2022-09-28 18:04:21 +02:00
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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2024-02-23 16:38:44 +01:00
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<!-- 2024-02-23 Fri 15:38 -->
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2022-09-28 18:04:21 +02:00
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<title>Nucleus</title>
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<meta name="author" content="TREX CoE" />
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/* additional languages in org.el's org-babel-load-languages alist */
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pre.src-io:before { content: 'IO'; }
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pre.src-makefile:before { content: 'Makefile'; }
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pre.src-picolisp:before { content: 'Pico Lisp'; }
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pre.src-scala:before { content: 'Scala'; }
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pre.src-shell:before { content: 'Shell Script'; }
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/* additional language identifiers per "defun org-babel-execute"
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in ob-*.el */
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pre.src-cpp:before { content: 'C++'; }
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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-mksh:before { content: 'mksh'; }
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pre.src-delphi:before { content: 'Delphi'; }
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pre.src-metapost:before { content: 'MetaPost'; }
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pre.src-modula-2:before { content: 'Modula-2'; }
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pre.src-pascal:before { content: 'Pascal'; }
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pre.src-ps:before { content: 'PostScript'; }
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pre.src-prolog:before { content: 'Prolog'; }
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pre.src-simula:before { content: 'Simula'; }
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pre.src-tcl:before { content: 'tcl'; }
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pre.src-tex:before { content: 'TeX'; }
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pre.src-plain-tex:before { content: 'Plain TeX'; }
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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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table { border-collapse:collapse; }
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dt { font-weight: bold; }
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.figure p { text-align: center; }
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2022-11-18 14:16:53 +01:00
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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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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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#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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.org-svg { width: 90%; }
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/*]]>*/-->
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</style>
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<link rel="stylesheet" title="Standard" href="qmckl.css" type="text/css" />
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<script type="text/javascript" src="org-info.js">
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/**
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*
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* @source: org-info.js
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*
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* @licstart The following is the entire license notice for the
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* JavaScript code in org-info.js.
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*
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2022-11-18 14:16:53 +01:00
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* Copyright (C) 2012-2020 Free Software Foundation, Inc.
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2022-09-28 18:04:21 +02:00
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*
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*
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* The JavaScript code in this tag is free software: you can
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* redistribute it and/or modify it under the terms of the GNU
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* General Public License (GNU GPL) as published by the Free Software
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* Foundation, either version 3 of the License, or (at your option)
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* any later version. The code is distributed WITHOUT ANY WARRANTY;
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* without even the implied warranty of MERCHANTABILITY or FITNESS
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* FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
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*
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* As additional permission under GNU GPL version 3 section 7, you
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* may distribute non-source (e.g., minimized or compacted) forms of
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* that code without the copy of the GNU GPL normally required by
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* section 4, provided you include this license notice and a URL
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* through which recipients can access the Corresponding Source.
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*
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* @licend The above is the entire license notice
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* for the JavaScript code in org-info.js.
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*
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*/
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</script>
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<script type="text/javascript">
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/*
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@licstart The following is the entire license notice for the
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JavaScript code in this tag.
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2022-11-18 14:16:53 +01:00
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Copyright (C) 2012-2020 Free Software Foundation, Inc.
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2022-09-28 18:04:21 +02:00
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The JavaScript code in this tag is free software: you can
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redistribute it and/or modify it under the terms of the GNU
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General Public License (GNU GPL) as published by the Free Software
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Foundation, either version 3 of the License, or (at your option)
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any later version. The code is distributed WITHOUT ANY WARRANTY;
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without even the implied warranty of MERCHANTABILITY or FITNESS
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FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
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As additional permission under GNU GPL version 3 section 7, you
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may distribute non-source (e.g., minimized or compacted) forms of
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that code without the copy of the GNU GPL normally required by
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section 4, provided you include this license notice and a URL
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through which recipients can access the Corresponding Source.
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@licend The above is the entire license notice
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for the JavaScript code in this tag.
