diff --git a/docs/.buildinfo b/docs/.buildinfo
index 9e19846..cb4f786 100644
--- a/docs/.buildinfo
+++ b/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
diff --git a/docs/build.html b/docs/build.html
index e0d1c77..78dcff3 100644
--- a/docs/build.html
+++ b/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 git@github.com: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
diff --git a/docs/cgyro.html b/docs/cgyro.html
index c013160..43d9769 100644
--- a/docs/cgyro.html
+++ b/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>
         <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>
@@ -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
@@ -141,7 +143,7 @@ <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>
@@ -149,11 +151,11 @@ <h2>Data input<a class="headerlink" href="#data-input" title="Permalink to this
 </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>
@@ -196,7 +198,7 @@ <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>
@@ -204,7 +206,7 @@ <h2>Running Cases<a class="headerlink" href="#running-cases" title="Permalink to
 </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>
diff --git a/docs/cgyro/FAQ.html b/docs/cgyro/FAQ.html
index 6242a55..c261d7b 100644
--- a/docs/cgyro/FAQ.html
+++ b/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>
diff --git a/docs/cgyro/cgyro_cori.html b/docs/cgyro/cgyro_cori.html
index e3308ed..17791db 100644
--- a/docs/cgyro/cgyro_cori.html
+++ b/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>
diff --git a/docs/cgyro/cgyro_list.html b/docs/cgyro/cgyro_list.html
index 34dfc45..87eed2a 100644
--- a/docs/cgyro/cgyro_list.html
+++ b/docs/cgyro/cgyro_list.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>Alphabetical list for input.cgyro</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Alphabetical list for input.cgyro</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/cgyro_list.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -89,9 +91,9 @@
            <div itemprop="articleBody">
              
   <section id="alphabetical-list-for-input-cgyro">
-<h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-list-for-input-cgyro" title="Permalink to this headline"></a></h1>
+<h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-list-for-input-cgyro" title="Permalink to this heading"></a></h1>
 <section id="amp">
-<span id="cgyro-amp"></span><h2>AMP<a class="headerlink" href="#amp" title="Permalink to this headline"></a></h2>
+<span id="cgyro-amp"></span><h2>AMP<a class="headerlink" href="#amp" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Initial amplitude of finite-<span class="math notranslate nohighlight">\(n\)</span> modes.</p>
 <p><strong>Comments</strong></p>
@@ -103,7 +105,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="amp0">
-<span id="cgyro-amp0"></span><h2>AMP0<a class="headerlink" href="#amp0" title="Permalink to this headline"></a></h2>
+<span id="cgyro-amp0"></span><h2>AMP0<a class="headerlink" href="#amp0" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Initial amplitude of <span class="math notranslate nohighlight">\(n = 0\)</span> modes.</p>
 <p><strong>Comments</strong></p>
@@ -113,7 +115,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="betae-unit">
-<span id="cgyro-betae-unit"></span><h2>BETAE_UNIT<a class="headerlink" href="#betae-unit" title="Permalink to this headline"></a></h2>
+<span id="cgyro-betae-unit"></span><h2>BETAE_UNIT<a class="headerlink" href="#betae-unit" title="Permalink to this heading"></a></h2>
 <p><strong>Comments</strong></p>
 <ul class="simple">
 <li><p>DEFAULT = 0.0</p></li>
@@ -129,7 +131,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="betae-unit-scale">
-<span id="cgyro-betae-unit-scale"></span><h2>BETAE_UNIT_SCALE<a class="headerlink" href="#betae-unit-scale" title="Permalink to this headline"></a></h2>
+<span id="cgyro-betae-unit-scale"></span><h2>BETAE_UNIT_SCALE<a class="headerlink" href="#betae-unit-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Scale factor for <a class="reference internal" href="#cgyro-betae-unit"><span class="std std-ref">BETAE_UNIT</span></a>.</p>
 <p><strong>Comments</strong></p>
@@ -139,7 +141,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="beta-star-scale">
-<span id="cgyro-beta-star-scale"></span><h2>BETA_STAR_SCALE<a class="headerlink" href="#beta-star-scale" title="Permalink to this headline"></a></h2>
+<span id="cgyro-beta-star-scale"></span><h2>BETA_STAR_SCALE<a class="headerlink" href="#beta-star-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Pressure gradient scaling factor.  Here, the pressure gradient factor is
 defined as</p>
@@ -154,7 +156,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="btccw">
-<span id="cgyro-btccw"></span><h2>BTCCW<a class="headerlink" href="#btccw" title="Permalink to this headline"></a></h2>
