mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-11-04 21:24:08 +01:00
org-html-themes | ||
examples.html | ||
examples.org | ||
index.html | ||
intro.html | ||
intro.org | ||
lib.html | ||
lib.org | ||
README.html | ||
templator_front.html | ||
templator_hdf5.html | ||
templator_text.html | ||
theme.setup | ||
trex_lib.png | ||
trex_specs.png | ||
trex.html | ||
trexio_logo.png | ||
trexio.css | ||
trexio.png | ||
tutorial_benzene.html |
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-03-13 Wed 13:26 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
<meta name="generator" content="Org mode" />
<meta name="author" content="TREX-CoE" />
<style type="text/css">
<!--/*--><![CDATA[/*><!--*/
.title { text-align: center;
margin-bottom: .2em; }
.subtitle { text-align: center;
font-size: medium;
font-weight: bold;
margin-top:0; }
.todo { font-family: monospace; color: red; }
.done { font-family: monospace; color: green; }
.priority { font-family: monospace; color: orange; }
.tag { background-color: #eee; font-family: monospace;
padding: 2px; font-size: 80%; font-weight: normal; }
.timestamp { color: #bebebe; }
.timestamp-kwd { color: #5f9ea0; }
.org-right { margin-left: auto; margin-right: 0px; text-align: right; }
.org-left { margin-left: 0px; margin-right: auto; text-align: left; }
.org-center { margin-left: auto; margin-right: auto; text-align: center; }
.underline { text-decoration: underline; }
#postamble p, #preamble p { font-size: 90%; margin: .2em; }
p.verse { margin-left: 3%; }
pre {
border: 1px solid #ccc;
box-shadow: 3px 3px 3px #eee;
padding: 8pt;
font-family: monospace;
overflow: auto;
margin: 1.2em;
}
pre.src {
position: relative;
overflow: visible;
padding-top: 1.2em;
}
pre.src:before {
display: none;
position: absolute;
background-color: white;
top: -10px;
right: 10px;
padding: 3px;
border: 1px solid black;
}
pre.src:hover:before { display: inline;}
/* Languages per Org manual */
pre.src-asymptote:before { content: 'Asymptote'; }
pre.src-awk:before { content: 'Awk'; }
pre.src-C:before { content: 'C'; }
/* pre.src-C++ doesn't work in CSS */
pre.src-clojure:before { content: 'Clojure'; }
pre.src-css:before { content: 'CSS'; }
pre.src-D:before { content: 'D'; }
pre.src-ditaa:before { content: 'ditaa'; }
pre.src-dot:before { content: 'Graphviz'; }
pre.src-calc:before { content: 'Emacs Calc'; }
pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
pre.src-fortran:before { content: 'Fortran'; }
pre.src-gnuplot:before { content: 'gnuplot'; }
pre.src-haskell:before { content: 'Haskell'; }
pre.src-hledger:before { content: 'hledger'; }
pre.src-java:before { content: 'Java'; }
pre.src-js:before { content: 'Javascript'; }
pre.src-latex:before { content: 'LaTeX'; }
pre.src-ledger:before { content: 'Ledger'; }
pre.src-lisp:before { content: 'Lisp'; }
pre.src-lilypond:before { content: 'Lilypond'; }
pre.src-lua:before { content: 'Lua'; }
pre.src-matlab:before { content: 'MATLAB'; }
pre.src-mscgen:before { content: 'Mscgen'; }
pre.src-ocaml:before { content: 'Objective Caml'; }
pre.src-octave:before { content: 'Octave'; }
pre.src-org:before { content: 'Org mode'; }
pre.src-oz:before { content: 'OZ'; }
pre.src-plantuml:before { content: 'Plantuml'; }
pre.src-processing:before { content: 'Processing.js'; }
pre.src-python:before { content: 'Python'; }
pre.src-R:before { content: 'R'; }
pre.src-ruby:before { content: 'Ruby'; }
pre.src-sass:before { content: 'Sass'; }
pre.src-scheme:before { content: 'Scheme'; }
pre.src-screen:before { content: 'Gnu Screen'; }
pre.src-sed:before { content: 'Sed'; }
pre.src-sh:before { content: 'shell'; }
pre.src-sql:before { content: 'SQL'; }
pre.src-sqlite:before { content: 'SQLite'; }
/* additional languages in org.el's org-babel-load-languages alist */
pre.src-forth:before { content: 'Forth'; }
