-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Documenter.jl
committed
Sep 11, 2023
1 parent
92df14e
commit bb3760e
Showing
6 changed files
with
18 additions
and
18 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| <!DOCTYPE html> | ||
| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · AtomsBase.jl</title><script data-outdated-warner src="assets/warner.js"></script><link rel="canonical" href="https://juliamolsim.github.io/AtomsBase.jl/"/><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/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/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="siteinfo.js"></script><script src="../versions.js"></script><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>AtomsBase.jl</a></span></div><form class="docs-search" action="search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Packages-using-AtomsBase"><span>Packages using AtomsBase</span></a></li></ul></li><li><a class="tocitem" href="tutorial/">Tutorial</a></li><li><a class="tocitem" href="overview/">Overview</a></li><li><a class="tocitem" href="testing/">Testing against the AtomsBase interface</a></li><li><a class="tocitem" href="apireference/">API reference</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"><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-edit-link" href="https://github.com/JuliaMolSim/AtomsBase.jl/blob/master/README.md#" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="AtomsBase"><a class="docs-heading-anchor" href="#AtomsBase">AtomsBase</a><a id="AtomsBase-1"></a><a class="docs-heading-anchor-permalink" href="#AtomsBase" title="Permalink"></a></h1><p><em>A Julian abstract interface for atomic structures.</em></p><p><a href="https://JuliaMolSim.github.io/AtomsBase.jl/stable"><img src="https://img.shields.io/badge/docs-stable-blue.svg" alt="Stable"/></a> <a href="https://JuliaMolSim.github.io/AtomsBase.jl/dev"><img src="https://img.shields.io/badge/docs-dev-blue.svg" alt="Dev"/></a> <a href="https://github.com/JuliaMolSim/AtomsBase.jl/actions"><img src="https://github.com/JuliaMolSim/AtomsBase.jl/workflows/CI/badge.svg" alt="Build Status"/></a> <a href="https://codecov.io/gh/JuliaMolSim/AtomsBase.jl"><img src="https://codecov.io/gh/JuliaMolSim/AtomsBase.jl/branch/master/graph/badge.svg" alt="Coverage"/></a></p><p>AtomsBase is an abstract interface for representation of atomic geometries in Julia. It aims to be a lightweight means of facilitating interoperability between various tools including ...</p><ul><li>Chemical simulation engines:<ul><li><a href="https://github.com/JuliaMolSim/DFTK.jl">DFTK.jl</a> (density-functional theory)</li><li><a href="https://github.com/JuliaMolSim/Molly.jl">Molly.jl</a> (molecular dynamics)</li></ul></li><li>Integration with third party-libraries:<ul><li><a href="https://github.com/mfherbst/ASEconvert.jl">ASEconvert.jl</a> (integration with the Atomistic Simulation Environment)</li></ul></li><li>I/O with standard file formats (.cif, .xyz, ...)<ul><li>E.g. <a href="https://github.com/mfherbst/AtomIO.jl">AtomIO.jl</a></li></ul></li><li>automatic differentiation and machine learning systems<ul><li><a href="https://github.com/Chemellia/ChemistryFeaturization.jl">ChemistryFeaturization.jl</a> (featurization of atomic systems)</li></ul></li><li>numerical tools: sampling, integration schemes, etc.</li><li>visualization (e.g. plot recipes)</li></ul><p>Currently, the design philosophy is to be as lightweight as possible with a small set of required function dispatches to make adopting the interface easy. We also provide a couple of <a href="https://juliamolsim.github.io/AtomsBase.jl/stable/atomicsystems/#atomic-systems">standard flexible implementations of the interface</a> that we envision to be broadly applicable. If features beyond these are required we encourage developers to open PRs or provide their own implementations. For more on how to use the package, see <a href="https://juliamolsim.github.io/AtomsBase.jl/stable">the documentation</a>.