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Documenter.jl committed Sep 25, 2024
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{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-25T00:45:18","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-25T11:51:33","documenter_version":"1.7.0"}}
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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>Home · Packmol.jl</title><meta name="title" content="Home · Packmol.jl"/><meta property="og:title" content="Home · Packmol.jl"/><meta property="twitter:title" content="Home · Packmol.jl"/><meta name="description" content="Documentation for Packmol.jl."/><meta property="og:description" content="Documentation for Packmol.jl."/><meta property="twitter:description" content="Documentation for Packmol.jl."/><script data-outdated-warner src="assets/warner.js"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 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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"><a class="docs-logo" href><img src="assets/logo.svg" alt="Packmol.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href>Packmol.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 class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#See-also"><span>See also</span></a></li><li class="toplevel"><a class="tocitem" href="#Reference"><span>Reference</span></a></li></ul></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 class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/m3g/Packmol.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/m3g/Packmol.jl/blob/main/docs/src/index.md" 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="Packmol.jl"><a class="docs-heading-anchor" href="#Packmol.jl">Packmol.jl</a><a id="Packmol.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Packmol.jl" title="Permalink"></a></h1><p><a href="https://github.com/m3g/Packmol.jl">Packmol.jl</a> is in very early stages of development.</p><h2 id="See-also"><a class="docs-heading-anchor" href="#See-also">See also</a><a id="See-also-1"></a><a class="docs-heading-anchor-permalink" href="#See-also" title="Permalink"></a></h2><p><a href="https://m3g.github.io/MolSimToolkit.jl/stable/system_setup/#Packmol-Input-Creator">MolSimToolkit.jl/Packmol-Input-Creator</a></p><h1 id="Reference"><a class="docs-heading-anchor" href="#Reference">Reference</a><a id="Reference-1"></a><a class="docs-heading-anchor-permalink" href="#Reference" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Packmol.run_packmol" href="#Packmol.run_packmol"><code>Packmol.run_packmol</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">run_packmol()
run_packmol(input_file::String)</code></pre><p>Runs the packmol executable with the input file <code>input_file</code>. This will run the classical <code>http://m3g.iqm.unicamp.br/packmol</code> program, which is a pre-compiled binary. The input file is a text file with the same syntax as the packmol input files.</p><p>If no input file is provided, a file explorer will be opened to choose the input file.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/Packmol.jl/blob/ef6eac3a23e1e3bac73089ca51a12a754b41f29c/src/packmol_runner.jl#L8-L20">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Packmol.pack_monoatomic!" href="#Packmol.pack_monoatomic!"><code>Packmol.pack_monoatomic!</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">pack_monoatomic!(positions::AbstractVector{&lt;:SVector{N,T}}, unitcell, tol)</code></pre><p>Pack a monoatomic system with iniital positions <code>x</code> and distance tolerance <code>tol</code>, into the unitcell defined by <code>unitcell</code>, considering periodic boundary conditions.</p><p>The unitcell can be a vector, in the case of orthorhombic cells, or a matrix, in the case of triclinic cells.</p><p>The coordinates and the unitcells can be two- or three-dimensional. </p><p><strong>Example</strong></p><pre><code class="language-julia-repl hljs">julia&gt; using Packmol, StaticArrays
run_packmol(input_file::String)</code></pre><p>Runs the packmol executable with the input file <code>input_file</code>. This will run the classical <code>http://m3g.iqm.unicamp.br/packmol</code> program, which is a pre-compiled binary. The input file is a text file with the same syntax as the packmol input files.</p><p>If no input file is provided, a file explorer will be opened to choose the input file.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/Packmol.jl/blob/288735c55d8be38e4544d18e32d326c02d0af3ae/src/packmol_runner.jl#L8-L20">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Packmol.pack_monoatomic!" href="#Packmol.pack_monoatomic!"><code>Packmol.pack_monoatomic!</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">pack_monoatomic!(positions::AbstractVector{&lt;:SVector{N,T}}, unitcell, tol)</code></pre><p>Pack a monoatomic system with iniital positions <code>x</code> and distance tolerance <code>tol</code>, into the unitcell defined by <code>unitcell</code>, considering periodic boundary conditions.</p><p>The unitcell can be a vector, in the case of orthorhombic cells, or a matrix, in the case of triclinic cells.</p><p>The coordinates and the unitcells can be two- or three-dimensional. </p><p><strong>Example</strong></p><pre><code class="language-julia-repl hljs">julia&gt; using Packmol, StaticArrays

julia&gt; coordinates = 100 * rand(SVector{3,Float64}, 10^5);

julia&gt; unitcell = [100.0, 100.0, 100.0]; tolerance = 2.0;

julia&gt; pack_monoatomic!(coordinates, unitcell, tolerance)</code></pre><p>After packing, the <code>coordinates</code> array will have updated positions for the atoms without overlaps. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/Packmol.jl/blob/ef6eac3a23e1e3bac73089ca51a12a754b41f29c/src/mono_atomic.jl#L82-L108">source</a></section></article></article><nav class="docs-footer"><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 1.7.0 on <span class="colophon-date" title="Wednesday 25 September 2024 00:45">Wednesday 25 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
julia&gt; pack_monoatomic!(coordinates, unitcell, tolerance)</code></pre><p>After packing, the <code>coordinates</code> array will have updated positions for the atoms without overlaps. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/Packmol.jl/blob/288735c55d8be38e4544d18e32d326c02d0af3ae/src/mono_atomic.jl#L82-L108">source</a></section></article></article><nav class="docs-footer"><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 1.7.0 on <span class="colophon-date" title="Wednesday 25 September 2024 11:51">Wednesday 25 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

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