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*/
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<!--/*--><![CDATA[/*><!--*/
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org_html_manager.set("TOC_DEPTH", "4");
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org_html_manager.set("LINK_HOME", "index.html");
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org_html_manager.set("LINK_UP", "");
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org_html_manager.set("LOCAL_TOC", "1");
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org_html_manager.set("VIEW_BUTTONS", "0");
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org_html_manager.set("MOUSE_HINT", "underline");
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org_html_manager.set("FIXED_TOC", "0");
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org_html_manager.set("TOC", "1");
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org_html_manager.set("VIEW", "info");
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org_html_manager.setup(); // activate after the parameters are set
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/*]]>*///-->
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</script>
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<script type="text/javascript">
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/*
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@licstart The following is the entire license notice for the
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JavaScript code in this tag.
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2022-11-18 14:16:53 +01:00
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Copyright (C) 2012-2020 Free Software Foundation, Inc.
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2022-09-28 18:04:21 +02:00
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The JavaScript code in this tag is free software: you can
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redistribute it and/or modify it under the terms of the GNU
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General Public License (GNU GPL) as published by the Free Software
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Foundation, either version 3 of the License, or (at your option)
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any later version. The code is distributed WITHOUT ANY WARRANTY;
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without even the implied warranty of MERCHANTABILITY or FITNESS
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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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</head>
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<body>
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<div id="org-div-home-and-up">
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<a accesskey="h" href=""> UP </a>
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<a accesskey="H" href="index.html"> HOME </a>
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</div><div id="content">
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<h1 class="title">Nucleus</h1>
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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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2024-02-23 16:38:44 +01:00
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<li><a href="#org48320de">1. Context</a>
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2022-09-28 18:04:21 +02:00
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<ul>
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2024-02-23 16:38:44 +01:00
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<li><a href="#orgf1f63b8">1.1. Data structure</a></li>
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<li><a href="#org12ff8c2">1.2. Access functions</a></li>
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<li><a href="#org096624e">1.3. Initialization functions</a></li>
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<li><a href="#orgc4c40c2">1.4. Test</a></li>
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2022-09-28 18:04:21 +02:00
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</ul>
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</li>
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2024-02-23 16:38:44 +01:00
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<li><a href="#orge87f1d8">2. Computation</a>
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2022-09-28 18:04:21 +02:00
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<ul>
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2024-02-23 16:38:44 +01:00
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<li><a href="#orgc490154">2.1. Nucleus-nucleus distances</a>
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2022-09-28 18:04:21 +02:00
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<ul>
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2024-02-23 16:38:44 +01:00
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<li><a href="#org02d312e">2.1.1. Get</a></li>
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<li><a href="#orgf2bf670">2.1.2. Compute</a></li>
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<li><a href="#orge7c0287">2.1.3. Test</a></li>
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2022-09-28 18:04:21 +02:00
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</ul>
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</li>
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2024-02-23 16:38:44 +01:00
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<li><a href="#org627978d">2.2. Nuclear repulsion energy</a>
|
2022-09-28 18:04:21 +02:00
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<ul>
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2024-02-23 16:38:44 +01:00
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<li><a href="#org17a64a7">2.2.1. Get</a></li>
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<li><a href="#orgd790c52">2.2.2. Compute</a></li>
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<li><a href="#org2452270">2.2.3. Test</a></li>
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2022-09-28 18:04:21 +02:00
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</ul>
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</li>
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</ul>
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</ul>
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</div>
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</div>
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2024-02-23 16:38:44 +01:00
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<div id="outline-container-org48320de" class="outline-2">
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<h2 id="org48320de"><span class="section-number-2">1</span> Context</h2>
|
2022-09-28 18:04:21 +02:00
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<div class="outline-text-2" id="text-1">
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<p>
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The following data stored in the context:
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</p>
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<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
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<col class="org-left" />
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<col class="org-left" />
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<col class="org-left" />
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</colgroup>
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<tbody>
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<tr>
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<td class="org-left"><code>uninitialized</code></td>
