mathjax-yard 0.1.0 → 1.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.gitignore +1 -1
- data/.yardopts +1 -1
- data/Rakefile +1 -0
- data/doc/MathJaxYard.html +141 -0
- data/doc/MathJaxYard/Command.html +1017 -0
- data/doc/_index.html +149 -0
- data/doc/class_list.html +58 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +57 -0
- data/doc/css/style.css +339 -0
- data/doc/file.Home.html +86 -0
- data/doc/file.README.html +144 -0
- data/doc/file.README_ja.html +162 -0
- data/doc/file.atom.html +211 -0
- data/doc/file.potential2.html +196 -0
- data/doc/file_list.html +72 -0
- data/doc/frames.html +26 -0
- data/doc/index.html +144 -0
- data/doc/js/app.js +219 -0
- data/doc/js/full_list.js +181 -0
- data/doc/js/jquery.js +4 -0
- data/doc/method_list.html +129 -0
- data/doc/top-level-namespace.html +158 -0
- data/lib/mathjax-yard.rb +48 -61
- data/lib/mathjax-yard/script.rb +20 -0
- data/lib/mathjax-yard/version.rb +1 -1
- data/mathjax-yard.gemspec +3 -1
- data/mathjax.yml +3 -3
- data/mathjax.yml.bk +28 -0
- metadata +40 -7
- data/docs/README_ja.md +0 -77
- data/docs/atom.md +0 -121
- data/docs/potential2.md +0 -103
data/doc/file.Home.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<script type="text/x-mathjax-config">
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tex2jax:{
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inlineMath: [ ['$','$'], ["\(","\)"] ],
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<title>
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File: Home
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— Documentation by YARD 0.8.7.6
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</title>
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<link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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<script type="text/javascript" charset="utf-8">
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hasFrames = window.top.frames.main ? true : false;
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framesUrl = "frames.html#!file.Home.html";
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<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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</head>
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<div id="menu">
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<a href="_index.html">Index</a> »
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<span class="title">File: Home</span>
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<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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<div id="search">
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href="class_list.html">
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Class List
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href="method_list.html">
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Method List
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href="file_list.html">
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File List
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<div id="content"><div id='filecontents'><p>Welcome to the mathjax-yard wiki!</p>
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<div id="footer">
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Generated on Thu Jun 23 14:03:52 2016 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.8.7.6 (ruby-2.2.2).
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</html>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<script type="text/x-mathjax-config">
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MathJax.Hub.Config({
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tex2jax:{
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inlineMath: [ ['$','$'], ["\(","\)"] ],
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displayMath: [ ['$$','$$'], ["\[","\]"] ]
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}
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});
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</script>
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<script type="text/javascript"
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src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML">
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</script>
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<meta http-equiv="X-UA-Compatible" CONTENT="IE=EmulateIE7" />
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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<title>
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File: README
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— Documentation by YARD 0.8.7.6
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</title>
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<link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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<link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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<script type="text/javascript" charset="utf-8">
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hasFrames = window.top.frames.main ? true : false;
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relpath = '';
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framesUrl = "frames.html#!file.README.html";
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</script>
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<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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</head>
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<div id="menu">
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<a href="_index.html">Index</a> »
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<span class="title">File: README</span>
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<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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</div>
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<div id="search">
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<a class="full_list_link" id="class_list_link"
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href="class_list.html">
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Class List
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</a>
