Merge branch 'master' of github.com:gafusion/doc

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: f94905812146c9caa357d14d3bfb54ae
+config: 7ba56bb446dec0fc07ee499e22e53cb2
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build.html

@@ -16,7 +16,9 @@
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="_static/doctools.js"></script>
+        <script src="_static/sphinx_highlight.js"></script>
         <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -83,8 +85,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Build from sources</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Build from sources</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/build.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -95,16 +97,16 @@
            <div itemprop="articleBody">
 
   <section id="build-from-sources">
-<h1>Build from sources<a class="headerlink" href="#build-from-sources" title="Permalink to this headline"></a></h1>
+<h1>Build from sources<a class="headerlink" href="#build-from-sources" title="Permalink to this heading"></a></h1>
 <section id="prerequisites">
-<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline"></a></h2>
+<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this heading"></a></h2>
 <p>These instructions assume you have a complete GACODE top-level directory, which can be cloned from GitHub:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ git clone [email protected]:gafusion/gacode.git
 </pre></div>
 </div>
 </section>
 <section id="environment-variables">
-<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline"></a></h2>
+<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this heading"></a></h2>
 <p>First, you need to locate a suitable platform, or make your own platform files.  After cloning the repository, you can query the existing platforms using:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ ./gacode/shared/bin/gacode_platforms
 </pre></div>
@@ -136,7 +138,7 @@ <h2>Environment variables<a class="headerlink" href="#environment-variables" tit
 <p>Numerous templates for each of these files can be found in the specific folders, and most often there will be an existing machine files that is almost exactly what you need.  So, the strategy is to copy a similar machine file to your new one, and tweak as required.</p>
 </section>
 <section id="building">
-<h2>Building<a class="headerlink" href="#building" title="Permalink to this headline"></a></h2>
+<h2>Building<a class="headerlink" href="#building" title="Permalink to this heading"></a></h2>
 <p>To build the entire GACODE project, type:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cd $GACODE_ROOT
 $ make

docs/cgyro.html

@@ -16,7 +16,9 @@
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
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+        <script src="_static/sphinx_highlight.js"></script>
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@@ -88,8 +90,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>CGYRO</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">CGYRO</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/cgyro.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -100,17 +102,17 @@
            <div itemprop="articleBody">
 
   <section id="cgyro">
-<h1>CGYRO<a class="headerlink" href="#cgyro" title="Permalink to this headline"></a></h1>
+<h1>CGYRO<a class="headerlink" href="#cgyro" title="Permalink to this heading"></a></h1>
 <a class="reference internal image-reference" href="_images/b250.png"><img alt="b250" src="_images/b250.png" style="width: 48%;" /></a>
 <a class="reference internal image-reference" href="_images/b990.png"><img alt="b990" src="_images/b990.png" style="width: 48%;" /></a>
 <a class="reference internal image-reference" href="_images/b1020.png"><img alt="b1020" src="_images/b1020.png" style="width: 48%;" /></a>
 <a class="reference internal image-reference" href="_images/b1480.png"><img alt="b1480" src="_images/b1480.png" style="width: 48%;" /></a>
 <section id="source-code">
-<h2>Source Code<a class="headerlink" href="#source-code" title="Permalink to this headline"></a></h2>
+<h2>Source Code<a class="headerlink" href="#source-code" title="Permalink to this heading"></a></h2>
 <p><a class="reference external" href="http://github.com/gafusion/gacode">CGYRO source code</a>  is available at GitHub.</p>
 </section>
 <section id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline"></a></h2>
+<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this heading"></a></h2>
 <p><strong>The past: GYRO</strong></p>
 <p>Over the past two decades, the fusion community has focused its modeling efforts
 primarily on the core region. A popular kinetic code used for this purpose
@@ -141,19 +143,19 @@ <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this head
 calculation of collisional transport in toroidal geometry.</p>
 </section>
 <section id="data-input">
-<h2>Data input<a class="headerlink" href="#data-input" title="Permalink to this headline"></a></h2>
+<h2>Data input<a class="headerlink" href="#data-input" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p><a class="reference internal" href="cgyro/cgyro_table.html"><span class="doc">Tabular list</span></a></p></li>
 <li><p><a class="reference internal" href="cgyro/cgyro_list.html"><span class="doc">Alphabetical list</span></a></p></li>
 <li><p>Profile data: <a class="reference internal" href="input_gacode.html#input-gacode"><span class="std std-ref">input.gacode</span></a>.</p></li>
 </ul>
 </section>
 <section id="data-output-and-plotting">
-<h2>Data output and plotting<a class="headerlink" href="#data-output-and-plotting" title="Permalink to this headline"></a></h2>
+<h2>Data output and plotting<a class="headerlink" href="#data-output-and-plotting" title="Permalink to this heading"></a></h2>
 <p>Although there is a description of <a class="reference internal" href="cgyro/outputs.html"><span class="doc">output data</span></a>, it is suggested that users use the python interface to output data.</p>
 </section>
 <section id="normalization">
-<h2>Normalization<a class="headerlink" href="#normalization" title="Permalink to this headline"></a></h2>
+<h2>Normalization<a class="headerlink" href="#normalization" title="Permalink to this heading"></a></h2>
 <table class="colwidths-given docutils align-default" id="id7">
 <caption><span class="caption-text"><strong>CGYRO Normalization</strong></span><a class="headerlink" href="#id7" title="Permalink to this table"></a></caption>
 <colgroup>
@@ -196,15 +198,15 @@ <h2>Normalization<a class="headerlink" href="#normalization" title="Permalink to
 </table>
 </section>
 <section id="running-cases">
-<h2>Running Cases<a class="headerlink" href="#running-cases" title="Permalink to this headline"></a></h2>
+<h2>Running Cases<a class="headerlink" href="#running-cases" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p><a class="reference internal" href="cgyro/running_cases.html"><span class="doc">running cases</span></a></p></li>
 <li><p><a class="reference internal" href="cgyro/cgyro_cori.html"><span class="doc">cori</span></a></p></li>
 <li><p><a class="reference internal" href="cgyro/cgyro_titan.html"><span class="doc">titan</span></a></p></li>
 </ul>
 </section>
 <section id="frequently-asked-questions">
-<h2>Frequently Asked Questions<a class="headerlink" href="#frequently-asked-questions" title="Permalink to this headline"></a></h2>
+<h2>Frequently Asked Questions<a class="headerlink" href="#frequently-asked-questions" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p><a class="reference internal" href="cgyro/FAQ.html"><span class="doc">FAQ</span></a></p></li>
 </ul>