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<td class="org-left">int32<sub>t</sub></td>
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<td class="org-left">Keeps bit set for uninitialized data</td>
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</tr>
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<tr>
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<td class="org-left"><code>num</code></td>
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<td class="org-left">int64<sub>t</sub></td>
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<td class="org-left">Total number of nuclei</td>
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</tr>
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<tr>
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<td class="org-left"><code>provided</code></td>
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<td class="org-left">bool</td>
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<td class="org-left">If true, <code>nucleus</code> is valid</td>
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</tr>
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<tr>
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<td class="org-left"><code>charge</code></td>
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<td class="org-left">qmckl<sub>vector</sub></td>
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<td class="org-left">Nuclear charges</td>
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</tr>
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<tr>
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<td class="org-left"><code>coord</code></td>
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<td class="org-left">qmckl<sub>matrix</sub></td>
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<td class="org-left">Nuclear coordinates, in transposed format</td>
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</tr>
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<tr>
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<td class="org-left"><code>coord_date</code></td>
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<td class="org-left">int64<sub>t</sub></td>
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<td class="org-left">Nuclear coordinates, date if modified</td>
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</tr>
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</tbody>
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</table>
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<p>
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Computed data:
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</p>
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<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
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<col class="org-left" />
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<col class="org-left" />
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</colgroup>
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<tbody>
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<tr>
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<td class="org-left"><code>nn_distance</code></td>
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<td class="org-left">qmckl<sub>matrix</sub></td>
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<td class="org-left">Nucleus-nucleus distances</td>
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</tr>
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<tr>
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<td class="org-left"><code>nn_distance_date</code></td>
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<td class="org-left">int64<sub>t</sub></td>
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<td class="org-left">Date when Nucleus-nucleus distances were computed</td>
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</tr>
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<tr>
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<td class="org-left"><code>repulsion</code></td>
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<td class="org-left">double</td>
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<td class="org-left">Nuclear repulsion energy</td>
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</tr>
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<tr>
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<td class="org-left"><code>repulsion_date</code></td>
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<td class="org-left">int64<sub>t</sub></td>
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<td class="org-left">Date when the nuclear repulsion energy was computed</td>
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</tr>
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</tbody>
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</table>
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</div>
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|
2024-02-23 16:38:44 +01:00
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<div id="outline-container-orgf1f63b8" class="outline-3">
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<h3 id="orgf1f63b8"><span class="section-number-3">1.1</span> Data structure</h3>
|
2022-09-28 18:04:21 +02:00
|
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<div class="outline-text-3" id="text-1-1">
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">qmckl_nucleus_struct</span> {
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|
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">num</span>;
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|
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">repulsion_date</span>;
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|
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">nn_distance_date</span>;
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<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">coord_date</span>;
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|
<span style="color: #228b22;">qmckl_vector</span> <span style="color: #a0522d;">charge</span>;
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|
<span style="color: #228b22;">qmckl_matrix</span> <span style="color: #a0522d;">coord</span>;
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<span style="color: #228b22;">qmckl_matrix</span> <span style="color: #a0522d;">nn_distance</span>;
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<span style="color: #228b22;">double</span> <span style="color: #a0522d;">repulsion</span>;
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|
<span style="color: #228b22;">int32_t</span> <span style="color: #a0522d;">uninitialized</span>;
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|
|
<span style="color: #228b22;">bool</span> <span style="color: #a0522d;">provided</span>;
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|
} <span style="color: #228b22;">qmckl_nucleus_struct</span>;
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</pre>
|
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|
</div>
|
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<p>
|
|
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|
|
The <code>uninitialized</code> integer contains one bit set to one for each
|
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|
|
initialization function which has not been called. It becomes equal
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|
|
to zero after all initialization functions have been called. The
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|
struct is then initialized and <code>provided == true</code>.
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|
Some values are initialized by default, and are not concerned by
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this mechanism.