+<span id="cgyro-btccw"></span><h2>BTCCW<a class="headerlink" href="#btccw" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the orientation of the toroidal magnetic field <span class="math notranslate nohighlight">\(B_t\)</span> relative to the toroidal angle <span class="math notranslate nohighlight">\(\varphi\)</span>.</p>
 <p><strong>Choices</strong></p>
@@ -171,7 +173,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="box-size">
-<span id="cgyro-box-size"></span><h2>BOX_SIZE<a class="headerlink" href="#box-size" title="Permalink to this headline"></a></h2>
+<span id="cgyro-box-size"></span><h2>BOX_SIZE<a class="headerlink" href="#box-size" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Integer multiplier to determine the radial box length, <span class="math notranslate nohighlight">\(L_x\)</span>, as a multiple of the distance between reference singular surfaces, <span class="math notranslate nohighlight">\(L_0 = r/(qs)\)</span>.</p>
 <div class="math notranslate nohighlight">
@@ -185,7 +187,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-model">
-<span id="cgyro-collision-model"></span><h2>COLLISION_MODEL<a class="headerlink" href="#collision-model" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-model"></span><h2>COLLISION_MODEL<a class="headerlink" href="#collision-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Collision operator selection.</p>
 <p><strong>Choices</strong></p>
@@ -205,7 +207,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-field-model">
-<span id="cgyro-collision-field-model"></span><h2>COLLISION_FIELD_MODEL<a class="headerlink" href="#collision-field-model" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-field-model"></span><h2>COLLISION_FIELD_MODEL<a class="headerlink" href="#collision-field-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to toggle self-consistent field update during collisions.</p>
 <p><strong>Choices</strong></p>
@@ -220,7 +222,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-mom-restore">
-<span id="cgyro-collision-mom-restore"></span><h2>COLLISION_MOM_RESTORE<a class="headerlink" href="#collision-mom-restore" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-mom-restore"></span><h2>COLLISION_MOM_RESTORE<a class="headerlink" href="#collision-mom-restore" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to toggle collisional momentum conservation.</p>
 <p><strong>Choices</strong></p>
@@ -236,7 +238,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-ene-restore">
-<span id="cgyro-collision-ene-restore"></span><h2>COLLISION_ENE_RESTORE<a class="headerlink" href="#collision-ene-restore" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-ene-restore"></span><h2>COLLISION_ENE_RESTORE<a class="headerlink" href="#collision-ene-restore" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to toggle collisional energy conservation.</p>
 <p><strong>Choices</strong></p>
@@ -252,7 +254,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-ene-diffusion">
-<span id="cgyro-collision-ene-diffusion"></span><h2>COLLISION_ENE_DIFFUSION<a class="headerlink" href="#collision-ene-diffusion" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-ene-diffusion"></span><h2>COLLISION_ENE_DIFFUSION<a class="headerlink" href="#collision-ene-diffusion" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to toggle collisional energy diffusion.</p>
 <p><strong>Choices</strong></p>
@@ -268,7 +270,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-kperp">
-<span id="cgyro-collision-kperp"></span><h2>COLLISION_KPERP<a class="headerlink" href="#collision-kperp" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-kperp"></span><h2>COLLISION_KPERP<a class="headerlink" href="#collision-kperp" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to toggle <span class="math notranslate nohighlight">\(k_\perp^2\)</span> terms in collision operator.</p>
 <p><strong>Choices</strong></p>
@@ -284,7 +286,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-precision-mode">
-<span id="cgyro-collision-precision-mode"></span><h2>COLLISION_PRECISION_MODE<a class="headerlink" href="#collision-precision-mode" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-precision-mode"></span><h2>COLLISION_PRECISION_MODE<a class="headerlink" href="#collision-precision-mode" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Control the precision of the Sugama cmat constants.</p>
 <p><strong>Choices</strong></p>
@@ -301,7 +303,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="collision-full-stripes">
-<span id="cgyro-collision-full-stripes"></span><h2>COLLISION_FULL_STRIPES<a class="headerlink" href="#collision-full-stripes" title="Permalink to this headline"></a></h2>