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<a class="full_list_link" id="method_list_link"
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href="method_list.html">
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Method List
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</a>
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<a class="full_list_link" id="file_list_link"
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href="file_list.html">
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File List
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</a>
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</div>
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<div class="clear"></div>
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</div>
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<iframe id="search_frame"></iframe>
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<div id="content"><div id='filecontents'><h1>MathJaxYard</h1>
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<p>mathjax-yard is a mathjax extension for markdown in yard.</p>
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<h2>Installation</h2>
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<p>Add this line to your application's Gemfile:</p>
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<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gem'>gem</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>mathjax-yard</span><span class='tstring_end'>'</span></span>
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</code></pre>
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<p>And then execute:</p>
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<pre class="code ruby"><code class="ruby">$ bundle
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</code></pre>
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<p>Or install it yourself as:</p>
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<pre class="code ruby"><code class="ruby">$ gem install mathjax-yard
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</code></pre>
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<h2>Usage</h2>
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<p>mathjax-yard is intended to be a command line tool, using in Rakefile as follows.</p>
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<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_desc'>desc</span> <span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>make documents by yard</span><span class='tstring_end'>"</span></span>
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<span class='id identifier rubyid_task'>task</span> <span class='symbol'>:yard</span> <span class='kw'>do</span>
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<span class='id identifier rubyid_system'>system</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>mathjax-yard</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span>
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<span class='const'>YARD</span><span class='op'>::</span><span class='const'>Rake</span><span class='op'>::</span><span class='const'>YardocTask</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
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<span class='kw'>end</span>
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<span class='id identifier rubyid_desc'>desc</span> <span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>make documents with yardmath</span><span class='tstring_end'>"</span></span>
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<span class='id identifier rubyid_task'>task</span> <span class='symbol'>:mathjax</span> <span class='kw'>do</span>
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<span class='id identifier rubyid_system'>system</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>mathjax-yard --post</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span>
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<span class='kw'>end</span>
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</code></pre>
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<p>mathjax-yard search ./<em>/</em>.md and replace '$...$' or '$$...$$' to $MATHJAX*<em>$ tags, and make 'mathjax.yml' for storing these relations. After the normal YARD operation has done, 'mathjax-yard --post' replacement will be done on 'doc/file.</em>.html'. The yard options are</p>
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<pre class="code ruby"><code class="ruby">-t mathjax -p templates
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</code></pre>
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<p>The mathjax layout should be included in yard layout.</p>
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<h2>Development</h2>
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<p>After checking out the repo, run <code>bin/setup</code> to install dependencies. Then, run <code>rake spec</code> to run the tests. You can also run <code>bin/console</code> for an interactive prompt that will allow you to experiment. Run <code>bundle exec mathjax-yard</code> to use the gem in this directory, ignoring other installed copies of this gem.</p>
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<p>To install this gem onto your local machine, run <code>bundle exec rake install</code>. To release a new version, update the version number in <code>version.rb</code>, and then run <code>bundle exec rake release</code>, which will create a git tag for the version, push git commits and tags, and push the <code>.gem</code> file to <a href="https://rubygems.org">rubygems.org</a>.</p>
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<h2>Contributing</h2>
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<p>Bug reports and pull requests are welcome on GitHub at <a href="https://github.com/%5BUSERNAME%5D/mathjax-yard">https://github.com/[USERNAME]/mathjax-yard</a>. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the <a href="http://contributor-covenant.org">Contributor Covenant</a> code of conduct.</p>
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<h2>License</h2>
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<p>The gem is available as open source under the terms of the <a href="http://opensource.org/licenses/MIT">MIT License</a>.</p>
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Generated on Thu Jun 23 14:03:52 2016 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.8.7.6 (ruby-2.2.2).