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</p>
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_init_nucleus</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>);
|
|
|
|
|
</pre>
|
|
|
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|
</div>
|
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<div class="org-src-container">
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|
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_init_nucleus</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>) {
|
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|
|
<span style="color: #a020f0;">if</span> (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
|
|
|
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">false</span>;
|
|
|
|
|
}
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|
|
<span style="color: #228b22;">qmckl_context_struct</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">ctx</span> = (<span style="color: #228b22;">qmckl_context_struct</span>*) context;
|
|
|
|
|
assert (ctx != <span style="color: #008b8b;">NULL</span>);
|
|
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|
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|
|
ctx->nucleus.uninitialized = (1 << 3) - 1;
|
|
|
|
|
|
2022-11-18 14:16:53 +01:00
|
|
|
/* <span style="color: #b22222;">Default values</span> */
|
2022-09-28 18:04:21 +02:00
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|
|
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|
|
<span style="color: #a020f0;">return</span> QMCKL_SUCCESS;
|
|
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|
|
}
|
|
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|
|
</pre>
|
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|
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|
</div>
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</div>
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</div>
|
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|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-org12ff8c2" class="outline-3">
|
|
|
|
|
<h3 id="org12ff8c2"><span class="section-number-3">1.2</span> Access functions</h3>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-3" id="text-1-2">
|
|
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|
<p>
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|
|
When all the data relative to nuclei have been set, the following
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|
function returns <code>true</code>.
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|
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|
</p>
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<div class="org-src-container">
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|
|
|
|
<pre class="src src-c"><span style="color: #228b22;">bool</span> <span style="color: #0000ff;">qmckl_nucleus_provided</span> (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>);
|
|
|
|
|
</pre>
|
|
|
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|
</div>
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|
</div>
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</div>
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|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-org096624e" class="outline-3">
|
|
|
|
|
<h3 id="org096624e"><span class="section-number-3">1.3</span> Initialization functions</h3>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-3" id="text-1-3">
|
|
|
|
|
<p>
|
|
|
|
|
To set the data relative to the nuclei in the context, the
|
|
|
|
|
following functions need to be called.
|
|
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|
</p>
|
|
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<div class="org-src-container">
|
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|
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span>
|
|
|
|
|
<span style="color: #0000ff;">qmckl_set_nucleus_num</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>,
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">num</span>);
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
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<p>
|
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Sets the number of nuclei.
|
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|
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|
</p>
|
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|
<div class="org-src-container">
|
|
|
|
|
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span>
|
|
|
|
|
<span style="color: #0000ff;">qmckl_set_nucleus_charge</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>,
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">charge</span>,
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size_max</span>);
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
|
|
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|
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<p>
|
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|
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Sets the nuclear charges of all the atoms.
|
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|
|
|
</p>
|
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|
|
|
|
<div class="org-src-container">
|
|
|
|
|
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span>
|
|
|
|
|
<span style="color: #0000ff;">qmckl_set_nucleus_coord</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>,
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span> <span style="color: #a0522d;">transp</span>,
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">coord</span>,
|
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|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size_max</span>);
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
|
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|
<p>
|
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|
Sets the nuclear coordinates of all the atoms. The coordinates
|
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|
|
|
are be given in atomic units.