+<span id="cgyro-collision-full-stripes"></span><h2>COLLISION_FULL_STRIPES<a class="headerlink" href="#collision-full-stripes" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of full 64-bit stripes to use close to the diagonal in low-precision mode.</p>
 <p><strong>Comments</strong></p>
@@ -312,7 +314,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="delta">
-<span id="cgyro-delta"></span><h2>DELTA<a class="headerlink" href="#delta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-delta"></span><h2>DELTA<a class="headerlink" href="#delta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Triangularity, <span class="math notranslate nohighlight">\(\delta\)</span>, of the flux surface:</p>
 <p><strong>Comments</strong></p>
@@ -324,7 +326,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="delta-t">
-<span id="cgyro-delta-t"></span><h2>DELTA_T<a class="headerlink" href="#delta-t" title="Permalink to this headline"></a></h2>
+<span id="cgyro-delta-t"></span><h2>DELTA_T<a class="headerlink" href="#delta-t" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Simulation timestep <span class="math notranslate nohighlight">\((c_s/a) \Delta t\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -335,7 +337,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="delta-t-method">
-<span id="cgyro-delta-t-method"></span><h2>DELTA_T_METHOD<a class="headerlink" href="#delta-t-method" title="Permalink to this headline"></a></h2>
+<span id="cgyro-delta-t-method"></span><h2>DELTA_T_METHOD<a class="headerlink" href="#delta-t-method" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Control for adaptive or fixed time-stepping.</p>
 <p><strong>Choices</strong></p>
@@ -353,7 +355,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="dens">
-<span id="cgyro-dens"></span><h2>DENS_*<a class="headerlink" href="#dens" title="Permalink to this headline"></a></h2>
+<span id="cgyro-dens"></span><h2>DENS_*<a class="headerlink" href="#dens" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale density.  First species density is DENS_1, and so on.</p>
 <div class="math notranslate nohighlight">
@@ -370,7 +372,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="dlnndr">
-<span id="cgyro-dlnndr"></span><h2>DLNNDR_*<a class="headerlink" href="#dlnndr" title="Permalink to this headline"></a></h2>
+<span id="cgyro-dlnndr"></span><h2>DLNNDR_*<a class="headerlink" href="#dlnndr" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale density gradient scale length:</p>
 <div class="math notranslate nohighlight">
@@ -387,7 +389,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="dlntdr">
-<span id="cgyro-dlntdr"></span><h2>DLNTDR_*<a class="headerlink" href="#dlntdr" title="Permalink to this headline"></a></h2>
+<span id="cgyro-dlntdr"></span><h2>DLNTDR_*<a class="headerlink" href="#dlntdr" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale temperature gradient scale length:</p>
 <div class="math notranslate nohighlight">
@@ -404,7 +406,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="dzmag">
-<span id="cgyro-dzmag"></span><h2>DZMAG<a class="headerlink" href="#dzmag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-dzmag"></span><h2>DZMAG<a class="headerlink" href="#dzmag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Rate of change of plasma elevation:</p>
 <div class="math notranslate nohighlight">
@@ -412,7 +414,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="e-max">
-<span id="cgyro-e-max"></span><h2>E_MAX<a class="headerlink" href="#e-max" title="Permalink to this headline"></a></h2>
+<span id="cgyro-e-max"></span><h2>E_MAX<a class="headerlink" href="#e-max" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum value of (pseudospectral) dimensionless energy, <span class="math notranslate nohighlight">\(\varepsilon_\mathrm{max}\)</span></p>
 <p><strong>Comments</strong></p>
@@ -423,7 +425,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="error-tol">
-<span id="cgyro-error-tol"></span><h2>ERROR_TOL<a class="headerlink" href="#error-tol" title="Permalink to this headline"></a></h2>
+<span id="cgyro-error-tol"></span><h2>ERROR_TOL<a class="headerlink" href="#error-tol" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Error tolerance for adaptive time-stepping.</p>
 <p><strong>Comments</strong></p>
@@ -434,7 +436,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="equilibrium-model">
-<span id="cgyro-equilibrium-model"></span><h2>EQUILIBRIUM_MODEL<a class="headerlink" href="#equilibrium-model" title="Permalink to this headline"></a></h2>
+<span id="cgyro-equilibrium-model"></span><h2>EQUILIBRIUM_MODEL<a class="headerlink" href="#equilibrium-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flux-surface shape specification parameter.</p>
 <p><strong>Choices</strong></p>
@@ -451,7 +453,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="field-print-flag">
