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 <!DOCTYPE html>
 <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Load Ar+Lennard-Jones dataset and postprocess · PotentialLearning.jl</title><meta name="title" content="Load Ar+Lennard-Jones dataset and postprocess · PotentialLearning.jl"/><meta property="og:title" content="Load Ar+Lennard-Jones dataset and postprocess · PotentialLearning.jl"/><meta property="twitter:title" content="Load Ar+Lennard-Jones dataset and postprocess · PotentialLearning.jl"/><meta name="description" content="Documentation for PotentialLearning.jl."/><meta property="og:description" content="Documentation for PotentialLearning.jl."/><meta property="twitter:description" content="Documentation for PotentialLearning.jl."/><meta property="og:url" content="https://cesmix-mit.github.io/PotentialLearning.jl/generated/LJ-Ar/lennard-jones-ar/"/><meta property="twitter:url" content="https://cesmix-mit.github.io/PotentialLearning.jl/generated/LJ-Ar/lennard-jones-ar/"/><link rel="canonical" href="https://cesmix-mit.github.io/PotentialLearning.jl/generated/LJ-Ar/lennard-jones-ar/"/><script data-outdated-warner src="../../../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="../../.."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../../../assets/documenter.js"></script><script src="../../../search_index.js"></script><script src="../../../siteinfo.js"></script><script src="../../../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../../assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../../assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../../assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../../assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../../../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../../../">PotentialLearning.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../../../">Home</a></li><li><a class="tocitem" href="../../../install-and-run-examples/">Install and run examples</a></li><li><span class="tocitem">Basic examples</span><ul><li><a class="tocitem" href="../../ACE-aHfO2/fit-ace-ahfo2/">Fit a-HfO2 dataset with ACE</a></li></ul></li><li><span class="tocitem">Intelligent subsampling</span><ul><li><a class="tocitem" href="../../DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2/">Subsample a-HfO2 dataset with DPP and fit with ACE</a></li><li><a class="tocitem" href="../../DPP-ACE-Na/fit-dpp-ace-na/">Subsample Na dataset with DPP and fit with ACE</a></li><li><a class="tocitem" href="../../DPP-ACE-Si/fit-dpp-ace-si/">Subsample Si dataset with DPP, fit with ACE, and cross validate</a></li></ul></li><li><span class="tocitem">Hyper-parameter optimization</span><ul><li><a class="tocitem" href="../../Opt-ACE-aHfO2/fit-opt-ace-ahfo2/">Optimize ACE hyper-parameters: minimize force time and fitting error</a></li></ul></li><li><span class="tocitem">Dimension reduction</span><ul><li><a class="tocitem" href="../../PCA-ACE-aHfO2/fit-pca-ace-ahfo2/">Reduce ACE descriptors with PCA and fit a-HfO2 dataset</a></li></ul></li><li><span class="tocitem">Misc</span><ul><li class="is-active"><a class="tocitem" href>Load Ar+Lennard-Jones dataset and postprocess</a><ul class="internal"><li><a class="tocitem" href="#a.-Load-packages-and-define-paths."><span>a. Load packages and define paths.</span></a></li><li><a class="tocitem" href="#b.-Load-atomistic-dataset."><span>b. Load atomistic dataset.</span></a></li><li><a class="tocitem" href="#c.-Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range."><span>c. Compute distance from origin, extract LJ energies, and define time range.</span></a></li><li><a class="tocitem" href="#d.-Post-process-data."><span>d. Post-process data.</span></a></li></ul></li></ul></li><li><a class="tocitem" href="../../../api/">API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Misc</a></li><li class="is-active"><a href>Load Ar+Lennard-Jones dataset and postprocess</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Load Ar+Lennard-Jones dataset and postprocess</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/cesmix-mit/PotentialLearning.jl/blob/main/examples/LJ-Ar/lennard-jones-ar.jl#" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Load-Ar-dataset-with-energies-computed-by-Lennard-Jones-and-postprocess"><a class="docs-heading-anchor" href="#Load-Ar-dataset-with-energies-computed-by-Lennard-Jones-and-postprocess">Load Ar dataset with energies computed by Lennard-Jones and postprocess</a><a id="Load-Ar-dataset-with-energies-computed-by-Lennard-Jones-and-postprocess-1"></a><a class="docs-heading-anchor-permalink" href="#Load-Ar-dataset-with-energies-computed-by-Lennard-Jones-and-postprocess" title="Permalink"></a></h1><h2 id="a.-Load-packages-and-define-paths."><a class="docs-heading-anchor" href="#a.-Load-packages-and-define-paths.">a. Load packages and define paths.</a><a id="a.-Load-packages-and-define-paths.-1"></a><a class="docs-heading-anchor-permalink" href="#a.-Load-packages-and-define-paths." title="Permalink"></a></h2><p>Load packages.</p><pre><code class="language-julia hljs">using Unitful, UnitfulAtomic
 using AtomsBase, InteratomicPotentials, PotentialLearning
-using LinearAlgebra, Plots, DisplayAs</code></pre><p>Define paths.</p><pre><code class="language-julia hljs">path = joinpath(dirname(pathof(PotentialLearning)), &quot;../examples/LJ-Ar&quot;)
-ds_path = &quot;$path/../data/LJ-AR/lj-ar.yaml&quot;;</code></pre><h2 id="b.-Load-atomistic-dataset."><a class="docs-heading-anchor" href="#b.-Load-atomistic-dataset.">b. Load atomistic dataset.</a><a id="b.-Load-atomistic-dataset.-1"></a><a class="docs-heading-anchor-permalink" href="#b.-Load-atomistic-dataset." title="Permalink"></a></h2><pre><code class="language-julia hljs">ds, thermo = load_data(ds_path, YAML(:Ar, u&quot;eV&quot;, u&quot;Å&quot;))
+using LinearAlgebra, Plots, DisplayAs</code></pre><p>Define paths.</p><pre><code class="language-julia hljs">base_path = haskey(ENV, &quot;BASE_PATH&quot;) ? ENV[&quot;BASE_PATH&quot;] : &quot;../../&quot;
+ds_path   = &quot;$base_path/examples/data/LJ-AR/lj-ar.yaml&quot;</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">&quot;/home/runner/work/PotentialLearning.jl/PotentialLearning.jl/docs/..//examples/data/LJ-AR/lj-ar.yaml&quot;</code></pre><h2 id="b.-Load-atomistic-dataset."><a class="docs-heading-anchor" href="#b.-Load-atomistic-dataset.">b. Load atomistic dataset.</a><a id="b.-Load-atomistic-dataset.-1"></a><a class="docs-heading-anchor-permalink" href="#b.-Load-atomistic-dataset." title="Permalink"></a></h2><pre><code class="language-julia hljs">ds, thermo = load_data(ds_path, YAML(:Ar, u&quot;eV&quot;, u&quot;Å&quot;))
 ds = @views ds[2:end] # Filter first configuration (zero energy)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">DataSet{num_configs = 10000} 
 	 Configuration{S, Energy, Forces, AtomsBase.FlexibleSystem{3, AtomsBase.Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(a₀, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}}
 	 Configuration{S, Energy, Forces, AtomsBase.FlexibleSystem{3, AtomsBase.Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(a₀, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}}
@@ -60,4 +60,4 @@
          xlabel = &quot;τ | ps&quot;,
          ylabel = &quot;Lennard Jones energy | eV&quot;,
          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="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>
+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="Sunday 14 July 2024 00:35">Sunday 14 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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