pre.src-io:before { content: 'IO'; }
pre.src-J:before { content: 'J'; }
pre.src-makefile:before { content: 'Makefile'; }
pre.src-maxima:before { content: 'Maxima'; }
pre.src-perl:before { content: 'Perl'; }
pre.src-picolisp:before { content: 'Pico Lisp'; }
pre.src-scala:before { content: 'Scala'; }
pre.src-shell:before { content: 'Shell Script'; }
pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
/* additional language identifiers per "defun org-babel-execute"
in ob-*.el */
pre.src-cpp:before { content: 'C++'; }
pre.src-abc:before { content: 'ABC'; }
pre.src-coq:before { content: 'Coq'; }
pre.src-groovy:before { content: 'Groovy'; }
/* additional language identifiers from org-babel-shell-names in
ob-shell.el: ob-shell is the only babel language using a lambda to put
the execution function name together. */
pre.src-bash:before { content: 'bash'; }
pre.src-csh:before { content: 'csh'; }
pre.src-ash:before { content: 'ash'; }
pre.src-dash:before { content: 'dash'; }
pre.src-ksh:before { content: 'ksh'; }
pre.src-mksh:before { content: 'mksh'; }
pre.src-posh:before { content: 'posh'; }
/* Additional Emacs modes also supported by the LaTeX listings package */
pre.src-ada:before { content: 'Ada'; }
pre.src-asm:before { content: 'Assembler'; }
pre.src-caml:before { content: 'Caml'; }
pre.src-delphi:before { content: 'Delphi'; }
pre.src-html:before { content: 'HTML'; }
pre.src-idl:before { content: 'IDL'; }
pre.src-mercury:before { content: 'Mercury'; }
pre.src-metapost:before { content: 'MetaPost'; }
pre.src-modula-2:before { content: 'Modula-2'; }
pre.src-pascal:before { content: 'Pascal'; }
pre.src-ps:before { content: 'PostScript'; }
pre.src-prolog:before { content: 'Prolog'; }
pre.src-simula:before { content: 'Simula'; }
pre.src-tcl:before { content: 'tcl'; }
pre.src-tex:before { content: 'TeX'; }
pre.src-plain-tex:before { content: 'Plain TeX'; }
pre.src-verilog:before { content: 'Verilog'; }
pre.src-vhdl:before { content: 'VHDL'; }
pre.src-xml:before { content: 'XML'; }
pre.src-nxml:before { content: 'XML'; }
/* add a generic configuration mode; LaTeX export needs an additional
(add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
pre.src-conf:before { content: 'Configuration File'; }
table { border-collapse:collapse; }
caption.t-above { caption-side: top; }
caption.t-bottom { caption-side: bottom; }
td, th { vertical-align:top; }
th.org-right { text-align: center; }
th.org-left { text-align: center; }
th.org-center { text-align: center; }
td.org-right { text-align: right; }
td.org-left { text-align: left; }
td.org-center { text-align: center; }
dt { font-weight: bold; }
.footpara { display: inline; }
.footdef { margin-bottom: 1em; }
.figure { padding: 1em; }
.figure p { text-align: center; }
.equation-container {
display: table;
text-align: center;
width: 100%;
}
.equation {
vertical-align: middle;
}
.equation-label {
display: table-cell;
text-align: right;
vertical-align: middle;
}
.inlinetask {
padding: 10px;
border: 2px solid gray;
margin: 10px;
background: #ffffcc;
}
#org-div-home-and-up
{ text-align: right; font-size: 70%; white-space: nowrap; }
textarea { overflow-x: auto; }
.linenr { font-size: smaller }
.code-highlighted { background-color: #ffff00; }
.org-info-js_info-navigation { border-style: none; }
#org-info-js_console-label
{ font-size: 10px; font-weight: bold; white-space: nowrap; }
.org-info-js_search-highlight
{ background-color: #ffff00; color: #000000; font-weight: bold; }
.org-svg { width: 90%; }
/*]]>*/-->
</style>
<link rel="stylesheet" title="Standard" href="trexio.css" type="text/css" />
<script type="text/javascript" src="org-info.js">
/**
*
* @source: org-info.js
*
* @licstart The following is the entire license notice for the
* JavaScript code in org-info.js.