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inlineMath: [ ['$','$'], ["\(","\)"] ],
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File: README_ja
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— Documentation by YARD 0.8.7.6
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hasFrames = window.top.frames.main ? true : false;
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relpath = '';
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framesUrl = "frames.html#!file.README_ja.html";
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</script>
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<div id="content"><div id='filecontents'><h1>MathJaxYard</h1>
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<p>mathjax-yardはyardによるmarkdown変換においてmathjaxを使えるようにする拡張機能です．</p>
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<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gem'>gem</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>mathjax-yard</span><span class='tstring_end'>'</span></span>
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<p>Or install it yourself as:</p>
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<p>mathjax-yardはcommand line toolとしての使用を意図して作られています．例えば，Rakefileでの使用例は次の通りです．</p>
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<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_desc'>desc</span> <span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>make documents by yard</span><span class='tstring_end'>"</span></span>
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<span class='id identifier rubyid_system'>system</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>mathjax-yard</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span>
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<span class='const'>YARD</span><span class='op'>::</span><span class='const'>Rake</span><span class='op'>::</span><span class='const'>YardocTask</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
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<span class='id identifier rubyid_desc'>desc</span> <span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>make documents with yardmath</span><span class='tstring_end'>"</span></span>
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<span class='id identifier rubyid_task'>task</span> <span class='symbol'>:mathjax</span> <span class='kw'>do</span>
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<span class='id identifier rubyid_system'>system</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>mathjax-yard --post</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span>
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<p>yardのデフォルトでの動作をなぞって，動作するように作られています．</p>
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<ul>
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<li>mathjax-yardは./<em>/</em>.mdを探索し，それらの中に'\$\$'あるいは'\$\$..\$\$'があると\$MATHJAX20\$などというタグに付け替え，</li>
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*また，同時に， 'mathjax.yml'にそれらのhash関係をyaml形式で保存します．</li>
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<li>通常のrake yardで変換したのち，</li>
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<li>'mathjax-yard --post'によって，'doc/file.*.html'に残されたtagを元に戻します．</li>
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<li>また同時に，backファイルを元に戻します．</li>
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<p>yardのoptionは，.yardoptsに</p>
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<pre class="code ruby"><code class="ruby">-t mathjax -p templates
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-
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spec/*.md
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</code></pre>
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<p>としています．また，htmlのhead部分にmathjaxのscriptを埋め込んだlayoutを用意しています．</p>
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<pre class="code csh"><code class="csh">bob% bundle exec exe/mathjax-yard --help
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Usage: yardmath [options] [DIRECTORY]
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-v, --version show program Version.
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-p, --post post operation.
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</code></pre>
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<h2>Development</h2>
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<p>After checking out the repo, run <code>bin/setup</code> to install dependencies. Then, run <code>rake spec</code> to run the tests. You can also run <code>bin/console</code> for an interactive prompt that will allow you to experiment. Run <code>bundle exec mathjax-yard</code> to use the gem in this directory, ignoring other installed copies of this gem.</p>
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<p>To install this gem onto your local machine, run <code>bundle exec rake install</code>. To release a new version, update the version number in <code>version.rb</code>, and then run <code>bundle exec rake release</code>, which will create a git tag for the version, push git commits and tags, and push the <code>.gem</code> file to <a href="https://rubygems.org">rubygems.org</a>.</p>
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<h2>Contributing</h2>
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<p>Bug reports and pull requests are welcome on GitHub at <a href="https://github.com/%5BUSERNAME%5D/mathjax-yard">https://github.com/[USERNAME]/mathjax-yard</a>. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the <a href="http://contributor-covenant.org">Contributor Covenant</a> code of conduct.</p>
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<h2>License</h2>
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<p>The gem is available as open source under the terms of the <a href="http://opensource.org/licenses/MIT">MIT License</a>.</p>
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Generated on Thu Jun 23 14:03:52 2016 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.8.7.6 (ruby-2.2.2).