</p><h2 id="Packages-using-AtomsBase"><a class="docs-heading-anchor" href="#Packages-using-AtomsBase">Packages using AtomsBase</a><a id="Packages-using-AtomsBase-1"></a><a class="docs-heading-anchor-permalink" href="#Packages-using-AtomsBase" title="Permalink"></a></h2><p>The following (not all yet-registered) packages currently make use of AtomsBase:</p><ul><li><a href="https://github.com/jrdegreeff/ASEPotential.jl">ASEPotential</a></li><li><a href="https://github.com/mfherbst/ASEconvert.jl">ASEconvert</a></li><li><a href="https://github.com/mfherbst/AtomIO.jl">AtomIO</a>: I/O for atomic structures, also wraps some ASE functionality</li><li><a href="https://github.com/cesmix-mit/Atomistic.jl/tree/263ec97b5f380f1b2ba593bf8feaf36e7f7cff9a">Atomistic</a>: integrated workflow for MD simulations, part of <a href="https://computing.mit.edu/cesmix/">CESMIX</a></li><li><a href="https://github.com/lxvm/AutoBZCore.jl/">AutoBZCore.jl</a>: Brillouin-zone integration</li><li><a href="https://github.com/GDufenshuoo/BFPIS.jl">BFPIS</a></li><li><a href="https://github.com/Chemellia/ChemistryFeaturization.jl">ChemistryFeaturization</a>: Interface for featurization of atomic structures for input into machine learning models, part of <a href="https://chemellia.org">Chemellia</a></li><li><a href="https://github.com/JuliaMolSim/DFTK.jl">DFTK</a>: density functional theory simulations</li><li><a href="https://github.com/libAtoms/ExtXYZ.jl">ExtXYZ</a>: Parser for extended XYZ files</li><li><a href="https://github.com/cesmix-mit/InteratomicPotentials.jl">InteratomicPotentials</a>: implementations of a variety of interatomic potentials, also part of <a href="https://computing.mit.edu/cesmix/">CESMIX</a></li><li><a href="https://github.com/JuliaMolSim/Molly.jl">Molly</a>: molecular dynamics simulations</li><li><a href="https://github.com/SimonEnsemble/Xtals.jl">Xtals</a>: I/O and structure representation for crystals</li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorial/">Tutorial »</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="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 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 21:44">Monday 21 August 2023</span>. Using Julia version 1.9.2.</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>Home · AtomsBase.jl</title><script data-outdated-warner src="assets/warner.js"></script><link rel="canonical" href="https://juliamolsim.github.io/AtomsBase.jl/"/><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/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/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="siteinfo.js"></script><script src="../versions.js"></script><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>AtomsBase.jl</a></span></div><form class="docs-search" action="search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Packages-using-AtomsBase"><span>Packages using AtomsBase</span></a></li></ul></li><li><a class="tocitem" href="tutorial/">Tutorial</a></li><li><a class="tocitem" href="overview/">Overview</a></li><li><a class="tocitem" href="testing/">Testing against the AtomsBase interface</a></li><li><a class="tocitem" href="apireference/">API reference</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"><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-edit-link" href="https://github.com/JuliaMolSim/AtomsBase.jl/blob/master/README.md#" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="AtomsBase"><a class="docs-heading-anchor" href="#AtomsBase">AtomsBase</a><a id="AtomsBase-1"></a><a class="docs-heading-anchor-permalink" href="#AtomsBase" title="Permalink"></a></h1><p><em>A Julian abstract interface for atomic structures.</em></p><p><a href="https://JuliaMolSim.github.io/AtomsBase.jl/stable"><img src="https://img.shields.io/badge/docs-stable-blue.svg" alt="Stable"/></a> <a href="https://JuliaMolSim.github.io/AtomsBase.jl/dev"><img src="https://img.shields.io/badge/docs-dev-blue.svg" alt="Dev"/></a> <a href="https://github.com/JuliaMolSim/AtomsBase.jl/actions"><img src="https://github.com/JuliaMolSim/AtomsBase.jl/workflows/CI/badge.svg" alt="Build Status"/></a> <a href="https://codecov.io/gh/JuliaMolSim/AtomsBase.jl"><img src="https://codecov.io/gh/JuliaMolSim/AtomsBase.jl/branch/master/graph/badge.svg" alt="Coverage"/></a></p><p>AtomsBase is an abstract interface for representation of atomic geometries in Julia. It aims to be a lightweight means of facilitating interoperability between various tools including ...