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1049 lines
67 KiB
HTML
1049 lines
67 KiB
HTML
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<?xml version="1.0" encoding="utf-8"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Common</title>
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<meta name="generator" content="Org mode" />
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<meta name="author" content="Anthony Scemama" />
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.underline { text-decoration: underline; }
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#postamble p, #preamble p { font-size: 90%; margin: .2em; }
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pre.src-css:before { content: 'CSS'; }
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pre.src-ditaa:before { content: 'ditaa'; }
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/* additional language identifiers per "defun org-babel-execute"
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in ob-*.el */
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ob-shell.el: ob-shell is the only babel language using a lambda to put
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the execution function name together. */
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pre.src-csh:before { content: 'csh'; }
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pre.src-dash:before { content: 'dash'; }
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pre.src-mksh:before { content: 'mksh'; }
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/* Additional Emacs modes also supported by the LaTeX listings package */
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pre.src-tcl:before { content: 'tcl'; }
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pre.src-verilog:before { content: 'Verilog'; }
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pre.src-vhdl:before { content: 'VHDL'; }
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pre.src-xml:before { content: 'XML'; }
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pre.src-nxml:before { content: 'XML'; }
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/* add a generic configuration mode; LaTeX export needs an additional
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(add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
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pre.src-conf:before { content: 'Configuration File'; }
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table { border-collapse:collapse; }
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caption.t-bottom { caption-side: bottom; }
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td, th { vertical-align:top; }
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th.org-right { text-align: center; }
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th.org-left { text-align: center; }
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th.org-center { text-align: center; }
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td.org-right { text-align: right; }
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td.org-left { text-align: left; }
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dt { font-weight: bold; }
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.footpara { display: inline; }
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.footdef { margin-bottom: 1em; }
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.figure { padding: 1em; }
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.figure p { text-align: center; }
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.equation-container {
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display: table;
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text-align: center;
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width: 100%;
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}
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.equation {
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vertical-align: middle;
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}
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display: table-cell;
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text-align: right;
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vertical-align: middle;
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}
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.inlinetask {
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padding: 10px;
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border: 2px solid gray;
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margin: 10px;
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background: #ffffcc;
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}
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#org-div-home-and-up
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{ text-align: right; font-size: 70%; white-space: nowrap; }
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textarea { overflow-x: auto; }
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.org-info-js_info-navigation { border-style: none; }
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#org-info-js_console-label
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{ font-size: 10px; font-weight: bold; white-space: nowrap; }
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.org-info-js_search-highlight
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{ background-color: #ffff00; color: #000000; font-weight: bold; }
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/*]]>*/-->
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</style>
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<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
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<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/readtheorg.css"/>
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
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<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
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<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/lib/js/jquery.stickytableheaders.min.js"></script>
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<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/js/readtheorg.js"></script>
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<script type="text/javascript">
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// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain
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function CodeHighlightOn(elem, id)
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function CodeHighlightOff(elem, id)
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{
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/*]]>*///-->
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// @license-end
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</script>
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<script type="text/x-mathjax-config">
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MathJax.Hub.Config({
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displayAlign: "center",
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displayIndent: "0em",
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"HTML-CSS": { scale: 100,
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linebreaks: { automatic: "false" },
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webFont: "TeX"
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},
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SVG: {scale: 100,