-<span id="cgyro-field-print-flag"></span><h2>FIELD_PRINT_FLAG<a class="headerlink" href="#field-print-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-field-print-flag"></span><h2>FIELD_PRINT_FLAG<a class="headerlink" href="#field-print-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Toggle printing of <span class="math notranslate nohighlight">\(\delta A_\parallel(k_x^0,k_y,t)\)</span> and <span class="math notranslate nohighlight">\(\delta B_\parallel(k_x^0,k_y,t)\)</span> .</p>
 <p><strong>Comments</strong></p>
@@ -463,7 +465,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="freq-tol">
-<span id="cgyro-freq-tol"></span><h2>FREQ_TOL<a class="headerlink" href="#freq-tol" title="Permalink to this headline"></a></h2>
+<span id="cgyro-freq-tol"></span><h2>FREQ_TOL<a class="headerlink" href="#freq-tol" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Eigenvalue convergence tolerance for linear simulations.</p>
 <p><strong>Comments</strong></p>
@@ -473,7 +475,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="gamma-e">
-<span id="cgyro-gamma-e"></span><h2>GAMMA_E<a class="headerlink" href="#gamma-e" title="Permalink to this headline"></a></h2>
+<span id="cgyro-gamma-e"></span><h2>GAMMA_E<a class="headerlink" href="#gamma-e" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shearing rate <span class="math notranslate nohighlight">\(\displaystyle \frac{a}{c_s} \gamma_E\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -484,7 +486,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="gamma-e-scale">
-<span id="cgyro-gamma-e-scale"></span><h2>GAMMA_E_SCALE<a class="headerlink" href="#gamma-e-scale" title="Permalink to this headline"></a></h2>
+<span id="cgyro-gamma-e-scale"></span><h2>GAMMA_E_SCALE<a class="headerlink" href="#gamma-e-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Scaling factor applied to experimental value of <span class="math notranslate nohighlight">\(\gamma_E\)</span> .</p>
 <p><strong>Comments</strong></p>
@@ -495,7 +497,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="gamma-p">
-<span id="cgyro-gamma-p"></span><h2>GAMMA_P<a class="headerlink" href="#gamma-p" title="Permalink to this headline"></a></h2>
+<span id="cgyro-gamma-p"></span><h2>GAMMA_P<a class="headerlink" href="#gamma-p" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized rotation shearing rate <span class="math notranslate nohighlight">\(\displaystyle \frac{a}{c_s} \gamma_p\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -506,7 +508,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="gamma-p-scale">
-<span id="cgyro-gamma-p-scale"></span><h2>GAMMA_P_SCALE<a class="headerlink" href="#gamma-p-scale" title="Permalink to this headline"></a></h2>
+<span id="cgyro-gamma-p-scale"></span><h2>GAMMA_P_SCALE<a class="headerlink" href="#gamma-p-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Scaling factor applied to experimental value of <span class="math notranslate nohighlight">\(\gamma_p\)</span> .</p>
 <p><strong>Comments</strong></p>
@@ -517,7 +519,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="gpu-bigmem-flag">
-<span id="cgyro-gpu-bigmem-flag"></span><h2>GPU_BIGMEM_FLAG<a class="headerlink" href="#gpu-bigmem-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-gpu-bigmem-flag"></span><h2>GPU_BIGMEM_FLAG<a class="headerlink" href="#gpu-bigmem-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Enable (or disable) memory intensive GPU offload.</p>
 <p><strong>Choices</strong></p>
@@ -534,7 +536,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="h-print-flag">
-<span id="cgyro-h-print-flag"></span><h2>H_PRINT_FLAG<a class="headerlink" href="#h-print-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-h-print-flag"></span><h2>H_PRINT_FLAG<a class="headerlink" href="#h-print-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Toggle printing of distribution for single-mode runs.</p>
 <p><strong>Comments</strong></p>
@@ -544,7 +546,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="ipccw">
-<span id="cgyro-ipccw"></span><h2>IPCCW<a class="headerlink" href="#ipccw" title="Permalink to this headline"></a></h2>
+<span id="cgyro-ipccw"></span><h2>IPCCW<a class="headerlink" href="#ipccw" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the orientation of the plasma current (and thus the poloidal magnetic field <span class="math notranslate nohighlight">\(B_p\)</span>) relative to the toroidal angle <span class="math notranslate nohighlight">\(\varphi\)</span>.</p>
 <p><strong>Choices</strong></p>
@@ -561,7 +563,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="kappa">
-<span id="cgyro-kappa"></span><h2>KAPPA<a class="headerlink" href="#kappa" title="Permalink to this headline"></a></h2>