docs/cgyro/FAQ.html

@@ -16,7 +16,9 @@
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
         <script src="../_static/underscore.js"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../_static/doctools.js"></script>
+        <script src="../_static/sphinx_highlight.js"></script>
         <script src="../_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
@@ -77,8 +79,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>FAQ</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">FAQ</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/FAQ.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -89,7 +91,7 @@
            <div itemprop="articleBody">
 
   <section id="faq">
-<h1>FAQ<a class="headerlink" href="#faq" title="Permalink to this headline"></a></h1>
+<h1>FAQ<a class="headerlink" href="#faq" title="Permalink to this heading"></a></h1>
 <div class="toggle-header docutils container">
 <p>What is <span class="math notranslate nohighlight">\(k_y \rho_s\)</span> and why does CGYRO modify <span class="math notranslate nohighlight">\(\rho_s\)</span> ?</p>
 </div>

docs/cgyro/cgyro_cori.html

@@ -16,7 +16,9 @@
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
         <script src="../_static/underscore.js"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../_static/doctools.js"></script>
+        <script src="../_static/sphinx_highlight.js"></script>
         <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -76,8 +78,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Running CGYRO on NERSC Cori</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Running CGYRO on NERSC Cori</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/cgyro_cori.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -88,17 +90,17 @@
            <div itemprop="articleBody">
 
   <section id="running-cgyro-on-nersc-cori">
-<h1>Running CGYRO on NERSC Cori<a class="headerlink" href="#running-cgyro-on-nersc-cori" title="Permalink to this headline"></a></h1>
+<h1>Running CGYRO on NERSC Cori<a class="headerlink" href="#running-cgyro-on-nersc-cori" title="Permalink to this heading"></a></h1>
 <p>NERSC Cori is one of the most popular platforms on which to run CGYRO.
 This document provides some guidance on how to best make use of its resources</p>
 <section id="cori-capabilities">
-<h2>Cori capabilities<a class="headerlink" href="#cori-capabilities" title="Permalink to this headline"></a></h2>
+<h2>Cori capabilities<a class="headerlink" href="#cori-capabilities" title="Permalink to this heading"></a></h2>
 <p>The bulk of the Cori compute power comes from the approximately 10k nodes, each hosting a single Xeon Phi CPU.
 For our purposes, each Xeon Phi provides 128 execution threads.
 Each node is also equiped with 96 GB of RAM.</p>
 </section>
 <section id="cgyro-platform-file">
-<h2>CGYRO Platform File<a class="headerlink" href="#cgyro-platform-file" title="Permalink to this headline"></a></h2>
+<h2>CGYRO Platform File<a class="headerlink" href="#cgyro-platform-file" title="Permalink to this heading"></a></h2>
 <p>There are two recommended platform files available:</p>
 <ul class="simple">
 <li><p>CORI_KNL_HT2_IFORT</p></li>
@@ -112,14 +114,14 @@ <h2>CGYRO Platform File<a class="headerlink" href="#cgyro-platform-file" title="
 </div>
 </section>
 <section id="balancing-mpi-rank-vs-omp">
-<h2>Balancing MPI Rank vs OMP<a class="headerlink" href="#balancing-mpi-rank-vs-omp" title="Permalink to this headline"></a></h2>
+<h2>Balancing MPI Rank vs OMP<a class="headerlink" href="#balancing-mpi-rank-vs-omp" title="Permalink to this heading"></a></h2>
 <p>When submitting a CGYRO job, you are asked to pick an MPI rank ( <em>-n</em> ) and the number of threads/process ( <em>-nomp</em> ).
 The product will determine the amount of compute resources you will use.</p>
 <p>The recommended setting is to pick <strong>nomp</strong> to be 4.</p>
 <p>For jobs that use only a few nodes, <strong>-nomp 2</strong> may be better, and for really big runs, you may get a marginal speedup using <strong>-nomp 8</strong> or even <strong>-nomp 16</strong>.</p>
 </section>
 <section id="trading-speed-vs-efficiency">
-<h2>Trading speed vs efficiency<a class="headerlink" href="#trading-speed-vs-efficiency" title="Permalink to this headline"></a></h2>
+<h2>Trading speed vs efficiency<a class="headerlink" href="#trading-speed-vs-efficiency" title="Permalink to this heading"></a></h2>
 <p>As with most HPC codes, CGYRO will run faster when using more compute resources (i.e. compute nodes).
 However, like most HPC codes, the efficiency will generally decrease as you use more resources, too.
 I.e. you will be able to get <strong>less computation done with the same amount of allocation time</strong>.</p>