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linebreaks: { automatic: "false" },
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font: "TeX"},
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NativeMML: {scale: 100},
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TeX: { equationNumbers: {autoNumber: "AMS"},
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MultLineWidth: "85%",
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TagSide: "right",
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TagIndent: ".8em"
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}
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});
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</script>
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||
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<script type="text/javascript"
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||
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src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML"></script>
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||
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</head>
|
||
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<body>
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||
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<div id="content">
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||
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<h1 class="title">Common</h1>
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||
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<div id="table-of-contents">
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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||
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<li><a href="#orgf947286">1. Electrons</a>
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||
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<ul>
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<li><a href="#orgb7eb1f5">1.1. Type</a></li>
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||
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<li><a href="#org2109b26">1.2. Creation</a></li>
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||
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<li><a href="#org2a36970">1.3. Access</a></li>
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||
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<li><a href="#org5e47047">1.4. Printers</a></li>
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||
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<li><a href="#orgc347c9f">1.5. Tests</a></li>
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||
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</ul>
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||
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</li>
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||
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<li><a href="#org25852ad">2. Element</a>
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||
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<ul>
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||
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<li><a href="#org038a472">2.1. Type</a></li>
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||
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<li><a href="#orgc0d1c8c">2.2. Conversion</a></li>
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||
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<li><a href="#orgf48d5b6">2.3. Database information</a></li>
|
||
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<li><a href="#org4e97465">2.4. Printers</a></li>
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||
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</ul>
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||
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</li>
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||
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<li><a href="#org4c5689f">3. Atomic mass</a></li>
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||
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<li><a href="#org6bd3bbb">4. Nuclei</a>
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||
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<ul>
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||
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<li><a href="#org91c1c84">4.1. Type</a></li>
|
||
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<li><a href="#org0e06d85">4.2. xyz file lexer/parser</a>
|
||
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<ul>
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||
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<li><a href="#orgd2a815e">4.2.1. Lexer</a></li>
|
||
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<li><a href="#orga0e9364">4.2.2. Parser</a></li>
|
||
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</ul>
|
||
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</li>
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||
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<li><a href="#org67c4576">4.3. Conversion</a></li>
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||
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<li><a href="#org31c8415">4.4. <span class="todo TODO">TODO</span> Query</a></li>
|
||
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<li><a href="#orga01f8b6">4.5. Printers</a></li>
|
||
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<li><a href="#orgf2e9bac">4.6. Tests</a></li>
|
||
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</ul>
|
||
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</li>
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||
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<li><a href="#org3573ea4">5. Z-matrix</a>
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||
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<ul>
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||
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<li><a href="#org7593a50">5.1. Type</a></li>
|
||
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<li><a href="#orgf0cdae8">5.2. Conversion</a></li>
|
||
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<li><a href="#org08080f5">5.3. Printers</a></li>
|
||
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</ul>
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||
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</li>
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||
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</ul>
|
||
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</div>
|
||
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</div>
|
||
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<div class="org-src-container">
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||
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<pre class="src src-ocaml" id="org62b2bfe"><span class="org-string">"Information relative to particles (electrons and nuclei)."</span>
|
||
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</pre>
|
||
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</div>
|
||
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<div id="outline-container-orgf947286" class="outline-2">
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|
|
<h2 id="orgf947286"><span class="section-number-2">1</span> Electrons</h2>
|
||
|
|
<div class="outline-text-2" id="text-1">
|
||
|
|
<p>
|
||
|
|
Data structure which contains the number of α and β electrons.