|
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|
|
|
</p>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-orgc4c40c2" class="outline-3">
|
|
|
|
|
<h3 id="orgc4c40c2"><span class="section-number-3">1.4</span> Test</h3>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-3" id="text-1-4">
|
|
|
|
|
<div class="org-src-container">
|
|
|
|
|
<pre class="src src-c"><span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">nucl_charge</span> = chbrclf_charge;
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">nucl_coord</span> = &(chbrclf_nucl_coord[0][0]);
|
|
|
|
|
|
2022-11-18 14:16:53 +01:00
|
|
|
/* <span style="color: #b22222;">---</span> */
|
2022-09-28 18:04:21 +02:00
|
|
|
|
|
|
|
|
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #a0522d;">rc</span>;
|
|
|
|
|
|
|
|
|
|
assert(!qmckl_nucleus_provided(context));
|
|
|
|
|
|
|
|
|
|
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">n</span>;
|
|
|
|
|
rc = qmckl_get_nucleus_num (context, &n);
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
rc = qmckl_set_nucleus_num (context, chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
assert(!qmckl_nucleus_provided(context));
|
|
|
|
|
|
|
|
|
|
rc = qmckl_get_nucleus_num (context, &n);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(n == chbrclf_nucl_num);
|
|
|
|
|
|
|
|
|
|
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">nucl_coord2</span>[3*chbrclf_nucl_num];
|
|
|
|
|
|
|
|
|
|
rc = qmckl_get_nucleus_coord (context, <span style="color: #8b2252;">'T'</span>, nucl_coord2, 3*chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
|
|
|
|
|
|
|
|
|
|
rc = qmckl_set_nucleus_coord (context, <span style="color: #8b2252;">'T'</span>, &(nucl_coord[0]), 3*chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
|
|
|
|
|
assert(!qmckl_nucleus_provided(context));
|
|
|
|
|
|
|
|
|
|
rc = qmckl_get_nucleus_coord (context, <span style="color: #8b2252;">'N'</span>, nucl_coord2, 3*chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">k</span>=0 ; k<3 ; ++k) {
|
|
|
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">i</span>=0 ; i<chbrclf_nucl_num ; ++i) {
|
|
|
|
|
assert( nucl_coord[chbrclf_nucl_num*k+i] == nucl_coord2[3*i+k] );
|
|
|
|
|
}
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
rc = qmckl_get_nucleus_coord (context, <span style="color: #8b2252;">'T'</span>, nucl_coord2, 3*chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">i</span>=0 ; i<3*chbrclf_nucl_num ; ++i) {
|
|
|
|
|
assert( nucl_coord[i] == nucl_coord2[i] );
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">nucl_charge2</span>[chbrclf_nucl_num];
|
|
|
|
|
|
|
|
|
|
rc = qmckl_get_nucleus_charge(context, nucl_charge2, chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
|
|
|
|
|
|
|
|
|
|
rc = qmckl_set_nucleus_charge(context, nucl_charge, chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
|
|
|
|
|
rc = qmckl_get_nucleus_charge(context, nucl_charge2, chbrclf_nucl_num);
|
|
|
|
|
<span style="color: #0000ff;">qmckl_check</span>(context, rc);
|
|
|
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">i</span>=0 ; i<chbrclf_nucl_num ; ++i) {
|
|
|
|
|
assert( nucl_charge[i] == nucl_charge2[i] );
|
|
|
|
|
}
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-orge87f1d8" class="outline-2">
|
|
|
|
|
<h2 id="orge87f1d8"><span class="section-number-2">2</span> Computation</h2>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-2" id="text-2">
|
|
|
|
|
<p>
|
|
|
|
|
The computed data is stored in the context so that it can be reused
|
|
|
|
|
by different kernels. To ensure that the data is valid, for each
|
|
|
|
|
computed data the date of the context is stored when it is computed.
|
|
|
|
|
To know if some data needs to be recomputed, we check if the date of
|
|
|
|
|
the dependencies are more recent than the date of the data to
|
|
|
|
|
compute. If it is the case, then the data is recomputed and the
|
|
|
|
|
current date is stored.