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|
data/doc/file.atom.html
ADDED
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@@ -0,0 +1,211 @@
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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File: atom
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— Documentation by YARD 0.8.7.6
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<span class="title">File: atom</span>
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|
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|
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|
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|
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|
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|
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+
<div id="content"><div id='filecontents'><h1>概要</h1>
|
|
77
|
+
|
|
78
|
+
<h1>EAM</h1>
|
|
79
|
+
|
|
80
|
+
<p>EAM(Embedded atom method)は1980年代以降に，盛んに使われるようになった経験的原子間ポテンシャルである．</p>
|
|
81
|
+
|
|
82
|
+
<h2>エネルギー表記</h2>
|
|
83
|
+
|
|
84
|
+
<p>EAMは原子$i$のエネルギーを</p>
|
|
85
|
+
|
|
86
|
+
<p>$$E_i = \sum_j\phi \left( r_j \right) + f(\rho)
|
|
87
|
+
$$
|
|
88
|
+
と表記する．右辺第1項は単なる2体間の相互作用を表わす．
|
|
89
|
+
右辺第2項が多体項と呼ばれるEAMに特徴的な項である．
|
|
90
|
+
この工夫によって原子空孔を初め多くの金属物性を
|
|
91
|
+
うまく表現することが可能となった．詳しくは西谷・赤本参照．</p>
|
|
92
|
+
|
|
93
|
+
<p>さて，$r_j$はこの場合原子$j$との距離を意味しており，$E_i$は原子$i$の周りの原子との和によって求まる．多体項は，一般的に</p>
|
|
94
|
+
|
|
95
|
+
<p>$$f(\rho) =\sqrt{\rho}=\sqrt{\sum_j h^2 \left( r_j \right) }
|
|
96
|
+
$$
|
|
97
|
+
によって求められる．$\rho$は強結合(tight binding)理論の2次モーメント近似と捉えると，電子密度を表わすとされている．</p>
|
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|
+
|
|
99
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+
<h2>具体例</h2>
|
|
100
|
+
|
|
101
|
+
<h3>for phi(r0)=-3.39, Ev=0.8, p=3.0 at r0=2.8577</h3>
|
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|
+
|
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|
+
<pre class="code maple"><code class="maple">
|
|
104
|
+
A0,B0,P,POQ,Q:=69.1378255, 12.47431958,
|
|
105
|
+
2.148157653, 2.893854749, 0.7423170267;
|
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+
|
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+
-3.39*32;
|
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|
+
-108.48
|
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|
+
</code></pre>
|
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|
+
|
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|
+
<pre class="code ruby"><code class="ruby">n:=12;
|
|
112
|
+
ene:=r->n*A0*exp(-P*r);
|
|
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|
+
h:=r->B0*exp(-Q*r);
|
|
114
|
+
rho:=r->12*h(r)^2;
|
|
115
|
+
plot(ene(r)-sqrt(rho(r)),r=2..4);
|
|
116
|
+
</code></pre>
|
|
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|
+
|
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|
+
<p><img src="eam_ev_plot.gif" alt=""></p>
|
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+
|
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+
<pre class="code ruby"><code class="ruby">r0:=fsolve(diff(ene(r)-sqrt(rho(r)),r),r=3);
|
|
121
|
+
2.857701344
|
|
122
|
+
evalf(subs(r=r0,ene(r)-sqrt(rho(r))));
|
|
123
|
+
-3.390000002
|
|
124
|
+
</code></pre>
|
|
125
|
+
|
|
126
|
+
<pre class="code math"><code class="math">E_i = \sum _ j\phi \left( r_{{j}} \right) + \h \left( r_{{j}} \right)
|
|
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|
+
</code></pre>
|
|
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|
+
|
|
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|
+
<h1>LJ</h1>
|
|
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|
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|
|
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|
+
<p>LJ(Lennard-Jones)はもっとも簡単な2体のポテンシャル．</p>
|
|
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+
|
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133
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+
<h2>エネルギー表記</h2>
|
|
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+
|
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135