|
||
|
|
</p>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orgb7eb1f5" class="outline-3">
|
||
|
|
<h3 id="orgb7eb1f5"><span class="section-number-3">1.1</span> Type</h3>
|
||
|
|
<div class="outline-text-3" id="text-1-1">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml" id="orge3b79fc"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org2109b26" class="outline-3">
|
||
|
|
<h3 id="org2109b26"><span class="section-number-3">1.2</span> Creation</h3>
|
||
|
|
<div class="outline-text-3" id="text-1-2">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> int <span class="org-tuareg-font-lock-operator">-></span> int <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_atoms</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">?multiplicity</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-label">?charge</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
<span class="org-comment-delimiter">(* </span><span class="org-comment">@param multiplicity default is 1</span>
|
||
|
|
<span class="org-comment"> @param charge default is 0</span>
|
||
|
|
<span class="org-comment"> @raise Invalid_argument if the spin multiplicity is not compatible with</span>
|
||
|
|
<span class="org-comment"> the molecule and the total charge.</span>
|
||
|
|
<span class="org-comment-delimiter">*)</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>make</code></td>
|
||
|
|
<td class="org-left"><code>make n_alfa n_beta</code></td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_atoms</code></td>
|
||
|
|
<td class="org-left">Creates the data relative to electrons for a molecular system described by <code>Nuclei.t</code> for a given total charge and spin multiplicity.</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org2a36970" class="outline-3">
|
||
|
|
<h3 id="org2a36970"><span class="section-number-3">1.3</span> Access</h3>
|
||
|
|
<div class="outline-text-3" id="text-1-3">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">charge</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Charge.</span>t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">n_elec</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">n_alfa</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">n_beta</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">multiplicity</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>charge</code></td>
|
||
|
|
<td class="org-left">Sum of the charges of the electrons</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>n_elec</code></td>
|
||
|
|
<td class="org-left">Number of electrons</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>n_alfa</code></td>
|
||
|
|
<td class="org-left">Number of alpha electrons</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>n_beta</code></td>
|
||
|
|
<td class="org-left">Number of beta electrons</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>multiplicity</code></td>
|
||
|
|
<td class="org-left">Spin multiplicity: \(2S+1\)</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org5e47047" class="outline-3">
|
||
|
|
<h3 id="org5e47047"><span class="section-number-3">1.4</span> Printers</h3>
|
||
|
|
<div class="outline-text-3" id="text-1-4">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orgc347c9f" class="outline-3">
|
||
|
|
<h3 id="orgc347c9f"><span class="section-number-3">1.5</span> Tests</h3>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org25852ad" class="outline-2">
|
||
|
|
<h2 id="org25852ad"><span class="section-number-2">2</span> Element</h2>
|
||
|
|
<div class="outline-text-2" id="text-2">
|
||
|
|
<p>
|
||
|
|
Chemical elements.
|
||
|
|
</p>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org038a472" class="outline-3">
|
||
|
|
<h3 id="org038a472"><span class="section-number-3">2.1</span> Type</h3>
|
||
|
|
<div class="outline-text-3" id="text-2-1">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml" id="org124f3ea"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">X</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">H</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">He</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Li</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Be</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">B</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">C</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">N</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">O</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">F</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ne</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Na</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Mg</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Al</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Si</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">P</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">S</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cl</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ar</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">K</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ca</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sc</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ti</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">V</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cr</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Mn</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Fe</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Co</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ni</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cu</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Zn</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ga</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ge</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">As</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Se</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Br</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Kr</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Rb</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sr</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Y</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Zr</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Nb</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Mo</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Tc</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ru</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Rh</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Pd</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ag</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cd</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">In</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sn</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sb</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Te</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">I</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Xe</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Pt</span>
|
||
|
|
|
||
|
|
<span class="org-keyword">exception</span> <span class="org-tuareg-font-lock-constructor">ElementError</span> <span class="org-keyword">of</span> string
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orgc0d1c8c" class="outline-3">
|
||
|
|
<h3 id="orgc0d1c8c"><span class="section-number-3">2.2</span> Conversion</h3>
|
||
|
|
<div class="outline-text-3" id="text-2-2">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> string
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_long_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> string
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_int</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_int</span> <span class="org-tuareg-font-lock-operator">:</span> int <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_charge</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Charge.</span>t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_charge</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Charge.</span>t <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_string</code></td>
|
||
|
|
<td class="org-left">Creates an <code>Element.t</code> from a chemical symbol or from the full name of the element (case insensitive)</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_string</code></td>
|
||
|
|
<td class="org-left">Gets the chemical symbol of the <code>Element.t</code> in a string</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_long_string</code></td>
|
||
|
|
<td class="org-left">Gets the full name of the <code>Element.t</code> in a string</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_int</code></td>
|
||
|
|
<td class="org-left">Convert to the atomic charge, with <code>int</code> type</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_int</code></td>
|
||
|
|
<td class="org-left">Create from the atomic charge, with <code>int</code> type</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_charge</code></td>
|
||
|
|
<td class="org-left">Convert to the atomic charge, with <code>Charge.t</code> type</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_charge</code></td>
|
||
|
|
<td class="org-left">Create from the atomic charge, with <code>Charge.t</code> type</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
|
||
|
|
<pre class="example" id="org227d844">
|
||
|
|
Element.of_string "Fe" ;;
|
||
|
|
- : Element.t = Particles.Element.Fe
|
||
|
|
|
||
|
|
Element.of_string "hydrogen" ;;
|
||
|
|
- : Element.t = Particles.Element.H
|
||
|
|
|
||
|
|
Element.of_string "Kryptonite" ;;
|
||
|
|
Exception: Particles.Element.ElementError "Element Kryptonite unknown".
