Skip to content

Commit 31289fb

Browse files
committed
update tglf DEBYE and add ref
1 parent 4487605 commit 31289fb

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

50 files changed

+844
-1091
lines changed

docs/.buildinfo

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: 556eb8091613b199f169c4c376f2cb96
3+
config: ffa9270b90cdd9fb560826aca3bd95a4
44
tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/README.html

Lines changed: 173 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,173 @@
1+
<!DOCTYPE html>
2+
<html class="writer-html5" lang="en" >
3+
<head>
4+
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
5+
6+
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
7+
<title>Using GACODE &mdash; GACODE</title>
8+
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
9+
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
10+
<link rel="stylesheet" href="_static/contentui.css" type="text/css" />
11+
<!--[if lt IE 9]>
12+
<script src="_static/js/html5shiv.min.js"></script>
13+
<![endif]-->
14+
15+
<script src="_static/documentation_options.js?v=5929fcd5"></script>
16+
<script src="_static/doctools.js?v=888ff710"></script>
17+
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
18+
<script src="_static/contentui.js"></script>
19+
<script src="_static/js/theme.js"></script>
20+
<link rel="index" title="Index" href="genindex.html" />
21+
<link rel="search" title="Search" href="search.html" />
22+
<link rel="next" title="Prebuilt Environments" href="setup.html" />
23+
<link rel="prev" title="The General Atomics GACODE Suite" href="index.html" />
24+
</head>
25+
26+
<body class="wy-body-for-nav">
27+
<div class="wy-grid-for-nav">
28+
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
29+
<div class="wy-side-scroll">
30+
<div class="wy-side-nav-search" >
31+
<a href="index.html" class="icon icon-home"> GACODE
32+
</a>
33+
<div role="search">
34+
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
35+
<input type="text" name="q" placeholder="Search docs" />
36+
<input type="hidden" name="check_keywords" value="yes" />
37+
<input type="hidden" name="area" value="default" />
38+
</form>
39+
</div>
40+
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
41+
<p class="caption" role="heading"><span class="caption-text">Software</span></p>
42+
<ul class="current">
43+
<li class="toctree-l1 current"><a class="current reference internal" href="#">Using GACODE</a><ul>
44+
<li class="toctree-l2"><a class="reference internal" href="#source-code-and-documentation">Source code and documentation</a></li>
45+
</ul>
46+
</li>
47+
<li class="toctree-l1"><a class="reference internal" href="setup.html">Prebuilt Environments</a></li>
48+
<li class="toctree-l1"><a class="reference internal" href="build.html">Build on your laptop</a></li>
49+
<li class="toctree-l1"><a class="reference internal" href="zreferences.html">References</a></li>
50+
</ul>
51+
<p class="caption" role="heading"><span class="caption-text">Codes</span></p>
52+
<ul>
53+
<li class="toctree-l1"><a class="reference internal" href="neo.html">NEO</a></li>
54+
<li class="toctree-l1"><a class="reference internal" href="tgyro.html">TGYRO</a></li>
55+
<li class="toctree-l1"><a class="reference internal" href="cgyro.html">CGYRO</a></li>
56+
<li class="toctree-l1"><a class="reference internal" href="gyro.html">GYRO</a></li>
57+
<li class="toctree-l1"><a class="reference internal" href="tglf.html">TGLF</a></li>
58+
<li class="toctree-l1"><a class="reference internal" href="prgen.html">profiles_gen</a></li>
59+
</ul>
60+
<p class="caption" role="heading"><span class="caption-text">Physics</span></p>
61+
<ul>
62+
<li class="toctree-l1"><a class="reference internal" href="geometry.html">FLUX-SURFACE GEOMETRY</a></li>
63+
<li class="toctree-l1"><a class="reference internal" href="rotation.html">PLASMA ROTATION THEORY</a></li>
64+
<li class="toctree-l1"><a class="reference internal" href="input_gacode.html">input.gacode</a></li>
65+
<li class="toctree-l1"><a class="reference internal" href="misc.html">Miscellaneous</a></li>
66+
</ul>
67+
68+
</div>
69+
</div>
70+
</nav>
71+
72+
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
73+
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
74+
<a href="index.html">GACODE</a>
75+
</nav>
76+
77+
<div class="wy-nav-content">
78+
<div class="rst-content">
79+
<div role="navigation" aria-label="Page navigation">
80+