|
+
<h2>具体例</h2>
|
|
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|
+
|
|
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|
+
<pre class="code maple"><code class="maple">A0:=1.587401051*0.7071067812/2.857701314;
|
|
138
|
+
E0:=-1*4.0/12.0;
|
|
139
|
+
|
|
140
|
+
A:=18.19007708;
|
|
141
|
+
B:=89.22765864;
|
|
142
|
+
phi:=r-> 12*(-A*(1/r**3)+B*(1/r**5));
|
|
143
|
+
r0:=fsolve(diff(phi(r),r),r=3);
|
|
144
|
+
2.859281101
|
|
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|
+
phi(r0);
|
|
146
|
+
-3.735125644
|
|
147
|
+
</code></pre>
|
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|
+
|
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+
<p><img src="lj_ev_plot.gif" alt=""></p>
|
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+
|
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+
<h1>EAM fitting</h1>
|
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+
|
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<p>EAM potentialの種々の構築手法を詳解する．</p>
|
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|
|
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|
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<h2>background</h2>
|
|
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|
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|
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<p>MCにおいて$NPT$一定の計算がうまくいっていない．</p>
|
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|
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|
+
<ul>
|
|
160
|
+
<li>覚埜式の$E-V$プロットをすると小体積でのエネルギの上がりが低い．</li>
|
|
161
|
+
<li>$T=0.1$[eV]で融けているよう
|
|
162
|
+
なので，もう少し精密にEAMポテンシャルを構築してみる．</li>
|
|
163
|
+
</ul>
|
|
164
|
+
|
|
165
|
+
<h2>poq fixed</h2>
|
|
166
|
+
|
|
167
|
+
<p>EAM potentialにおいて単原子空孔の生成エネルギ$E_v$は</p>
|
|
168
|
+
|
|
169
|
+
<p>$$E_v = -\frac{E_c}{2} \frac{2-poq}{1-poq}
|
|
170
|
+
$$
|
|
171
|
+
の関係がある．したがって，</p>
|
|
172
|
+
|
|
173
|
+
<pre class="code maple"><code class="maple">Ev:=0.8;
|
|
174
|
+
Ec:=3.39;
|
|
175
|
+
eq1:=Ev=Ec/2*(2-poq)/(1-poq);
|
|
176
|
+
solve(eq1,poq);
|
|
177
|
+
2.893854749
|
|
178
|
+
</code></pre>
|
|
179
|
+
|
|
180
|
+
<p>さらにこの値を使ってポテンシャルのパラメータを求めるのは以下の通り．ここで，$q$を設定している．</p>
|
|
181
|
+
|
|
182
|
+
<pre class="code ruby"><code class="ruby">phi:=r->12.0*A*exp(-p*r)-sqrt(12.0*(B*exp(-q*r))^2);
|
|
183
|
+
poq:=2.893854749;
|
|
184
|
+
q:=3.00*0.2474390089;
|
|
185
|
+
a0:=8.0828/2;
|
|
186
|
+
r0:=evalf(a0*sqrt(2)/2.0); #2.857701345
|
|
187
|
+
eq1:=phi(r0)=-3.39;
|
|
188
|
+
s2:=solve(eq1,A);
|
|
189
|
+
p:=poq*q; #2.148157653
|
|
190
|
+
eq2:=subs(r=r0,diff(phi(r),r));
|
|
191
|
+
#plot(subs(A=s2,eq2),B=0..20);
|
|
192
|
+
b0:=fsolve(subs(A=s2,eq2),B=10);
|
|
193
|
+
a0:=subs(B=b0,s2);
|
|
194
|
+
phi0:=unapply(subs({A=a0,B=b0},phi(r)),r);
|
|
195
|
+
plot(phi0(r),r=2..5);
|
|
196
|
+
phi0(r0);
|
|
197
|
+
a0,b0,p,poq,q;
|
|
198
|
+
#69.1378255, 12.47431958, 2.148157653, 2.893854749, 0.7423170267
|
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199
|
+
</code></pre>
|
|
200
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+
|
|
201
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+
<p><img src="eam_ev.png" alt=""></p>
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202
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+
</div></div>
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203
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+
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204
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+
<div id="footer">
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205
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Generated on Thu Jun 23 14:03:52 2016 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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207
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0.8.7.6 (ruby-2.2.2).
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</div>
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</body>
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</html>
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