|
||
|
|
|
||
|
|
Element.(to_long_string Fe) ;;
|
||
|
|
- : string = "Iron"
|
||
|
|
|
||
|
|
Element.(to_string Fe);;
|
||
|
|
- : string = "Fe"
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orgf48d5b6" class="outline-3">
|
||
|
|
<h3 id="orgf48d5b6"><span class="section-number-3">2.3</span> Database information</h3>
|
||
|
|
<div class="outline-text-3" id="text-2-3">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">covalent_radius</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Non_negative_float.</span>t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">vdw_radius</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Non_negative_float.</span>t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">mass</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Mass.</span>t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">small_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">large_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>covalent_radius</code></td>
|
||
|
|
<td class="org-left">Covalent radii of the elements, in atomic units</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>vdw_radius</code></td>
|
||
|
|
<td class="org-left">Van der Waals radii of the elements, in atomic units</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>mass</code></td>
|
||
|
|
<td class="org-left">Atomic mass of the elements, in atomic units)</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>small_core</code></td>
|
||
|
|
<td class="org-left">Number of electrons in the small core model (all except the outermost two shells)</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>large_core</code></td>
|
||
|
|
<td class="org-left">Number of electrons in the large core model (all except the outermost shell)</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org4e97465" class="outline-3">
|
||
|
|
<h3 id="org4e97465"><span class="section-number-3">2.4</span> Printers</h3>
|
||
|
|
<div class="outline-text-3" id="text-2-4">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp_long</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org4c5689f" class="outline-2">
|
||
|
|
<h2 id="org4c5689f"><span class="section-number-2">3</span> Atomic mass</h2>
|
||
|
|
<div class="outline-text-2" id="text-3">
|
||
|
|
<p>
|
||
|
|
Atomic mass, a non-negative float.
|
||
|
|
</p>
|
||
|
|
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml" id="orgb624991"><span class="org-tuareg-font-lock-governing">include</span> <span class="org-tuareg-font-lock-governing">module type of</span> <span class="org-tuareg-font-lock-module">Common.Non_negative_float</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org6bd3bbb" class="outline-2">
|
||
|
|
<h2 id="org6bd3bbb"><span class="section-number-2">4</span> Nuclei</h2>
|
||
|
|
<div class="outline-text-2" id="text-4">
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org91c1c84" class="outline-3">
|
||
|
|
<h3 id="org91c1c84"><span class="section-number-3">4.1</span> Type</h3>
|
||
|
|
<div class="outline-text-3" id="text-4-1">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml" id="org3d3e724"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">(</span><span class="org-tuareg-font-lock-module">Element.</span>t <span class="org-tuareg-font-lock-operator">*</span> <span class="org-tuareg-font-lock-module">Coordinate.</span>t<span class="org-tuareg-font-lock-operator">)</span> array
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org0e06d85" class="outline-3">
|
||
|
|
<h3 id="org0e06d85"><span class="section-number-3">4.2</span> xyz file lexer/parser</h3>
|
||
|
|
<div class="outline-text-3" id="text-4-2">
|
||
|
|
</div>
|
||
|
|
<div id="outline-container-orgd2a815e" class="outline-4">
|
||
|
|
<h4 id="orgd2a815e"><span class="section-number-4">4.2.1</span> Lexer</h4>
|
||
|
|
<div class="outline-text-4" id="text-4-2-1">
|
||
|
|
<p>
|
||
|
|
<code>nuclei_lexer.mll</code> contains the description of the lexemes used in
|
||
|
|
an xyz file.
