build based on 66b1242

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-09T18:38:10","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-12T23:11:36","documenter_version":"1.5.0"}}

dev/generated/LJ-Ar/lennard-jones-ar/index.html

@@ -60,4 +60,4 @@
          xlabel = "τ | ps",
          ylabel = "Lennard Jones energy | eV",
          dpi = 300, fontsize = 12)
-DisplayAs.PNG(p)</code></pre><img src="4bd94ae8.png" alt="Example block output"/><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../PCA-ACE-aHfO2/fit-pca-ace-ahfo2/">« Reduce ACE descriptors with PCA and fit a-HfO2 dataset</a><a class="docs-footer-nextpage" href="../../../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Tuesday 9 July 2024 18:38">Tuesday 9 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+DisplayAs.PNG(p)</code></pre><img src="4bd94ae8.png" alt="Example block output"/><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../PCA-ACE-aHfO2/fit-pca-ace-ahfo2/">« Reduce ACE descriptors with PCA and fit a-HfO2 dataset</a><a class="docs-footer-nextpage" href="../../../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Friday 12 July 2024 23:11">Friday 12 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -11,4 +11,4 @@
 end
 iap, res = hyperlearn!(model, pars, conf_train; loss = custom_loss);</code></pre><p>2 - Export optimal values to your molecular dynamic workflow.</p><p>See <a href="https://cesmix-mit.github.io/PotentialLearning.jl/dev/generated/Opt-ACE-aHfO2/fit-opt-ace-ahfo2/">example</a>.</p><p>The models are compatible with the interfaces of our sister package <a href="https://github.com/cesmix-mit/InteratomicPotentials.jl">InteratomicPotentials.jl</a>. In particular, we are interested in maintaining compatibility with <a href="https://github.com/ACEsuit">ACESuit</a>, as well as integrating <a href="https://www.lammps.org/">LAMMPS</a> based potentials such as <a href="https://docs.lammps.org/Packages_details.html#pkg-ml-pod">ML-POD</a> and <a href="https://docs.lammps.org/Packages_details.html#ml-pace-package">ML-PACE</a>. We are also working to provide neural network potential architecture optimization.</p><h2 id="Compress-interatomic-potential-data-and-model"><a class="docs-heading-anchor" href="#Compress-interatomic-potential-data-and-model">Compress interatomic potential data and model</a><a id="Compress-interatomic-potential-data-and-model-1"></a><a class="docs-heading-anchor-permalink" href="#Compress-interatomic-potential-data-and-model" title="Permalink"></a></h2><p>Compress interatomic potential data and model using dimensionality reduction of energy and force descriptors:</p><p>1 - Define a PCA state, fit PCA with your the energy and force descriptors of your dataset, and transform all dataset descriptors.</p><pre><code class="language-julia hljs">pca = PCAState(tol = n_desc)
 fit!(ds_train, pca)
-transform!(ds_train, pca)</code></pre><p>2 - Export PCA fitted data to be used in your workflow.</p><p>See <a href="https://cesmix-mit.github.io/PotentialLearning.jl/dev/generated/PCA-ACE-aHfO2/fit-pca-ace-ahfo2/">example</a>.</p><p>We are working to provide feature selection of energy and force descriptors based on <a href="https://github.com/JuliaLinearAlgebra/LowRankApprox.jl">CUR</a>.</p><p>Additionally, this package includes utilities for loading input data (such as XYZ files), computing various metrics (including MAE, MSE, RSQ, and COV), exporting results, and generating plots.</p><h2 id="Acknowledgment"><a class="docs-heading-anchor" href="#Acknowledgment">Acknowledgment</a><a id="Acknowledgment-1"></a><a class="docs-heading-anchor-permalink" href="#Acknowledgment" title="Permalink"></a></h2><p>Center for the Exascale Simulation of Materials in Extreme Environments (<a href="https://computing.mit.edu/cesmix/">CESMIX</a>). Massachusetts Institute of Technology (<a href="https://www.mit.edu/">MIT</a>).</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="install-and-run-examples/">Install and run examples »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Tuesday 9 July 2024 18:38">Tuesday 9 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+transform!(ds_train, pca)</code></pre><p>2 - Export PCA fitted data to be used in your workflow.</p><p>See <a href="https://cesmix-mit.github.io/PotentialLearning.jl/dev/generated/PCA-ACE-aHfO2/fit-pca-ace-ahfo2/">example</a>.</p><p>We are working to provide feature selection of energy and force descriptors based on <a href="https://github.com/JuliaLinearAlgebra/LowRankApprox.jl">CUR</a>.</p><p>Additionally, this package includes utilities for loading input data (such as XYZ files), computing various metrics (including MAE, MSE, RSQ, and COV), exporting results, and generating plots.</p><h2 id="Acknowledgment"><a class="docs-heading-anchor" href="#Acknowledgment">Acknowledgment</a><a id="Acknowledgment-1"></a><a class="docs-heading-anchor-permalink" href="#Acknowledgment" title="Permalink"></a></h2><p>Center for the Exascale Simulation of Materials in Extreme Environments (<a href="https://computing.mit.edu/cesmix/">CESMIX</a>). Massachusetts Institute of Technology (<a href="https://www.mit.edu/">MIT</a>).</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="install-and-run-examples/">Install and run examples »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Friday 12 July 2024 23:11">Friday 12 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/install-and-run-examples/index.html

