build based on 2c994c3

previews/PR74/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-18T00:11:24","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-18T00:12:49","documenter_version":"1.4.1"}}

previews/PR74/generated/LJ-Ar/lennard-jones-ar/index.html

@@ -4,10 +4,10 @@
 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><pre class="documenter-example-output"><code class="nohighlight hljs ansi">&quot;/home/runner/work/PotentialLearning.jl/PotentialLearning.jl/src/../examples/LJ-Ar/../data/LJ-AR/lj-ar.yaml&quot;</code></pre><h2 id="Load-atomistic-dataset"><a class="docs-heading-anchor" href="#Load-atomistic-dataset">Load atomistic dataset</a><a id="Load-atomistic-dataset-1"></a><a class="docs-heading-anchor-permalink" href="#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, 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}}}, Energy, Forces}
-	 Configuration{S, 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}}}, Energy, Forces}
+	 Configuration{S, Energy, 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}}}, Forces}
+	 Configuration{S, Energy, 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}}}, Forces}
 	 ⋮
-	 Configuration{S, 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}}}, Energy, Forces}</code></pre><h2 id="Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range."><a class="docs-heading-anchor" href="#Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range.">Compute distance from origin, extract LJ energies, and define time range.</a><a id="Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range.-1"></a><a class="docs-heading-anchor-permalink" href="#Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range." title="Permalink"></a></h2><p>Get atom positions and compute distance from origin.</p><pre><code class="language-julia hljs">systems = get_system.(ds)
+	 Configuration{S, Energy, 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}}}, Forces}</code></pre><h2 id="Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range."><a class="docs-heading-anchor" href="#Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range.">Compute distance from origin, extract LJ energies, and define time range.</a><a id="Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range.-1"></a><a class="docs-heading-anchor-permalink" href="#Compute-distance-from-origin,-extract-LJ-energies,-and-define-time-range." title="Permalink"></a></h2><p>Get atom positions and compute distance from origin.</p><pre><code class="language-julia hljs">systems = get_system.(ds)
 n_atoms = length(first(systems)) # Note: in this dataset all systems contain the same no. of atoms
 positions = position.(systems)
 dists_origin = map(x-&gt;ustrip.(norm.(x)), positions)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">10000-element Vector{Vector{Float64}}:
@@ -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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 18 June 2024 00:11">Tuesday 18 June 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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 18 June 2024 00:12">Tuesday 18 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>