|
||
|
|
</p>
|
||
|
|
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Xyz_parser</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">eol</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">'\n'</span><span class="org-tuareg-font-lock-operator">]</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">white</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">' '</span> <span class="org-string">'\t'</span><span class="org-tuareg-font-lock-operator">]+</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">word</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[^</span><span class="org-string">' '</span> <span class="org-string">'\t'</span> <span class="org-string">'\n'</span><span class="org-tuareg-font-lock-operator">]+</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">letter</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">'A'</span><span class="org-tuareg-font-lock-operator">-</span><span class="org-string">'Z'</span> <span class="org-string">'a'</span><span class="org-tuareg-font-lock-operator">-</span><span class="org-string">'z'</span><span class="org-tuareg-font-lock-operator">]</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">integer</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">'0'</span><span class="org-tuareg-font-lock-operator">-</span><span class="org-string">'9'</span><span class="org-tuareg-font-lock-operator">]+</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">real</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-string">'-'</span><span class="org-tuareg-font-lock-operator">?</span> <span class="org-tuareg-font-lock-operator">(</span>integer <span class="org-string">'.'</span> integer <span class="org-tuareg-font-lock-operator">|</span> integer <span class="org-string">'.'</span> <span class="org-tuareg-font-lock-operator">|</span> <span class="org-string">'.'</span> integer<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">([</span><span class="org-string">'e'</span> <span class="org-string">'E'</span><span class="org-tuareg-font-lock-operator">]</span> <span class="org-tuareg-font-lock-operator">(</span><span class="org-string">'+'</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-string">'-'</span><span class="org-tuareg-font-lock-operator">)?</span> integer<span class="org-tuareg-font-lock-operator">)?</span>
|
||
|
|
|
||
|
|
|
||
|
|
rule read_all <span class="org-tuareg-font-lock-operator">=</span> parse
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> eof <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">EOF</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> eol <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> white <span class="org-keyword">as</span> w <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> w <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> integer <span class="org-keyword">as</span> i <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-operator">(</span>int_of_string i<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> real <span class="org-keyword">as</span> f <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-operator">(</span>float_of_string f<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> word <span class="org-keyword">as</span> w <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">WORD</span> w <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
<span class="org-comment-delimiter">(* </span><span class="org-comment">DEBUG</span>
|
||
|
|
<span class="org-comment"> let () =</span>
|
||
|
|
<span class="org-comment"> let ic = open_in "h2o.xyz" in</span>
|
||
|
|
<span class="org-comment"> let lexbuf = Lexing.from_channel ic in</span>
|
||
|
|
<span class="org-comment"> while true do</span>
|
||
|
|
<span class="org-comment"> let s =</span>
|
||
|
|
<span class="org-comment"> match read_all lexbuf with</span>
|
||
|
|
<span class="org-comment"> | EOL -> "EOL"</span>
|
||
|
|
<span class="org-comment"> | SPACE w -> "SPACE("^w^")"</span>
|
||
|
|
<span class="org-comment"> | INTEGER i -> "INTEGER("^(string_of_int i)^")"</span>
|
||
|
|
<span class="org-comment"> | FLOAT f -> "FLOAT("^(string_of_float f)^")"</span>
|
||
|
|
<span class="org-comment"> | WORD w -> "WORD("^w^")"</span>
|
||
|
|
<span class="org-comment"> | EOF -> "EOF"</span>
|
||
|
|
<span class="org-comment"> in</span>
|
||
|
|
<span class="org-comment"> print_endline s</span>
|
||
|
|
<span class="org-comment"> done;</span>
|
||
|
|
<span class="org-comment-delimiter">*)</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orga0e9364" class="outline-4">
|
||
|
|
<h4 id="orga0e9364"><span class="section-number-4">4.2.2</span> Parser</h4>
|
||
|
|
<div class="outline-text-4" id="text-4-2-2">
|
||
|
|
<p>
|
||
|
|
<code>xyz_parser.mly</code> parses nuclear coordinates in xyz format.