</p><ul><li>Chemical simulation engines:<ul><li><a href="https://github.com/JuliaMolSim/DFTK.jl">DFTK.jl</a> (density-functional theory)</li><li><a href="https://github.com/JuliaMolSim/Molly.jl">Molly.jl</a> (molecular dynamics)</li></ul></li><li>Integration with third party-libraries:<ul><li><a href="https://github.com/mfherbst/ASEconvert.jl">ASEconvert.jl</a> (integration with the Atomistic Simulation Environment)</li></ul></li><li>I/O with standard file formats (.cif, .xyz, ...)<ul><li>E.g. <a href="https://github.com/mfherbst/AtomIO.jl">AtomIO.jl</a></li></ul></li><li>automatic differentiation and machine learning systems<ul><li><a href="https://github.com/Chemellia/ChemistryFeaturization.jl">ChemistryFeaturization.jl</a> (featurization of atomic systems)</li></ul></li><li>numerical tools: sampling, integration schemes, etc.</li><li>visualization (e.g. plot recipes)</li></ul><p>Currently, the design philosophy is to be as lightweight as possible with a small set of required function dispatches to make adopting the interface easy. We also provide a couple of <a href="https://juliamolsim.github.io/AtomsBase.jl/stable/atomicsystems/#atomic-systems">standard flexible implementations of the interface</a> that we envision to be broadly applicable. If features beyond these are required we encourage developers to open PRs or provide their own implementations. For more on how to use the package, see <a href="https://juliamolsim.github.io/AtomsBase.jl/stable">the documentation</a>.</p><h2 id="Packages-using-AtomsBase"><a class="docs-heading-anchor" href="#Packages-using-AtomsBase">Packages using AtomsBase</a><a id="Packages-using-AtomsBase-1"></a><a class="docs-heading-anchor-permalink" href="#Packages-using-AtomsBase" title="Permalink"></a></h2><p>The following (not all yet-registered) packages currently make use of AtomsBase:</p><ul><li><a href="https://github.com/jrdegreeff/ASEPotential.jl">ASEPotential</a></li><li><a href="https://github.com/mfherbst/ASEconvert.jl">ASEconvert</a></li><li><a href="https://github.com/mfherbst/AtomIO.jl">AtomIO</a>: I/O for atomic structures, also wraps some ASE functionality</li><li><a href="https://github.com/cesmix-mit/Atomistic.jl/tree/263ec97b5f380f1b2ba593bf8feaf36e7f7cff9a">Atomistic</a>: integrated workflow for MD simulations, part of <a href="https://computing.mit.edu/cesmix/">CESMIX</a></li><li><a href="https://github.com/lxvm/AutoBZCore.jl/">AutoBZCore.jl</a>: Brillouin-zone integration</li><li><a href="https://github.com/GDufenshuoo/BFPIS.jl">BFPIS</a></li><li><a href="https://github.com/Chemellia/ChemistryFeaturization.jl">ChemistryFeaturization</a>: Interface for featurization of atomic structures for input into machine learning models, part of <a href="https://chemellia.org">Chemellia</a></li><li><a href="https://github.com/JuliaMolSim/DFTK.jl">DFTK</a>: density functional theory simulations</li><li><a href="https://github.com/libAtoms/ExtXYZ.jl">ExtXYZ</a>: Parser for extended XYZ files</li><li><a href="https://github.com/cesmix-mit/InteratomicPotentials.jl">InteratomicPotentials</a>: implementations of a variety of interatomic potentials, also part of <a href="https://computing.mit.edu/cesmix/">CESMIX</a></li><li><a href="https://github.com/JuliaMolSim/Molly.jl">Molly</a>: molecular dynamics simulations</li><li><a href="https://github.com/SimonEnsemble/Xtals.jl">Xtals</a>: I/O and structure representation for crystals</li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorial/">Tutorial »</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="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 0.27.25 on <span class="colophon-date" title="Monday 11 September 2023 04:53">Monday 11 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
Oops, something went wrong.