|
|
|
|
|
</p>
|
|
|
|
|
</div>
|
|
|
|
|
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-orgc490154" class="outline-3">
|
|
|
|
|
<h3 id="orgc490154"><span class="section-number-3">2.1</span> Nucleus-nucleus distances</h3>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-3" id="text-2-1">
|
|
|
|
|
</div>
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-org02d312e" class="outline-4">
|
|
|
|
|
<h4 id="org02d312e"><span class="section-number-4">2.1.1</span> Get</h4>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-4" id="text-2-1-1">
|
|
|
|
|
<div class="org-src-container">
|
|
|
|
|
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span>
|
|
|
|
|
<span style="color: #0000ff;">qmckl_get_nucleus_nn_distance</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>,
|
|
|
|
|
<span style="color: #228b22;">double</span>* <span style="color: #a0522d;">distance</span>,
|
|
|
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size_max</span>);
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-orgf2bf670" class="outline-4">
|
|
|
|
|
<h4 id="orgf2bf670"><span class="section-number-4">2.1.2</span> Compute</h4>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-4" id="text-2-1-2">
|
2024-02-23 16:38:44 +01:00
|
|
|
<table id="org7783fc8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
2022-09-28 18:04:21 +02:00
|
|
|
|
|
|
|
|
|
|
|
|
|
<colgroup>
|
|
|
|
|
<col class="org-left" />
|
|
|
|
|
|
|
|
|
|
<col class="org-left" />
|
|
|
|
|
|
|
|
|
|
<col class="org-left" />
|
|
|
|
|
|
|
|
|
|
<col class="org-left" />
|
|
|
|
|
</colgroup>
|
|
|
|
|
<tbody>
|
|
|
|
|
<tr>
|
|
|
|
|
<td class="org-left">qmckl<sub>context</sub></td>
|
|
|
|
|
<td class="org-left">context</td>
|
|
|
|
|
<td class="org-left">in</td>
|
|
|
|
|
<td class="org-left">Global state</td>
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
<td class="org-left">int64<sub>t</sub></td>
|
|
|
|
|
<td class="org-left">nucl<sub>num</sub></td>
|
|
|
|
|
<td class="org-left">in</td>
|
|
|
|
|
<td class="org-left">Number of nuclei</td>
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
<td class="org-left">double</td>
|
|
|
|
|
<td class="org-left">coord[3][nucl<sub>num</sub>]</td>
|
|
|
|
|
<td class="org-left">in</td>
|
|
|
|
|
<td class="org-left">Nuclear coordinates (au)</td>
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
<td class="org-left">double</td>
|
|
|
|
|
<td class="org-left">nn<sub>distance</sub>[nucl<sub>num</sub>][nucl<sub>num</sub>]</td>
|
|
|
|
|
<td class="org-left">out</td>
|
|
|
|
|
<td class="org-left">Nucleus-nucleus distances (au)</td>
|
|
|
|
|
</tr>
|
|
|
|
|
</tbody>
|
|
|
|
|
</table>
|
|
|
|
|
|
|
|
|
|
<div class="org-src-container">
|
|
|
|
|
<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_compute_nn_distance_f</span><span style="color: #000000; background-color: #ffffff;">(context, nucl_num, coord, nn_distance)</span><span style="color: #a0522d;"> </span><span style="color: #a020f0;">&</span>
|
|
|
|
|
<span style="color: #a020f0;">result</span>(info)
|
|
|
|
|
<span style="color: #a020f0;">use</span> <span style="color: #0000ff;">qmckl</span>
|
|
|
|
|
<span style="color: #a020f0;">implicit</span> <span style="color: #228b22;">none</span>
|
|
|
|
|
<span style="color: #228b22;">integer</span>(qmckl_context), <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> context</span>
|
|
|
|
|
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_num</span>
|
|
|
|
|
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> coord(nucl_num,3)</span>
|
|
|
|
|
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(out) ::<span style="color: #a0522d;"> nn_distance(nucl_num,nucl_num)</span>
|
|
|
|
|
|
|
|
|
|
<span style="color: #228b22;">integer</span>*8 ::<span style="color: #a0522d;"> k</span>
|
|
|
|
|
|
|
|
|
|
info = QMCKL_SUCCESS
|
|
|
|
|
|
|
|
|
|
<span style="color: #a020f0;">if</span> (context == QMCKL_NULL_CONTEXT) <span style="color: #a020f0;">then</span>
|
|
|
|
|
info = QMCKL_INVALID_CONTEXT
|
|
|
|
|
<span style="color: #a020f0;">return</span>
|
|
|
|
|
<span style="color: #a020f0;">endif</span>
|
|
|
|
|
|
|
|
|
|
<span style="color: #a020f0;">if</span> (nucl_num <= 0) <span style="color: #a020f0;">then</span>
|
|
|
|
|
info = QMCKL_INVALID_ARG_2
|
|
|
|
|
<span style="color: #a020f0;">return</span>
|
|
|
|
|
<span style="color: #a020f0;">endif</span>
|
|
|
|
|
|
|
|
|
|
info = qmckl_distance(context, <span style="color: #8b2252;">'T'</span>, <span style="color: #8b2252;">'T'</span>, nucl_num, nucl_num, <span style="color: #a020f0;">&</span>
|
|
|
|
|
coord, nucl_num, <span style="color: #a020f0;">&</span>
|
|
|
|
|
coord, nucl_num, <span style="color: #a020f0;">&</span>
|
|
|
|
|
nn_distance, nucl_num)
|
|
|
|
|
|
|
|
|
|
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_nn_distance_f</span>
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-orge7c0287" class="outline-4">
|
|
|
|
|
<h4 id="orge7c0287"><span class="section-number-4">2.1.3</span> Test</h4>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-4" id="text-2-1-3">
|
|
|
|
|
<div class="org-src-container">
|
2022-11-18 14:16:53 +01:00
|
|
|
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data</span> */
|
2022-09-28 18:04:21 +02:00
|
|
|
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
|
|
|
|
|
|
|
|
|
|
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">distance</span>[chbrclf_nucl_num*chbrclf_nucl_num];
|
|
|
|
|
rc = qmckl_get_nucleus_nn_distance(context, distance, chbrclf_nucl_num*chbrclf_nucl_num);
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<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[0] == 0.);