*
* Copyright (C) 2012-2020 Free Software Foundation, Inc.
*
*
* The JavaScript code in this tag is free software: you can
* redistribute it and/or modify it under the terms of the GNU
* General Public License (GNU GPL) as published by the Free Software
* Foundation, either version 3 of the License, or (at your option)
* any later version. The code is distributed WITHOUT ANY WARRANTY;
* without even the implied warranty of MERCHANTABILITY or FITNESS
* FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
*
* As additional permission under GNU GPL version 3 section 7, you
* may distribute non-source (e.g., minimized or compacted) forms of
* that code without the copy of the GNU GPL normally required by
* section 4, provided you include this license notice and a URL
* through which recipients can access the Corresponding Source.
*
* @licend The above is the entire license notice
* for the JavaScript code in org-info.js.
*
*/
</script>
<script type="text/javascript">
/*
@licstart The following is the entire license notice for the
JavaScript code in this tag.
Copyright (C) 2012-2020 Free Software Foundation, Inc.
The JavaScript code in this tag is free software: you can
redistribute it and/or modify it under the terms of the GNU
General Public License (GNU GPL) as published by the Free Software
Foundation, either version 3 of the License, or (at your option)
any later version. The code is distributed WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
As additional permission under GNU GPL version 3 section 7, you
may distribute non-source (e.g., minimized or compacted) forms of
that code without the copy of the GNU GPL normally required by
section 4, provided you include this license notice and a URL
through which recipients can access the Corresponding Source.
@licend The above is the entire license notice
for the JavaScript code in this tag.
*/
<!--/*--><![CDATA[/*><!--*/
org_html_manager.set("TOC_DEPTH", "4");
org_html_manager.set("LINK_HOME", "index.html");
org_html_manager.set("LINK_UP", "");
org_html_manager.set("LOCAL_TOC", "1");
org_html_manager.set("VIEW_BUTTONS", "0");
org_html_manager.set("MOUSE_HINT", "underline");
org_html_manager.set("FIXED_TOC", "0");
org_html_manager.set("TOC", "0");
org_html_manager.set("VIEW", "info");
org_html_manager.setup(); // activate after the parameters are set
/*]]>*///-->
</script>
<script type="text/javascript">
/*
@licstart The following is the entire license notice for the
JavaScript code in this tag.
Copyright (C) 2012-2020 Free Software Foundation, Inc.
The JavaScript code in this tag is free software: you can
redistribute it and/or modify it under the terms of the GNU
General Public License (GNU GPL) as published by the Free Software
Foundation, either version 3 of the License, or (at your option)
any later version. The code is distributed WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
As additional permission under GNU GPL version 3 section 7, you
may distribute non-source (e.g., minimized or compacted) forms of
that code without the copy of the GNU GPL normally required by
section 4, provided you include this license notice and a URL
through which recipients can access the Corresponding Source.
@licend The above is the entire license notice
for the JavaScript code in this tag.
