build based on f2d862d

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-21T05:50:31","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-21T05:53:43","documenter_version":"1.8.0"}}

dev/tutorial/index.html

@@ -16,12 +16,12 @@
  0.0 nm s^-1
  0.0 nm s^-1</code></pre><p>See <a href="https://github.com/JuliaMolSim/AtomsBase.jl/blob/master/src/implementation/atom.jl"><code>atom.jl</code></a> and the respective API documentation for details. Notice in particular that <a href="../apireference/#AtomsBase.atomic_number"><code>atomic_number</code></a> specifies the element whereas <a href="../apireference/#AtomsBase.species"><code>species</code></a> and also <a href="../apireference/#AtomsBase.atomic_symbol"><code>atomic_symbol</code></a> may be more specific and may e.g. specify isotopes such as deuterium</p><pre><code class="language-julia hljs">deuterium = Atom(:D, [0, 1, 2.]u&quot;bohr&quot;)
 atomic_number(deuterium) == 1
-atomic_symbol(deuterium) == :D</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">true</code></pre><p>An equivalent dict-like interface based on <code>keys</code>, <code>haskey</code>, <code>get</code> and <code>pairs</code> is also available. For example</p><pre><code class="language-julia hljs">keys(atom)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(:position, :velocity, :species, :mass)</code></pre><pre><code class="language-julia hljs">atom[:species]</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">C</code></pre><pre><code class="language-julia hljs">pairs(atom)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Base.Generator{NTuple{4, Symbol}, AtomsBase.var&quot;#57#58&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}}(AtomsBase.var&quot;#57#58&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}(Atom(C,  [       0,        1,        2]u&quot;a₀&quot;)), (:position, :velocity, :species, :mass))</code></pre><p>This interface seamlessly generalises to working with user-specific atomic properties as will be discussed next.</p><h3 id="Optional-atomic-properties"><a class="docs-heading-anchor" href="#Optional-atomic-properties">Optional atomic properties</a><a id="Optional-atomic-properties-1"></a><a class="docs-heading-anchor-permalink" href="#Optional-atomic-properties" title="Permalink"></a></h3><p>Custom properties can be attached to an <code>Atom</code> by supplying arbitrary keyword arguments upon construction. For example to attach a pseudopotential for using the structure with <a href="https://dftk.org">DFTK</a>, construct the atom as</p><pre><code class="language-julia hljs">atom = Atom(:C, [0, 1, 2.]u&quot;bohr&quot;, pseudopotential=&quot;hgh/lda/c-q4&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Atom(C, Z = 6, m = 12.011 u):
+atomic_symbol(deuterium) == :D</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">true</code></pre><p>An equivalent dict-like interface based on <code>keys</code>, <code>haskey</code>, <code>get</code> and <code>pairs</code> is also available. For example</p><pre><code class="language-julia hljs">keys(atom)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(:position, :velocity, :species, :mass)</code></pre><pre><code class="language-julia hljs">atom[:species]</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">C</code></pre><pre><code class="language-julia hljs">pairs(atom)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Base.Generator{NTuple{4, Symbol}, AtomsBase.var&quot;#58#59&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}}(AtomsBase.var&quot;#58#59&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}(Atom(C,  [       0,        1,        2]u&quot;a₀&quot;)), (:position, :velocity, :species, :mass))</code></pre><p>This interface seamlessly generalises to working with user-specific atomic properties as will be discussed next.</p><h3 id="Optional-atomic-properties"><a class="docs-heading-anchor" href="#Optional-atomic-properties">Optional atomic properties</a><a id="Optional-atomic-properties-1"></a><a class="docs-heading-anchor-permalink" href="#Optional-atomic-properties" title="Permalink"></a></h3><p>Custom properties can be attached to an <code>Atom</code> by supplying arbitrary keyword arguments upon construction. For example to attach a pseudopotential for using the structure with <a href="https://dftk.org">DFTK</a>, construct the atom as</p><pre><code class="language-julia hljs">atom = Atom(:C, [0, 1, 2.]u&quot;bohr&quot;, pseudopotential=&quot;hgh/lda/c-q4&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Atom(C, Z = 6, m = 12.011 u):
     position          : [0,1,2]u&quot;a₀&quot;
     species           : C
     pseudopotential   : hgh/lda/c-q4
 </code></pre><p>which will make the pseudopotential identifier available as</p><pre><code class="language-julia hljs">atom[:pseudopotential]</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">&quot;hgh/lda/c-q4&quot;</code></pre><p>Notice that such custom properties are fully integrated with the standard atomic properties, e.g. automatically available from the <code>keys</code>, <code>haskey</code> and <code>pairs</code> functions, e.g.:</p><pre><code class="language-julia hljs">@show haskey(atom, :pseudopotential)
-pairs(atom)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Base.Generator{NTuple{5, Symbol}, AtomsBase.var&quot;#57#58&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}}(AtomsBase.var&quot;#57#58&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}(Atom(C,  [       0,        1,        2]u&quot;a₀&quot;)), (:position, :velocity, :species, :mass, :pseudopotential))</code></pre><p>Updating an atomic property proceeds similarly. E.g.</p><pre><code class="language-julia hljs">newatom = Atom(atom; atomic_mass=13u&quot;u&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Atom(C, Z = 6, m = 12.011 u):
+pairs(atom)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Base.Generator{NTuple{5, Symbol}, AtomsBase.var&quot;#58#59&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}}(AtomsBase.var&quot;#58#59&quot;{Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(nm, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}}(Atom(C,  [       0,        1,        2]u&quot;a₀&quot;)), (:position, :velocity, :species, :mass, :pseudopotential))</code></pre><p>Updating an atomic property proceeds similarly. E.g.</p><pre><code class="language-julia hljs">newatom = Atom(atom; atomic_mass=13u&quot;u&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Atom(C, Z = 6, m = 12.011 u):
     position          : [0,1,2]u&quot;a₀&quot;
     species           : C
     atomic_mass       : 13 u
@@ -87,4 +87,4 @@
 
     Atom(H,  [       0,        0,        1]u&quot;a₀&quot;)
     Atom(H,  [       0,        0,        3]u&quot;a₀&quot;)
-</code></pre><p>Again these custom properties are fully integrated with <code>keys</code>, <code>haskey</code>, <code>pairs</code> and <code>get</code>.</p><pre><code class="language-julia hljs">@show keys(system)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(:cell_vectors, :periodicity, :extra_data)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../implementations/">« Implementations</a><a class="docs-footer-nextpage" href="../apireference/">Reference »</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 1.8.0 on <span class="colophon-date" title="Thursday 21 November 2024 05:50">Thursday 21 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>Again these custom properties are fully integrated with <code>keys</code>, <code>haskey</code>, <code>pairs</code> and <code>get</code>.</p><pre><code class="language-julia hljs">@show keys(system)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(:cell_vectors, :periodicity, :extra_data)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../implementations/">« Implementations</a><a class="docs-footer-nextpage" href="../apireference/">Reference »</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 1.8.0 on <span class="colophon-date" title="Thursday 21 November 2024 05:53">Thursday 21 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>