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<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[1] == distance[chbrclf_nucl_num]);
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<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">distance</span>[1]-2.070304721365169) < 1.e-12);
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</pre>
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</div>
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</div>
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</div>
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</div>
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2024-02-23 16:38:44 +01:00
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<div id="outline-container-org627978d" class="outline-3">
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<h3 id="org627978d"><span class="section-number-3">2.2</span> Nuclear repulsion energy</h3>
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2022-09-28 18:04:21 +02:00
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<div class="outline-text-3" id="text-2-2">
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<p>
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\[
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V_{NN} = \sum_{A=1}^{N-1} \sum_{B>A}^N \frac{Q_A Q_B}{R_{AB}}
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\]
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</p>
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</div>
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2024-02-23 16:38:44 +01:00
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<div id="outline-container-org17a64a7" class="outline-4">
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<h4 id="org17a64a7"><span class="section-number-4">2.2.1</span> Get</h4>
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2022-09-28 18:04:21 +02:00
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<div class="outline-text-4" id="text-2-2-1">
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_nucleus_repulsion</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">energy</span>);
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</pre>
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</div>
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</div>
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</div>
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2024-02-23 16:38:44 +01:00
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<div id="outline-container-orgd790c52" class="outline-4">
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<h4 id="orgd790c52"><span class="section-number-4">2.2.2</span> Compute</h4>
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2022-09-28 18:04:21 +02:00
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<div class="outline-text-4" id="text-2-2-2">
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2024-02-23 16:38:44 +01:00
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<table id="org38278ad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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2022-09-28 18:04:21 +02:00
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<colgroup>
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<col class="org-left" />
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<col class="org-left" />
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<col class="org-left" />
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<col class="org-left" />
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</colgroup>
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<tbody>
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<tr>
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<td class="org-left">qmckl<sub>context</sub></td>
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<td class="org-left">context</td>
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<td class="org-left">in</td>
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<td class="org-left">Global state</td>
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</tr>
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<tr>
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<td class="org-left">int64<sub>t</sub></td>
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<td class="org-left">nucl<sub>num</sub></td>
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<td class="org-left">in</td>
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<td class="org-left">Number of nuclei</td>
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</tr>
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<tr>
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<td class="org-left">double</td>
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<td class="org-left">charge[nucl<sub>num</sub>]</td>
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<td class="org-left">in</td>
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<td class="org-left">Nuclear charges (au)</td>
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</tr>
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<tr>
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<td class="org-left">double</td>
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<td class="org-left">nn<sub>distance</sub>[nucl<sub>num</sub>][nucl<sub>num</sub>]</td>
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<td class="org-left">in</td>
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<td class="org-left">Nucleus-nucleus distances (au)</td>