<ul class="wy-breadcrumbs">
81+
<li><a href="index.html" class="icon icon-home"></a></li>
82+
<li class="breadcrumb-item active">Using GACODE</li>
83+
<li class="wy-breadcrumbs-aside">
84+
<a href="_sources/README.rst.txt" rel="nofollow"> View page source</a>
85+
</li>
86+
</ul>
87+
<hr/>
88+
</div>
89+
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
90+
<div itemprop="articleBody">
91+
92+
<section id="using-gacode">
93+
<h1>Using GACODE<a class="headerlink" href="#using-gacode" title="Link to this heading"></a></h1>
94+
<p>GACODE is free software released under the Apache 2.0 license. The developers of GACODE recommend the following <strong>best practices</strong></p>
95+
<ol class="arabic simple">
96+
<li><p>Compile/use the Software source code AS IS for publication purposes. You are welcome and encouraged to request changes through the <a class="reference external" href="https://github.com/gafusion/gacode/issues">github issues system</a>, to make code modifications for testing purposes, or to issue pull requests</p></li>
97+
<li><p>In published results or presentations, include the code name(s) and appropriate references in the table below</p></li>
98+
</ol>
99+
<table class="docutils align-default" id="id1">
100+
<caption><span class="caption-text"><strong>Appropriate References</strong></span><a class="headerlink" href="#id1" title="Link to this table"></a></caption>
101+
<colgroup>
102+
<col style="width: 27.3%" />
103+
<col style="width: 36.4%" />
104+
<col style="width: 36.4%" />
105+
</colgroup>
106+
<thead>
107+
<tr class="row-odd"><th class="head"><p>Physics code</p></th>
108+
<th class="head"><p>Topical Area</p></th>
109+
<th class="head"><p>Suitable citation</p></th>
110+
</tr>
111+
</thead>
112+
<tbody>
113+
<tr class="row-even"><td><p>CGYRO</p></td>
114+
<td><p>gyrokinetic simulation</p></td>
115+
<td><p><a class="reference external" href="https://doi.org/10.1016/j.jcp.2016.07.039">JCP2016</a></p></td>
116+
</tr>
117+
<tr class="row-odd"><td><p>GYRO</p></td>
118+
<td><p>gyrokinetic simulation</p></td>
119+
<td><p><a class="reference external" href="https://doi.org/10.1016/S0021-9991(03)00079-2">JCP2003</a></p></td>
120+
</tr>
121+
<tr class="row-even"><td><p>NEO</p></td>
122+
<td><p>neoclassical simulation</p></td>
123+
<td><p><a class="reference external" href="https://doi.org/10.1088/0741-3335/50/9/095010">PPCF2008</a> | <a class="reference external" href="https://doi.org/10.1088/0741-3335/54/1/015015">PPCF2012</a></p></td>
124+
</tr>
125+
<tr class="row-odd"><td><p>TGLF</p></td>
126+
<td><p>transport model</p></td>
127+
<td><p><a class="reference external" href="https://doi.org/10.1063/1.2436852">POP2007</a> | <a class="reference external" href="https://doi.org/10.1063/1.3505308">POP2010</a></p></td>
128+
</tr>
129+
<tr class="row-even"><td><p>TGYRO</p></td>
130+
<td><p>profile evolution</p></td>
131+
<td><p><a class="reference external" href="https://doi.org/10.1063/1.3167820">POP2009</a></p></td>
132+
</tr>
133+
</tbody>
134+
</table>
135+
<section id="source-code-and-documentation">
136+
<h2>Source code and documentation<a class="headerlink" href="#source-code-and-documentation" title="Link to this heading"></a></h2>
137+
<p>Source code is found in the <a class="reference external" href="https://github.com/gafusion">gacode repository</a>.
138+
For technical documentation, please refer to the <a class="reference external" href="https://gacode.io">GACODE website</a>.</p>
139+
</section>
140+
</section>
141+
142+
143+
</div>
144+
</div>
145+
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
146+
<a href="index.html" class="btn btn-neutral float-left" title="The General Atomics GACODE Suite" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
147+
<a href="setup.html" class="btn btn-neutral float-right" title="Prebuilt Environments" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
148+
</div>
149+
150+
<hr/>
151+
152+
<div role="contentinfo">
153+
<p>&#169; Copyright 2010-2025.</p>
154+
</div>
155+
156+
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
157+
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
158+
provided by <a href="https://readthedocs.org">Read the Docs</a>.
159+
160+
161+
</footer>
162+
</div>
163+
</div>
164+
</section>
165+
</div>
166+
<script>
167+
jQuery(function () {
168+
SphinxRtdTheme.Navigation.enable(true);
169+
});
170+
</script>
171+
172+
</body>
173+
</html>

