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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-16T04:16:04","documenter_version":"1.8.0"}}
{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-20T16:10:55","documenter_version":"1.8.0"}}
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16 changes: 8 additions & 8 deletions dev/examples/index.html
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simulate!(sys, simulator, 5_000; run_loggers=:skipzero)
end

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="Step",
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end
end

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="End-to-end distance / nm",
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end
end

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="Angle with adjacent monomers / degrees",
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forces_direct = force_direct.(dists)
forces_grad = force_grad.(dists)

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="Distance / nm",
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end
end

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="Distance / nm",
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end
end

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="Distance / nm",
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end
end

f = Figure(resolution=(600, 400))
f = Figure(size=(600, 400))
ax = Axis(
f[1, 1],
xlabel="Distance / nm",
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# Check that the constraints are satisfied at the end of the simulation
@test check_position_constraints(sys, shake)
@test check_velocity_constraints(sys, shake)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../differentiable/">« Differentiable simulation</a><a class="docs-footer-nextpage" href="../exercises/">Exercises »</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="Monday 16 December 2024 04:16">Monday 16 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
@test check_velocity_constraints(sys, shake)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../differentiable/">« Differentiable simulation</a><a class="docs-footer-nextpage" href="../exercises/">Exercises »</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="Friday 20 December 2024 16:10">Friday 20 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/exercises/index.html
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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>Exercises · Molly.jl</title><meta name="title" content="Exercises · Molly.jl"/><meta property="og:title" content="Exercises · Molly.jl"/><meta property="twitter:title" content="Exercises · Molly.jl"/><meta name="description" content="Documentation for Molly.jl."/><meta property="og:description" content="Documentation for Molly.jl."/><meta property="twitter:description" content="Documentation for Molly.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 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" 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(Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../documentation/">Documentation</a></li><li><a class="tocitem" href="../differentiable/">Differentiable simulation</a></li><li><a class="tocitem" href="../examples/">Examples</a></li><li class="is-active"><a class="tocitem" href>Exercises</a></li><li><a class="tocitem" href="../publications/">Publications</a></li><li><a class="tocitem" href="../related/">Related software</a></li><li><a class="tocitem" href="../development/">Development</a></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 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title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Molly-exercises"><a class="docs-heading-anchor" href="#Molly-exercises">Molly exercises</a><a id="Molly-exercises-1"></a><a class="docs-heading-anchor-permalink" href="#Molly-exercises" title="Permalink"></a></h1><p>A notebook with exercises covering various parts of Molly is available <a href="https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/molly_average.ipynb">here</a>, with answers available <a href="https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/molly_average_answers.ipynb">here</a>.</p><p>Another notebook with exercises on computing transport coefficients with Molly is available <a href="https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/shear_viscosity.ipynb">here</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../examples/">« Examples</a><a class="docs-footer-nextpage" href="../publications/">Publications »</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="Monday 16 December 2024 04:16">Monday 16 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Exercises · Molly.jl</title><meta name="title" content="Exercises · Molly.jl"/><meta property="og:title" content="Exercises · Molly.jl"/><meta property="twitter:title" content="Exercises · Molly.jl"/><meta name="description" content="Documentation for Molly.jl."/><meta property="og:description" content="Documentation for Molly.jl."/><meta property="twitter:description" content="Documentation for Molly.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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(Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../documentation/">Documentation</a></li><li><a class="tocitem" href="../differentiable/">Differentiable simulation</a></li><li><a class="tocitem" href="../examples/">Examples</a></li><li class="is-active"><a class="tocitem" href>Exercises</a></li><li><a class="tocitem" href="../publications/">Publications</a></li><li><a class="tocitem" href="../related/">Related software</a></li><li><a class="tocitem" href="../development/">Development</a></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 class="is-active"><a href>Exercises</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Exercises</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/JuliaMolSim/Molly.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/JuliaMolSim/Molly.jl/blob/master/docs/src/exercises.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="Molly-exercises"><a class="docs-heading-anchor" href="#Molly-exercises">Molly exercises</a><a id="Molly-exercises-1"></a><a class="docs-heading-anchor-permalink" href="#Molly-exercises" title="Permalink"></a></h1><p>A notebook with exercises covering various parts of Molly is available <a href="https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/molly_average.ipynb">here</a>, with answers available <a href="https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/molly_average_answers.ipynb">here</a>.</p><p>Another notebook with exercises on computing transport coefficients with Molly is available <a href="https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/shear_viscosity.ipynb">here</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../examples/">« Examples</a><a class="docs-footer-nextpage" href="../publications/">Publications »</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="Friday 20 December 2024 16:10">Friday 20 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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