+<span id="cgyro-kappa"></span><h2>KAPPA<a class="headerlink" href="#kappa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Elongation, <span class="math notranslate nohighlight">\(\kappa\)</span>, of the flux surface.</p>
 <p><strong>Comments</strong></p>
@@ -573,7 +575,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="gflux-print-flag">
-<span id="cgyro-gflux-print-flag"></span><h2>GFLUX_PRINT_FLAG<a class="headerlink" href="#gflux-print-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-gflux-print-flag"></span><h2>GFLUX_PRINT_FLAG<a class="headerlink" href="#gflux-print-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Toggle printing of global flux profiles.</p>
 <p><strong>Comments</strong></p>
@@ -584,7 +586,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="ky">
-<span id="cgyro-ky"></span><h2>KY<a class="headerlink" href="#ky" title="Permalink to this headline"></a></h2>
+<span id="cgyro-ky"></span><h2>KY<a class="headerlink" href="#ky" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Selector for value of <span class="math notranslate nohighlight">\(k_\theta \rho_s\)</span> .</p>
 <p><strong>Comments</strong></p>
@@ -596,17 +598,17 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="lambda-debye">
-<span id="cgyro-lambda-debye"></span><h2>LAMBDA_DEBYE<a class="headerlink" href="#lambda-debye" title="Permalink to this headline"></a></h2>
+<span id="cgyro-lambda-debye"></span><h2>LAMBDA_DEBYE<a class="headerlink" href="#lambda-debye" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="lambda-debye-scale">
-<span id="cgyro-lambda-debye-scale"></span><h2>LAMBDA_DEBYE_SCALE<a class="headerlink" href="#lambda-debye-scale" title="Permalink to this headline"></a></h2>
+<span id="cgyro-lambda-debye-scale"></span><h2>LAMBDA_DEBYE_SCALE<a class="headerlink" href="#lambda-debye-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="mach">
-<span id="cgyro-mach"></span><h2>MACH<a class="headerlink" href="#mach" title="Permalink to this headline"></a></h2>
+<span id="cgyro-mach"></span><h2>MACH<a class="headerlink" href="#mach" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Rotation speed (Mach number) <span class="math notranslate nohighlight">\(M\)</span></p>
 <p><strong>Comments</strong></p>
@@ -617,7 +619,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="mach-scale">
-<span id="cgyro-mach-scale"></span><h2>MACH_SCALE<a class="headerlink" href="#mach-scale" title="Permalink to this headline"></a></h2>
+<span id="cgyro-mach-scale"></span><h2>MACH_SCALE<a class="headerlink" href="#mach-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Scaling factor applied to experimental value of <span class="math notranslate nohighlight">\(M\)</span> .</p>
 <p><strong>Comments</strong></p>
@@ -628,7 +630,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="mass">
-<span id="cgyro-mass"></span><h2>MASS_*<a class="headerlink" href="#mass" title="Permalink to this headline"></a></h2>
+<span id="cgyro-mass"></span><h2>MASS_*<a class="headerlink" href="#mass" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The species mass normalized to deuterium mass: MASS_1, and so on.</p>
 <div class="math notranslate nohighlight">
@@ -648,13 +650,13 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="max-time">
-<span id="cgyro-max-time"></span><h2>MAX_TIME<a class="headerlink" href="#max-time" title="Permalink to this headline"></a></h2>
+<span id="cgyro-max-time"></span><h2>MAX_TIME<a class="headerlink" href="#max-time" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum simulation time in units of <span class="math notranslate nohighlight">\(a/c_s\)</span></p>
 <hr class="docutils" />
 </section>
 <section id="moment-print-flag">
-<span id="cgyro-moment-print-flag"></span><h2>MOMENT_PRINT_FLAG<a class="headerlink" href="#moment-print-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-moment-print-flag"></span><h2>MOMENT_PRINT_FLAG<a class="headerlink" href="#moment-print-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Toggle printing of <span class="math notranslate nohighlight">\(\delta n_a(k_x^0,k_y,t)\)</span>
 and <span class="math notranslate nohighlight">\(\delta E_a(k_x^0,k_y,t)\)</span> .</p>
@@ -665,7 +667,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="mpi-rank-order">
-<span id="cgyro-mpi-rank-order"></span><h2>MPI_RANK_ORDER<a class="headerlink" href="#mpi-rank-order" title="Permalink to this headline"></a></h2>
+<span id="cgyro-mpi-rank-order"></span><h2>MPI_RANK_ORDER<a class="headerlink" href="#mpi-rank-order" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Specify the relative ordering of MPI ranks.</p>
 <p><strong>Choices</strong></p>
@@ -681,7 +683,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="nonlinear-flag">