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</tr>
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<tr>
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<td class="org-left">double</td>
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<td class="org-left">energy</td>
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<td class="org-left">out</td>
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<td class="org-left">Nuclear repulsion energy</td>
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</tr>
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</tbody>
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</table>
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_compute_nucleus_repulsion_f</span><span style="color: #000000; background-color: #ffffff;">(context, nucl_num, charge, nn_distance, energy)</span><span style="color: #a0522d;"> </span><span style="color: #a020f0;">&</span>
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<span style="color: #a020f0;">result</span>(info)
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<span style="color: #a020f0;">use</span> <span style="color: #0000ff;">qmckl</span>
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<span style="color: #a020f0;">implicit</span> <span style="color: #228b22;">none</span>
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|
<span style="color: #228b22;">integer</span>(qmckl_context), <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> context</span>
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<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_num</span>
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|
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|
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> charge(nucl_num)</span>
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|
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|
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nn_distance(nucl_num,nucl_num)</span>
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|
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(out) ::<span style="color: #a0522d;"> energy</span>
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|
<span style="color: #228b22;">integer</span>*8 ::<span style="color: #a0522d;"> i, j</span>
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|
|
info = QMCKL_SUCCESS
|
|
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|
|
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|
|
<span style="color: #a020f0;">if</span> (context == QMCKL_NULL_CONTEXT) <span style="color: #a020f0;">then</span>
|
|
|
|
|
info = QMCKL_INVALID_CONTEXT
|
|
|
|
|
<span style="color: #a020f0;">return</span>
|
|
|
|
|
<span style="color: #a020f0;">endif</span>
|
|
|
|
|
|
|
|
|
|
<span style="color: #a020f0;">if</span> (nucl_num <= 0) <span style="color: #a020f0;">then</span>
|
|
|
|
|
info = QMCKL_INVALID_ARG_2
|
|
|
|
|
<span style="color: #a020f0;">return</span>
|
|
|
|
|
<span style="color: #a020f0;">endif</span>
|
|
|
|
|
|
|
|
|
|
energy = 0.d0
|
|
|
|
|
<span style="color: #a020f0;">do</span> j=2, nucl_num
|
|
|
|
|
<span style="color: #a020f0;">do</span> i=1, j-1
|
|
|
|
|
<span style="color: #a020f0;">if</span> (dabs(nn_distance(i,j)) > 1e-5) <span style="color: #a020f0;">then</span>
|
|
|
|
|
energy = energy + charge(i) * charge(j) / nn_distance(i,j)
|
|
|
|
|
<span style="color: #a020f0;">endif</span>
|
|
|
|
|
<span style="color: #a020f0;">end do</span>
|
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|
<span style="color: #a020f0;">end do</span>
|
|
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|
|
|
|
|
|
|
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_nucleus_repulsion_f</span>
|
|
|
|
|
</pre>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
</div>
|
|
|
|
|
|
2024-02-23 16:38:44 +01:00
|
|
|
<div id="outline-container-org2452270" class="outline-4">
|
|
|
|
|
<h4 id="org2452270"><span class="section-number-4">2.2.3</span> Test</h4>
|
2022-09-28 18:04:21 +02:00
|
|
|
<div class="outline-text-4" id="text-2-2-3">
|
|
|
|
|
<div class="org-src-container">
|
2022-11-18 14:16:53 +01:00
|
|
|
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data</span> */
|
2022-09-28 18:04:21 +02:00
|
|
|
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
|
|
|
|
|
|
|
|
|
|
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">rep</span>;
|
|
|
|
|
rc = qmckl_get_nucleus_repulsion(context, &rep);
|
|
|
|
|
<span style="color: #0000ff;">assert</span>(rep - 318.2309879436158 < 1.e-10);
|
|
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|
|
|
|
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|
|
</pre>
|
|
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|
|
</div>
|
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|
</div>
|
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|
</div>
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|
</div>
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|
</div>
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|
</div>
|
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|
|
<div id="postamble" class="status">
|
|
|
|
|
<p class="author">Author: TREX CoE</p>
|
2024-02-23 16:38:44 +01:00
|
|
|
<p class="date">Created: 2024-02-23 Fri 15:38</p>
|
2022-09-28 18:04:21 +02:00
|
|
|
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
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</div>
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</body>
|
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</html>
|