|
||
|
|
</p>
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-operator">%{</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-function-name">make_angstrom</span><span class="org-variable-name"> x y z</span> <span class="org-tuareg-font-lock-operator">=</span>
|
||
|
|
<span class="org-tuareg-font-lock-module">Coordinate.</span><span class="org-tuareg-font-lock-operator">(</span>make_angstrom <span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
x <span class="org-tuareg-font-lock-operator">;</span> y <span class="org-tuareg-font-lock-operator">;</span> z
|
||
|
|
<span class="org-tuareg-font-lock-operator">})</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-function-name">output_of</span><span class="org-variable-name"> f x y z</span> <span class="org-tuareg-font-lock-operator">=</span>
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">a</span> <span class="org-tuareg-font-lock-operator">=</span> make_angstrom x y z <span class="org-tuareg-font-lock-governing">in</span>
|
||
|
|
<span class="org-keyword">fun</span> <span class="org-variable-name">e</span> <span class="org-tuareg-font-lock-operator">-></span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
<span class="org-tuareg-font-lock-module">Xyz_ast.</span>
|
||
|
|
element <span class="org-tuareg-font-lock-operator">=</span> f e<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
coord <span class="org-tuareg-font-lock-operator">=</span> a <span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">output_of_string</span> <span class="org-tuareg-font-lock-operator">=</span> output_of <span class="org-tuareg-font-lock-module">Element.</span>of_string
|
||
|
|
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">output_of_int</span> <span class="org-tuareg-font-lock-operator">=</span> output_of <span class="org-tuareg-font-lock-module">Element.</span>of_int
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-operator">%}</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-constructor">EOL</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator"><</span>string<span class="org-tuareg-font-lock-operator">></span> <span class="org-tuareg-font-lock-constructor">SPACE</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator"><</span>string<span class="org-tuareg-font-lock-operator">></span> <span class="org-tuareg-font-lock-constructor">WORD</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator"><</span>int<span class="org-tuareg-font-lock-operator">></span> <span class="org-tuareg-font-lock-constructor">INTEGER</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator"><</span>float<span class="org-tuareg-font-lock-operator">></span> <span class="org-tuareg-font-lock-constructor">FLOAT</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-constructor">EOF</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span>start input
|
||
|
|
<span class="org-tuareg-font-lock-operator">%</span><span class="org-tuareg-font-lock-governing">type</span> <span class="org-tuareg-font-lock-operator"><</span><span class="org-tuareg-font-lock-module">Xyz_ast.</span>xyz_file<span class="org-tuareg-font-lock-operator">></span> input
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-operator">%%</span> <span class="org-tuareg-font-lock-operator">/*</span> <span class="org-tuareg-font-lock-constructor">Grammar</span> rules <span class="org-tuareg-font-lock-governing">and</span> <span class="org-function-name">actions</span><span class="org-variable-name"> follow</span> <span class="org-tuareg-font-lock-operator">*/</span>
|
||
|
|
|
||
|
|
input<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> integer title atoms_xyz <span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
number_of_atoms <span class="org-tuareg-font-lock-operator">=</span> $1<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
file_title <span class="org-tuareg-font-lock-operator">=</span> $2<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
nuclei <span class="org-tuareg-font-lock-operator">=</span> $3<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
|
||
|
|
|
||
|
|
integer<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $2 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $2 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
|
||
|
|
title<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> title_list <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
|
||
|
|
text<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">(</span>string_of_float $1<span class="org-tuareg-font-lock-operator">)}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">(</span>string_of_int $1<span class="org-tuareg-font-lock-operator">)}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
|
||
|
|
title_list<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-string">""</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> title_list text <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">(</span>$1 <span class="org-tuareg-font-lock-operator">^</span> $2<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
|
||
|
|
atoms_xyz<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-module">List.</span>rev $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">EOF</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-module">List.</span>rev $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
|
||
|
|
atoms_list<span class="org-tuareg-font-lock-operator">:</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">[]</span> <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<p>
|
||
|
|
When an xyz file is read by <code>xyz_parser.mly</code>, it is converted into
|
||
|
|
an <code>xyz_file</code> data structure.
