </div>
 </div>