build based on 3b5c8bc

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-09T19:19:04","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-09T19:30:18","documenter_version":"1.7.0"}}

dev/index.html

@@ -9,13 +9,13 @@
 all_frames = read_frames("seq.xyz")  # read all frames, returns Vector{Dict{String}{Any}}
 frames = read_frames("seq.xyz", 1:4) # specific range of frames
 
-write_frames(&quot;output.xyz&quot;, frames, append=true) # append four frames to output</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/211127d5122fa90c33ad9ae9ccb911e22948b2b0/src/ExtXYZ.jl#L1-L30">source</a></section></article><h2 id="Functions"><a class="docs-heading-anchor" href="#Functions">Functions</a><a id="Functions-1"></a><a class="docs-heading-anchor-permalink" href="#Functions" title="Permalink"></a></h2><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="ExtXYZ.read_frame" href="#ExtXYZ.read_frame"><code>ExtXYZ.read_frame</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">read_frame(file)</code></pre><p>Read a single frame from the ExtXYZ file <code>file</code>, which can be a file pointer, open IO stream or a string filename.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/211127d5122fa90c33ad9ae9ccb911e22948b2b0/src/fileio.jl#L257-L262">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="ExtXYZ.read_frames" href="#ExtXYZ.read_frames"><code>ExtXYZ.read_frames</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">read_frames(file[, range])</code></pre><p>Read a sequence of frames from the ExtXYZ <code>file</code>, which can be specified by a file pointer, filename or IOStream.</p><p><code>range</code> can be a single integer, range object or integer array of frame indices.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/211127d5122fa90c33ad9ae9ccb911e22948b2b0/src/fileio.jl#L339-L345">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="ExtXYZ.iread_frames" href="#ExtXYZ.iread_frames"><code>ExtXYZ.iread_frames</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">iread_frames(file[, range])</code></pre><p>Return a Channel for reading from an ExtXYZ file. Frames are yielded one by one. <code>range</code> can be a single integer, range object or integer array of frame indices.</p><p>Example usage:</p><pre><code class="language-julia hljs">ch = iread_frames(&quot;file.xyz&quot;)
+write_frames(&quot;output.xyz&quot;, frames, append=true) # append four frames to output</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/3b5c8bc82c1db1ce1e54ad6e5afa092992b14bb1/src/ExtXYZ.jl#L1-L30">source</a></section></article><h2 id="Functions"><a class="docs-heading-anchor" href="#Functions">Functions</a><a id="Functions-1"></a><a class="docs-heading-anchor-permalink" href="#Functions" title="Permalink"></a></h2><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="ExtXYZ.read_frame" href="#ExtXYZ.read_frame"><code>ExtXYZ.read_frame</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">read_frame(file)</code></pre><p>Read a single frame from the ExtXYZ file <code>file</code>, which can be a file pointer, open IO stream or a string filename.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/3b5c8bc82c1db1ce1e54ad6e5afa092992b14bb1/src/fileio.jl#L257-L262">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="ExtXYZ.read_frames" href="#ExtXYZ.read_frames"><code>ExtXYZ.read_frames</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">read_frames(file[, range])</code></pre><p>Read a sequence of frames from the ExtXYZ <code>file</code>, which can be specified by a file pointer, filename or IOStream.</p><p><code>range</code> can be a single integer, range object or integer array of frame indices.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/3b5c8bc82c1db1ce1e54ad6e5afa092992b14bb1/src/fileio.jl#L339-L345">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="ExtXYZ.iread_frames" href="#ExtXYZ.iread_frames"><code>ExtXYZ.iread_frames</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">iread_frames(file[, range])</code></pre><p>Return a Channel for reading from an ExtXYZ file. Frames are yielded one by one. <code>range</code> can be a single integer, range object or integer array of frame indices.</p><p>Example usage:</p><pre><code class="language-julia hljs">ch = iread_frames(&quot;file.xyz&quot;)
 for frame in ch
     process(frame)
-end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/211127d5122fa90c33ad9ae9ccb911e22948b2b0/src/fileio.jl#L297-L311">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="ExtXYZ.write_frame" href="#ExtXYZ.write_frame"><code>ExtXYZ.write_frame</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">write_frame(file, dict)</code></pre><p>Write a single atomic configuration represented by <code>dict</code> to <code>file</code>, which  can be a file pointer, open IO stream or string filename.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/211127d5122fa90c33ad9ae9ccb911e22948b2b0/src/fileio.jl#L384-L389">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="ExtXYZ.write_frames" href="#ExtXYZ.write_frames"><code>ExtXYZ.write_frames</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">write_frames(file, dicts)</code></pre><p>Write a sequence of atomic configurations to <code>file</code>. Can also be used asynchronously by passing a Channel in place of <code>dicts</code>, e.g.</p><pre><code class="language-julia hljs">Channel() do ch
+end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/3b5c8bc82c1db1ce1e54ad6e5afa092992b14bb1/src/fileio.jl#L297-L311">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="ExtXYZ.write_frame" href="#ExtXYZ.write_frame"><code>ExtXYZ.write_frame</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">write_frame(file, dict)</code></pre><p>Write a single atomic configuration represented by <code>dict</code> to <code>file</code>, which  can be a file pointer, open IO stream or string filename.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/3b5c8bc82c1db1ce1e54ad6e5afa092992b14bb1/src/fileio.jl#L384-L389">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="ExtXYZ.write_frames" href="#ExtXYZ.write_frames"><code>ExtXYZ.write_frames</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">write_frames(file, dicts)</code></pre><p>Write a sequence of atomic configurations to <code>file</code>. Can also be used asynchronously by passing a Channel in place of <code>dicts</code>, e.g.</p><pre><code class="language-julia hljs">Channel() do ch
     @async write_frames(outfile, ch)
 