@@ -3,4 +3,4 @@
     pkg> registry add https://github.com/cesmix-mit/CESMIX.git 
     pkg> registry add https://github.com/JuliaMolSim/MolSim.git
     pkg&gt; registry add https://github.com/ACEsuit/ACEregistry</code></pre><p>Then, add PotentialLearning:</p><pre><code class="language-julia hljs">    pkg&gt; add PotentialLearning
-</code></pre><h2 id="Clone-repository-and-access-an-example-folder"><a class="docs-heading-anchor" href="#Clone-repository-and-access-an-example-folder">Clone repository and access an example folder</a><a id="Clone-repository-and-access-an-example-folder-1"></a><a class="docs-heading-anchor-permalink" href="#Clone-repository-and-access-an-example-folder" title="Permalink"></a></h2><p>Clone <code>PotentialLearning.jl</code> repository in your working directory.</p><pre><code class="language-shell hljs">    $ git clone [email protected]:cesmix-mit/PotentialLearning.jl.git</code></pre><p>Access to any folder within <code>PotentialLearning.jl/examples</code>. E.g.</p><pre><code class="language-shell hljs">    $ cd PotentialLearning.jl/examples/DPP-ACE-aHfO2-1</code></pre><h2 id="Run-example"><a class="docs-heading-anchor" href="#Run-example">Run example</a><a id="Run-example-1"></a><a class="docs-heading-anchor-permalink" href="#Run-example" title="Permalink"></a></h2><p>Open a Julia REPL, activate the <code>examples</code> folder project, and define the number of threads.</p><pre><code class="language-julia hljs">    $ julia --project=./ --threads=4</code></pre><p>Type <code>]</code> to enter the Pkg REPL and instantiate.</p><pre><code class="language-julia hljs">    pkg&gt; instantiate</code></pre><p>Finally, include the example file.</p><pre><code class="language-julia hljs">    julia&gt; include(&quot;fit-dpp-ace-ahfo2.jl&quot;)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../generated/ACE-aHfO2/fit-ace-ahfo2/">Fit a-HfO2 dataset with ACE »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Tuesday 9 July 2024 18:38">Tuesday 9 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><h2 id="Clone-repository-and-access-an-example-folder"><a class="docs-heading-anchor" href="#Clone-repository-and-access-an-example-folder">Clone repository and access an example folder</a><a id="Clone-repository-and-access-an-example-folder-1"></a><a class="docs-heading-anchor-permalink" href="#Clone-repository-and-access-an-example-folder" title="Permalink"></a></h2><p>Clone <code>PotentialLearning.jl</code> repository in your working directory.</p><pre><code class="language-shell hljs">    $ git clone [email protected]:cesmix-mit/PotentialLearning.jl.git</code></pre><p>Access to any folder within <code>PotentialLearning.jl/examples</code>. E.g.</p><pre><code class="language-shell hljs">    $ cd PotentialLearning.jl/examples/DPP-ACE-aHfO2-1</code></pre><h2 id="Run-example"><a class="docs-heading-anchor" href="#Run-example">Run example</a><a id="Run-example-1"></a><a class="docs-heading-anchor-permalink" href="#Run-example" title="Permalink"></a></h2><p>Open a Julia REPL, activate the <code>examples</code> folder project, and define the number of threads.</p><pre><code class="language-julia hljs">    $ julia --project=./ --threads=4</code></pre><p>Type <code>]</code> to enter the Pkg REPL and instantiate.</p><pre><code class="language-julia hljs">    pkg&gt; instantiate</code></pre><p>Finally, include the example file.</p><pre><code class="language-julia hljs">    julia&gt; include(&quot;fit-dpp-ace-ahfo2.jl&quot;)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../generated/ACE-aHfO2/fit-ace-ahfo2/">Fit a-HfO2 dataset with ACE »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Friday 12 July 2024 23:11">Friday 12 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>