docs/build.html

Lines changed: 10 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,19 @@
11
<!DOCTYPE html>
2-
<html class="writer-html5" lang="en" data-content_root="./">
2+
<html class="writer-html5" lang="en" >
33
<head>
44
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
55

66
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
77
<title>Build on your laptop &mdash; GACODE</title>
8-
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
9-
<link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
10-
<link rel="stylesheet" type="text/css" href="_static/contentui.css" />
11-
12-
13-
<link rel="shortcut icon" href="_static/favicon.ico"/>
8+
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
9+
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
10+
<link rel="stylesheet" href="_static/contentui.css" type="text/css" />
1411
<!--[if lt IE 9]>
1512
<script src="_static/js/html5shiv.min.js"></script>
1613
<![endif]-->
1714

18-
<script src="_static/jquery.js?v=5d32c60e"></script>
19-
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
2015
<script src="_static/documentation_options.js?v=5929fcd5"></script>
21-
<script src="_static/doctools.js?v=9a2dae69"></script>
16+
<script src="_static/doctools.js?v=888ff710"></script>
2217
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
2318
<script src="_static/contentui.js"></script>
2419
<script src="_static/js/theme.js"></script>
@@ -33,24 +28,19 @@
3328
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
3429
<div class="wy-side-scroll">
3530
<div class="wy-side-nav-search" >
36-
37-
38-
39-
<a href="index.html" class="icon icon-home">
40-
GACODE
31+
<a href="index.html" class="icon icon-home"> GACODE
4132
</a>
4233
<div role="search">
4334
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
44-
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
35+
<input type="text" name="q" placeholder="Search docs" />
4536
<input type="hidden" name="check_keywords" value="yes" />
4637
<input type="hidden" name="area" value="default" />
4738
</form>
4839
</div>
4940
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
5041
<p class="caption" role="heading"><span class="caption-text">Software</span></p>
5142
<ul class="current">
52-
<li class="toctree-l1"><a class="reference internal" href="license.html">GACODE License</a></li>
53-
<li class="toctree-l1"><a class="reference internal" href="download.html">Download and user agreement</a></li>
43+
<li class="toctree-l1"><a class="reference internal" href="README.html">Using GACODE</a></li>
5444
<li class="toctree-l1"><a class="reference internal" href="setup.html">Prebuilt Environments</a></li>
5545
<li class="toctree-l1 current"><a class="current reference internal" href="#">Build on your laptop</a><ul>
5646
<li class="toctree-l2"><a class="reference internal" href="#first-step">First step</a></li>
@@ -93,7 +83,7 @@
9383
<div class="rst-content">
9484
<div role="navigation" aria-label="Page navigation">
9585
<ul class="wy-breadcrumbs">
96-
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
86+
<li><a href="index.html" class="icon icon-home"></a></li>
9787
<li class="breadcrumb-item active">Build on your laptop</li>
9888
<li class="wy-breadcrumbs-aside">
9989
<a href="_sources/build.rst.txt" rel="nofollow"> View page source</a>
@@ -191,7 +181,7 @@ <h2>Building<a class="headerlink" href="#building" title="Link to this heading">
191181
<hr/>
192182

