mathjax-yard 0.1.0 → 1.0.1
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- 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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File: Home
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— Documentation by YARD 0.8.7.6
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<div id="content"><div id='filecontents'><p>Welcome to the mathjax-yard wiki!</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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tex2jax:{
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inlineMath: [ ['$','$'], ["\(","\)"] ],
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displayMath: [ ['$$','$$'], ["\[","\]"] ]
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src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML">
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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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<div id="search">
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<a class="full_list_link" id="class_list_link"
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Class List
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href="method_list.html">
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Method List
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File List
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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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spec/*.md
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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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</div></div>
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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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<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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<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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<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_ja
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— Documentation by YARD 0.8.7.6
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</title>
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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_ja.html";
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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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<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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<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_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='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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ADDED
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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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+
<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
|
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|
|
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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|
+
|
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99
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+
<h2>具体例</h2>
|
|
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|
+
|
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101
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+
<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,
|
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|
+
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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|
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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;
|
|
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|
+
plot(ene(r)-sqrt(rho(r)),r=2..4);
|
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|
+
</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);
|
|
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|
+
2.857701344
|
|
122
|
+
evalf(subs(r=r0,ene(r)-sqrt(rho(r))));
|
|
123
|
+
-3.390000002
|
|
124
|
+
</code></pre>
|
|
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|
+
|
|
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|
+
<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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|
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<h1>LJ</h1>
|
|
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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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|
+
<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);
|
|
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|
+
-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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<h2>background</h2>
|
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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>
|
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+
<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>
|
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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);
|
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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
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+
</code></pre>
|
|
200
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+
|
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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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+
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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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0.8.7.6 (ruby-2.2.2).
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</body>
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