-<span id="cgyro-nonlinear-flag"></span><h2>NONLINEAR_FLAG<a class="headerlink" href="#nonlinear-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-nonlinear-flag"></span><h2>NONLINEAR_FLAG<a class="headerlink" href="#nonlinear-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Toggle inclusion of nonlinear terms.</p>
 <p><strong>Choices</strong></p>
@@ -696,7 +698,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-field">
-<span id="cgyro-n-field"></span><h2>N_FIELD<a class="headerlink" href="#n-field" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-field"></span><h2>N_FIELD<a class="headerlink" href="#n-field" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Selector for number of fluctuating fields</p>
 <p><strong>Choices</strong></p>
@@ -712,7 +714,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-global">
-<span id="cgyro-n-global"></span><h2>N_GLOBAL<a class="headerlink" href="#n-global" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-global"></span><h2>N_GLOBAL<a class="headerlink" href="#n-global" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Control number of global output harmonics</p>
 <p><strong>Comments</strong></p>
@@ -723,7 +725,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="nu-global">
-<span id="cgyro-nu-global"></span><h2>NU_GLOBAL<a class="headerlink" href="#nu-global" title="Permalink to this headline"></a></h2>
+<span id="cgyro-nu-global"></span><h2>NU_GLOBAL<a class="headerlink" href="#nu-global" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Source rate</p>
 <p><strong>Comments</strong></p>
@@ -734,17 +736,17 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="nup-radial">
-<span id="cgyro-nup-radial"></span><h2>NUP_RADIAL<a class="headerlink" href="#nup-radial" title="Permalink to this headline"></a></h2>
+<span id="cgyro-nup-radial"></span><h2>NUP_RADIAL<a class="headerlink" href="#nup-radial" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="up-theta">
-<span id="cgyro-up-theta"></span><h2>UP_THETA<a class="headerlink" href="#up-theta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-up-theta"></span><h2>UP_THETA<a class="headerlink" href="#up-theta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="nup-theta">
-<span id="cgyro-nup-theta"></span><h2>NUP_THETA<a class="headerlink" href="#nup-theta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-nup-theta"></span><h2>NUP_THETA<a class="headerlink" href="#nup-theta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Accuracy control for the poloidal discretization scheme.</p>
 <p><strong>Choices</strong></p>
@@ -761,17 +763,17 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="up-alpha">
-<span id="cgyro-up-alpha"></span><h2>UP_ALPHA<a class="headerlink" href="#up-alpha" title="Permalink to this headline"></a></h2>
+<span id="cgyro-up-alpha"></span><h2>UP_ALPHA<a class="headerlink" href="#up-alpha" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="nup-alpha">
-<span id="cgyro-nup-alpha"></span><h2>NUP_ALPHA<a class="headerlink" href="#nup-alpha" title="Permalink to this headline"></a></h2>
+<span id="cgyro-nup-alpha"></span><h2>NUP_ALPHA<a class="headerlink" href="#nup-alpha" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="nu-ee">
-<span id="cgyro-nu-ee"></span><h2>NU_EE<a class="headerlink" href="#nu-ee" title="Permalink to this headline"></a></h2>
+<span id="cgyro-nu-ee"></span><h2>NU_EE<a class="headerlink" href="#nu-ee" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Electron-electron collision frequency <span class="math notranslate nohighlight">\(\nu_{ee}\)</span>, in units of <span class="math notranslate nohighlight">\(c_s/a\)</span>.</p>
 <div class="math notranslate nohighlight">
@@ -785,7 +787,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-radial">
-<span id="cgyro-n-radial"></span><h2>N_RADIAL<a class="headerlink" href="#n-radial" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-radial"></span><h2>N_RADIAL<a class="headerlink" href="#n-radial" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of radial wavenumbers (radial Fourier harmonics) to retain in simulation.</p>
 <p><strong>Comments</strong></p>
@@ -798,7 +800,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-theta">
-<span id="cgyro-n-theta"></span><h2>N_THETA<a class="headerlink" href="#n-theta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-theta"></span><h2>N_THETA<a class="headerlink" href="#n-theta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of poloidal gridpoints <span class="math notranslate nohighlight">\(\theta_i\)</span>.  There is a single poloidal mesh for both the distribution function and the fields (unlike GYRO).</p>
 <p><strong>Comments</strong></p>
@@ -809,7 +811,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-xi">