*/
<!--/*--><![CDATA[/*><!--*/
function CodeHighlightOn(elem, id)
{
var target = document.getElementById(id);
if(null != target) {
elem.cacheClassElem = elem.className;
elem.cacheClassTarget = target.className;
target.className = "code-highlighted";
elem.className = "code-highlighted";
}
}
function CodeHighlightOff(elem, id)
{
var target = document.getElementById(id);
if(elem.cacheClassElem)
elem.className = elem.cacheClassElem;
if(elem.cacheClassTarget)
target.className = elem.cacheClassTarget;
}
/*]]>*///-->
</script>
</head>
<body>
<div id="org-div-home-and-up">
<a accesskey="h" href=""> UP </a>
|
<a accesskey="H" href="index.html"> HOME </a>
</div><div id="content">
<h1 class="title">TREXIO source code documentation</h1>
<hr />
<script async src="https://cse.google.com/cse.js?cx=a67f8ab65a66f97f2"></script>
<div class="gcse-search"></div>
<hr />
<p>
TREXIO is an open-source file format and library developed for the storage and
manipulation of data produced by quantum chemistry calculations. It was
designed with the goal of providing a reliable and efficient method of storing
and exchanging wave function parameters and matrix elements.
</p>
<p>
The library consists of a front-end implemented in the C programming language
and two different back-ends: a text back-end and a binary back-end utilizing
the HDF5 library enabling fast read and write speeds. It is compatible with a
variety of platforms and has interfaces for Fortran, Python, and OCaml.
</p>
<p>
If you use TREXIO, please cite this article published in the <a href="https://doi.org/10.1063/5.0148161">Journal of Chemical Physics</a>:
</p>
<div class="org-src-container">
<pre class="src src-latex">@article{trexio_2023,
author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Micha{<span style="color: #a020f0;">\l</span>} and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josu{<span style="color: #a020f0;">\'</span>{e}} and Filippi, Claudia and Nakano, Kosuke and Kohul{<span style="color: #a020f0;">\'</span>{a}}k, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and R{<span style="color: #a020f0;">\'</span>{<span style="color: #a020f0;">\i</span>}}os, Pablo L{<span style="color: #a020f0;">\'</span>{o}}pez and Alavi, Ali and Scemama, Anthony},
title = {{TREXIO: A file format and library for quantum chemistry}},
journal = {J. Chem. Phys.},
volume = {158},
number = {17},
year = {2023},
month = may,
issn = {0021-9606},
publisher = {AIP Publishing},
doi = {10.1063/5.0148161}
}
</pre>
</div>
<p>
If you don't have access to the journal, you can access the manuscript on
<a href="https://doi.org/10.48550/arXiv.2302.14793">arXiv:2302.14793</a>.
</p>
<hr />
<table style="width:100%">
<tr><td style="width:50%">
<ul class="org-ul">
<li><a href="./intro.html">Motivation</a></li>
<li><a href="./lib.html">The TREXIO library</a></li>
<li><a href="./trex.html">Data stored with TREXIO</a></li>
<li><a href="./tutorial_benzene.html">Tutorial</a></li>
<li><a href="./examples.html">Examples</a></li>
<li><a href="./templator_front.html">Front end API</a></li>
<li><a href="./templator_hdf5.html">HDF5 back end</a></li>
<li><a href="./templator_text.html">TEXT back end</a></li>
</ul>
</td>
<td>
<img src="trexio.png" alt="T-Rex talking about chemistry"
align="right" width="300"/>
</td></tr>
</table>
<hr />
<p>
The source code of the library is available at
<a href="https://github.com/trex-coe/trexio">https://github.com/trex-coe/trexio</a>
and bug reports should be submitted at
<a href="https://github.com/trex-coe/trexio/issues">https://github.com/trex-coe/trexio/issues</a>.
</p>
<p>
The TREXIO library is licensed under the open-source 3-clause BSD license.
</p>
<hr />
<p>
<img src="https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg" alt="euflag.jpg" /> <a href="https://trex-coe.eu">TREX: Targeting Real Chemical Accuracy at the Exascale</a> project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.
</p>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-13 Wed 13:26</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>