193183
<div role="contentinfo">
194-
<p>&#169; Copyright 2010-2024.</p>
184+
<p>&#169; Copyright 2010-2025.</p>
195185
</div>
196186

197187
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/build/pre_linux.html

Lines changed: 10 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,19 @@
11
<!DOCTYPE html>
2-
<html class="writer-html5" lang="en" data-content_root="../">
2+
<html class="writer-html5" lang="en" >
33
<head>
44
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
55

66
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
77
<title>Ubuntu/Mint &mdash; GACODE</title>
8-
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
9-
<link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
10-
<link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
11-
12-
13-
<link rel="shortcut icon" href="../_static/favicon.ico"/>
8+
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
9+
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
10+
<link rel="stylesheet" href="../_static/contentui.css" type="text/css" />
1411
<!--[if lt IE 9]>
1512
<script src="../_static/js/html5shiv.min.js"></script>
1613
<![endif]-->
1714

18-
<script src="../_static/jquery.js?v=5d32c60e"></script>
19-
<script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
2015
<script src="../_static/documentation_options.js?v=5929fcd5"></script>
21-
<script src="../_static/doctools.js?v=9a2dae69"></script>
16+
<script src="../_static/doctools.js?v=888ff710"></script>
2217
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
2318
<script src="../_static/contentui.js"></script>
2419
<script src="../_static/js/theme.js"></script>
@@ -31,24 +26,19 @@
3126
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
3227
<div class="wy-side-scroll">
3328
<div class="wy-side-nav-search" >
34-
35-
36-
37-
<a href="../index.html" class="icon icon-home">
38-
GACODE
29+
<a href="../index.html" class="icon icon-home"> GACODE
3930
</a>
4031
<div role="search">
4132
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
42-
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
33+
<input type="text" name="q" placeholder="Search docs" />
4334
<input type="hidden" name="check_keywords" value="yes" />
4435
<input type="hidden" name="area" value="default" />
4536
</form>
4637
</div>
4738
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
4839
<p class="caption" role="heading"><span class="caption-text">Software</span></p>
4940
<ul>
50-
<li class="toctree-l1"><a class="reference internal" href="../license.html">GACODE License</a></li>
51-
<li class="toctree-l1"><a class="reference internal" href="../download.html">Download and user agreement</a></li>
41+
<li class="toctree-l1"><a class="reference internal" href="../README.html">Using GACODE</a></li>
5242
<li class="toctree-l1"><a class="reference internal" href="../setup.html">Prebuilt Environments</a></li>
5343
<li class="toctree-l1"><a class="reference internal" href="../build.html">Build on your laptop</a></li>
5444
<li class="toctree-l1"><a class="reference internal" href="../zreferences.html">References</a></li>
@@ -83,7 +73,7 @@
8373
<div class="rst-content">
8474
<div role="navigation" aria-label="Page navigation">
8575
<ul class="wy-breadcrumbs">
86-
<li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
76+
<li><a href="../index.html" class="icon icon-home"></a></li>
8777
<li class="breadcrumb-item active">Ubuntu/Mint</li>
8878
<li class="wy-breadcrumbs-aside">
8979
<a href="../_sources/build/pre_linux.rst.txt" rel="nofollow"> View page source</a>
@@ -112,7 +102,7 @@ <h1>Ubuntu/Mint<a class="headerlink" href="#ubuntu-mint" title="Link to this hea
112102
<hr/>
113103

114104
<div role="contentinfo">
115-
<p>&#169; Copyright 2010-2024.</p>
105+
<p>&#169; Copyright 2010-2025.</p>
116106
</div>
117107

118108
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

0 commit comments

Comments
 (0)