-<span id="cgyro-n-xi"></span><h2>N_XI<a class="headerlink" href="#n-xi" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-xi"></span><h2>N_XI<a class="headerlink" href="#n-xi" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of Legendre pseudospectral meshpoints <span class="math notranslate nohighlight">\(\xi_i\)</span> to retain in simulation.</p>
 <p><strong>Comments</strong></p>
@@ -821,7 +823,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-energy">
-<span id="cgyro-n-energy"></span><h2>N_ENERGY<a class="headerlink" href="#n-energy" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-energy"></span><h2>N_ENERGY<a class="headerlink" href="#n-energy" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of generalized-Laguerre pseudospectral meshpoints <span class="math notranslate nohighlight">\(v_i\)</span> to retain in simulation</p>
 <p><strong>Comments</strong></p>
@@ -833,7 +835,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-toroidal">
-<span id="cgyro-n-toroidal"></span><h2>N_TOROIDAL<a class="headerlink" href="#n-toroidal" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-toroidal"></span><h2>N_TOROIDAL<a class="headerlink" href="#n-toroidal" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of toroidal harmonics (binormal Fourier modes).</p>
 <p><strong>Comments</strong></p>
@@ -843,7 +845,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="n-species">
-<span id="cgyro-n-species"></span><h2>N_SPECIES<a class="headerlink" href="#n-species" title="Permalink to this headline"></a></h2>
+<span id="cgyro-n-species"></span><h2>N_SPECIES<a class="headerlink" href="#n-species" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of kinetic species (includes electrons and all ions).</p>
 <p><strong>Comments</strong></p>
@@ -853,12 +855,12 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="print-step">
-<span id="cgyro-print-step"></span><h2>PRINT_STEP<a class="headerlink" href="#print-step" title="Permalink to this headline"></a></h2>
+<span id="cgyro-print-step"></span><h2>PRINT_STEP<a class="headerlink" href="#print-step" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="profile-model">
-<span id="cgyro-profile-model"></span><h2>PROFILE_MODEL<a class="headerlink" href="#profile-model" title="Permalink to this headline"></a></h2>
+<span id="cgyro-profile-model"></span><h2>PROFILE_MODEL<a class="headerlink" href="#profile-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Selector for profile data input.</p>
 <p><strong>Choices</strong></p>
@@ -873,7 +875,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="q">
-<span id="cgyro-q"></span><h2>Q<a class="headerlink" href="#q" title="Permalink to this headline"></a></h2>
+<span id="cgyro-q"></span><h2>Q<a class="headerlink" href="#q" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Safety factor, <span class="math notranslate nohighlight">\(q\)</span>, of the flux surface.</p>
 <p><strong>Comments</strong></p>
@@ -885,7 +887,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="quasineutral-flag">
-<span id="cgyro-quasineutral-flag"></span><h2>QUASINEUTRAL_FLAG<a class="headerlink" href="#quasineutral-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-quasineutral-flag"></span><h2>QUASINEUTRAL_FLAG<a class="headerlink" href="#quasineutral-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Enforce quasineutrality when using experimental profiles.</p>
 <p><strong>Choices</strong></p>
@@ -901,10 +903,10 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="restart-step">
-<span id="cgyro-restart-step"></span><h2>RESTART_STEP<a class="headerlink" href="#restart-step" title="Permalink to this headline"></a></h2>
+<span id="cgyro-restart-step"></span><h2>RESTART_STEP<a class="headerlink" href="#restart-step" title="Permalink to this heading"></a></h2>
 </section>
 <section id="rmin">
-<span id="cgyro-rmin"></span><h2>RMIN<a class="headerlink" href="#rmin" title="Permalink to this headline"></a></h2>
+<span id="cgyro-rmin"></span><h2>RMIN<a class="headerlink" href="#rmin" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio <span class="math notranslate nohighlight">\(r/a\)</span>, where <span class="math notranslate nohighlight">\(r\)</span> is the <a class="reference internal" href="../geometry.html"><span class="doc">minor radius</span></a> and <span class="math notranslate nohighlight">\(a\)</span> is the radius of the LCFS.</p>
 <p><strong>Comments</strong></p>
@@ -914,7 +916,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="rmaj">
-<span id="cgyro-rmaj"></span><h2>RMAJ<a class="headerlink" href="#rmaj" title="Permalink to this headline"></a></h2>
+<span id="cgyro-rmaj"></span><h2>RMAJ<a class="headerlink" href="#rmaj" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio <span class="math notranslate nohighlight">\(R_0/a\)</span>, where <span class="math notranslate nohighlight">\(R_0\)</span> is the <a class="reference internal" href="../geometry.html"><span class="doc">major radius</span></a> and <span class="math notranslate nohighlight">\(a\)</span> is the radius of the LCFS.</p>