|
||
|
|
</p>
|
||
|
|
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">nucleus</span> <span class="org-tuareg-font-lock-operator">=</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
element<span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Element.</span>t <span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
coord <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Coordinate.</span>angstrom <span class="org-tuareg-font-lock-module">Coordinate.</span>point<span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">xyz_file</span> <span class="org-tuareg-font-lock-operator">=</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">{</span>
|
||
|
|
number_of_atoms <span class="org-tuareg-font-lock-operator">:</span> int <span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
file_title <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
nuclei <span class="org-tuareg-font-lock-operator">:</span> nucleus list <span class="org-tuareg-font-lock-operator">;</span>
|
||
|
|
<span class="org-tuareg-font-lock-operator">}</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org67c4576" class="outline-3">
|
||
|
|
<h3 id="org67c4576"><span class="section-number-3">4.3</span> Conversion</h3>
|
||
|
|
<div class="outline-text-3" id="text-4-3">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> string
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_xyz_file</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_zmt_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_zmt_file</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> string
|
||
|
|
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_filename</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_xyz_string</code></td>
|
||
|
|
<td class="org-left">Create from a string, in xyz format</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_xyz_file</code></td>
|
||
|
|
<td class="org-left">Create from a file, in xyz format</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_zmt_string</code></td>
|
||
|
|
<td class="org-left">Create from a string, in z-matrix format</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_zmt_file</code></td>
|
||
|
|
<td class="org-left">Create from a file, in z-matrix format</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_string</code></td>
|
||
|
|
<td class="org-left">Transform to a string, for printing</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_filename</code></td>
|
||
|
|
<td class="org-left">Detects the type of file (xyz, z-matrix) and reads the file</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org31c8415" class="outline-3">
|
||
|
|
<h3 id="org31c8415"><span class="section-number-3">4.4</span> <span class="todo TODO">TODO</span> Query</h3>
|
||
|
|
<div class="outline-text-3" id="text-4-4">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">formula</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> string
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">repulsion</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> float
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">charge</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Charge.</span>t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">small_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">large_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>formula</code></td>
|
||
|
|
<td class="org-left">Returns the chemical formula</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>repulsion</code></td>
|
||
|
|
<td class="org-left">Nuclear repulsion energy, in atomic units</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>charge</code></td>
|
||
|
|
<td class="org-left">Sum of the charges of the nuclei</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>small_core</code></td>
|
||
|
|
<td class="org-left">Number of core electrons in the small core model</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>large_core</code></td>
|
||
|
|
<td class="org-left">Number of core electrons in the large core model</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orga01f8b6" class="outline-3">
|
||
|
|
<h3 id="orga01f8b6"><span class="section-number-3">4.5</span> Printers</h3>
|
||
|
|
<div class="outline-text-3" id="text-4-5">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orgf2e9bac" class="outline-3">
|
||
|
|
<h3 id="orgf2e9bac"><span class="section-number-3">4.6</span> Tests</h3>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org3573ea4" class="outline-2">
|
||
|
|
<h2 id="org3573ea4"><span class="section-number-2">5</span> Z-matrix</h2>
|
||
|
|
<div class="outline-text-2" id="text-5">
|
||
|
|
<p>
|
||
|
|
Z-matrix representation of nuclear coordinates.