     for frame in frames
         put!(ch, frame)
     end
-end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/211127d5122fa90c33ad9ae9ccb911e22948b2b0/src/fileio.jl#L399-L414">source</a></section></article><h2 id="Index"><a class="docs-heading-anchor" href="#Index">Index</a><a id="Index-1"></a><a class="docs-heading-anchor-permalink" href="#Index" title="Permalink"></a></h2><ul><li><a href="#ExtXYZ.ExtXYZ"><code>ExtXYZ.ExtXYZ</code></a></li><li><a href="#ExtXYZ.iread_frames"><code>ExtXYZ.iread_frames</code></a></li><li><a href="#ExtXYZ.read_frame"><code>ExtXYZ.read_frame</code></a></li><li><a href="#ExtXYZ.read_frames"><code>ExtXYZ.read_frames</code></a></li><li><a href="#ExtXYZ.write_frame"><code>ExtXYZ.write_frame</code></a></li><li><a href="#ExtXYZ.write_frames"><code>ExtXYZ.write_frames</code></a></li></ul></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="Monday 9 September 2024 19:19">Monday 9 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/libAtoms/ExtXYZ.jl/blob/3b5c8bc82c1db1ce1e54ad6e5afa092992b14bb1/src/fileio.jl#L399-L414">source</a></section></article><h2 id="Index"><a class="docs-heading-anchor" href="#Index">Index</a><a id="Index-1"></a><a class="docs-heading-anchor-permalink" href="#Index" title="Permalink"></a></h2><ul><li><a href="#ExtXYZ.ExtXYZ"><code>ExtXYZ.ExtXYZ</code></a></li><li><a href="#ExtXYZ.iread_frames"><code>ExtXYZ.iread_frames</code></a></li><li><a href="#ExtXYZ.read_frame"><code>ExtXYZ.read_frame</code></a></li><li><a href="#ExtXYZ.read_frames"><code>ExtXYZ.read_frames</code></a></li><li><a href="#ExtXYZ.write_frame"><code>ExtXYZ.write_frame</code></a></li><li><a href="#ExtXYZ.write_frames"><code>ExtXYZ.write_frames</code></a></li></ul></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="Monday 9 September 2024 19:30">Monday 9 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>