|
||
|
|
</p>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-org7593a50" class="outline-3">
|
||
|
|
<h3 id="org7593a50"><span class="section-number-3">5.1</span> Type</h3>
|
||
|
|
<div class="outline-text-3" id="text-5-1">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml" id="org742f0bb"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<div id="outline-container-orgf0cdae8" class="outline-3">
|
||
|
|
<h3 id="orgf0cdae8"><span class="section-number-3">5.2</span> Conversion</h3>
|
||
|
|
<div class="outline-text-3" id="text-5-2">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-></span> t
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-operator">(</span><span class="org-tuareg-font-lock-module">Element.</span>t <span class="org-tuareg-font-lock-operator">*</span> float <span class="org-tuareg-font-lock-operator">*</span> float <span class="org-tuareg-font-lock-operator">*</span> float<span class="org-tuareg-font-lock-operator">)</span> array
|
||
|
|
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> string
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||
|
|
|
||
|
|
|
||
|
|
<colgroup>
|
||
|
|
<col class="org-left" />
|
||
|
|
|
||
|
|
<col class="org-left" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody>
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>of_string</code></td>
|
||
|
|
<td class="org-left">Reads a z-matrix from a string</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_xyz</code></td>
|
||
|
|
<td class="org-left">Converts to xyz format, as in the <code>Nuclei</code> module</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
<tr>
|
||
|
|
<td class="org-left"><code>to_xyz_string</code></td>
|
||
|
|
<td class="org-left">Converts to xyz format, as a string</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
|
||
|
|
<pre class="example" id="org22200dd">
|
||
|
|
let zmt = Zmatrix.of_string "
|
||
|
|
n
|
||
|
|
n 1 nn
|
||
|
|
h 1 hn 2 hnn
|
||
|
|
h 2 hn 1 hnn 3 dih4
|
||
|
|
h 1 hn 2 hnn 4 dih5
|
||
|
|
h 2 hn 1 hnn 3 dih5
|
||
|
|
|
||
|
|
nn 1.446
|
||
|
|
hn 1.016
|
||
|
|
hnn 106.0
|
||
|
|
dih4 -54.38
|
||
|
|
dih5 54.38
|
||
|
|
" ;;
|
||
|
|
- : Zmatrix.t = N
|
||
|
|
N 1 1.446000
|
||
|
|
H 1 1.016000 2 106.000000
|
||
|
|
H 2 1.016000 1 106.000000 3 -54.380000
|
||
|
|
H 1 1.016000 2 106.000000 4 54.380000
|
||
|
|
H 2 1.016000 1 106.000000 3 54.380000
|
||
|
|
|
||
|
|
|
||
|
|
Zmatrix.to_xyz zmt ;;
|
||
|
|
- : (Element.t * float * float * float) array =
|
||
|
|
[|(N, 0., 0., 0.); (N, 0., 0., 1.446);
|
||
|
|
(H, -0.976641883073332107, 0., -0.280047553510071046);
|
||
|
|
(H, -0.568802835186988709, 0.793909757123734683, 1.726047553510071);
|
||
|
|
(H, 0.314092649983635563, 0.924756819385119, -0.280047553510071101);
|
||
|
|
(H, -0.568802835186988709, -0.793909757123734683, 1.726047553510071)|]
|
||
|
|
|
||
|
|
|
||
|
|
Zmatrix.to_xyz_string zmt ;;
|
||
|
|
- : string =
|
||
|
|
"N 0.000000 0.000000 0.000000
|
||
|
|
N 0.000000 0.000000 1.446000
|
||
|
|
H -0.976642 0.000000 -0.280048
|
||
|
|
H -0.568803 0.793910 1.726048
|
||
|
|
H 0.314093 0.924757 -0.280048
|
||
|
|
H -0.568803 -0.793910 1.726048"
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
|
||
|
|
<div id="outline-container-org08080f5" class="outline-3">
|
||
|
|
<h3 id="org08080f5"><span class="section-number-3">5.3</span> Printers</h3>
|
||
|
|
<div class="outline-text-3" id="text-5-3">
|
||
|
|
<div class="org-src-container">
|
||
|
|
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||
|
|
</pre>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
<div id="postamble" class="status">
|
||
|
|
<p class="author">Author: Anthony Scemama</p>
|
||
|
|
<p class="date">Created: 2021-01-01 Fri 16:37</p>
|
||
|
|
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||
|
|
</div>
|
||
|
|
</body>
|
||
|
|
</html>
|