 <p><strong>Comments</strong></p>
@@ -924,7 +926,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="rotation-model">
-<span id="cgyro-rotation-model"></span><h2>ROTATION_MODEL<a class="headerlink" href="#rotation-model" title="Permalink to this headline"></a></h2>
+<span id="cgyro-rotation-model"></span><h2>ROTATION_MODEL<a class="headerlink" href="#rotation-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -938,7 +940,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="s">
-<span id="cgyro-s"></span><h2>S<a class="headerlink" href="#s" title="Permalink to this headline"></a></h2>
+<span id="cgyro-s"></span><h2>S<a class="headerlink" href="#s" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Magnetic shear, <span class="math notranslate nohighlight">\(s\)</span>, of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -952,7 +954,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shift">
-<span id="cgyro-shift"></span><h2>SHIFT<a class="headerlink" href="#shift" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shift"></span><h2>SHIFT<a class="headerlink" href="#shift" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Shafranov shift, <span class="math notranslate nohighlight">\(\Delta\)</span>, of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -966,7 +968,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-cos0">
-<span id="cgyro-shape-cos0"></span><h2>SHAPE_COS0<a class="headerlink" href="#shape-cos0" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-cos0"></span><h2>SHAPE_COS0<a class="headerlink" href="#shape-cos0" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>0th antisymmetric moment.</p>
 <ul class="simple">
@@ -975,7 +977,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos0">
-<span id="cgyro-shape-s-cos0"></span><h2>SHAPE_S_COS0<a class="headerlink" href="#shape-s-cos0" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-s-cos0"></span><h2>SHAPE_S_COS0<a class="headerlink" href="#shape-s-cos0" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>0th antisymmetric moment shear.</p>
 <ul class="simple">
@@ -984,7 +986,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-cos1">
-<span id="cgyro-shape-cos1"></span><h2>SHAPE_COS1<a class="headerlink" href="#shape-cos1" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-cos1"></span><h2>SHAPE_COS1<a class="headerlink" href="#shape-cos1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>1st antisymmetric moment.</p>
 <ul class="simple">
@@ -993,7 +995,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos1">
-<span id="cgyro-shape-s-cos1"></span><h2>SHAPE_S_COS1<a class="headerlink" href="#shape-s-cos1" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-s-cos1"></span><h2>SHAPE_S_COS1<a class="headerlink" href="#shape-s-cos1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>1th antisymmetric moment shear.</p>
 <ul class="simple">
@@ -1002,7 +1004,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-cos2">
-<span id="cgyro-shape-cos2"></span><h2>SHAPE_COS2<a class="headerlink" href="#shape-cos2" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-cos2"></span><h2>SHAPE_COS2<a class="headerlink" href="#shape-cos2" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>2nd antisymmetric moment.</p>
 <ul class="simple">
@@ -1011,7 +1013,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos2">
-<span id="cgyro-shape-s-cos2"></span><h2>SHAPE_S_COS2<a class="headerlink" href="#shape-s-cos2" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-s-cos2"></span><h2>SHAPE_S_COS2<a class="headerlink" href="#shape-s-cos2" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>2th antisymmetric moment shear.</p>
 <ul class="simple">
@@ -1020,7 +1022,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-cos3">
-<span id="cgyro-shape-cos3"></span><h2>SHAPE_COS3<a class="headerlink" href="#shape-cos3" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-cos3"></span><h2>SHAPE_COS3<a class="headerlink" href="#shape-cos3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd antisymmetric moment.</p>
 <ul class="simple">
@@ -1029,7 +1031,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos3">
-<span id="cgyro-shape-s-cos3"></span><h2>SHAPE_S_COS3<a class="headerlink" href="#shape-s-cos3" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-s-cos3"></span><h2>SHAPE_S_COS3<a class="headerlink" href="#shape-s-cos3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd antisymmetric moment.</p>
 <ul class="simple">
@@ -1038,7 +1040,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-sin3">
-<span id="cgyro-shape-sin3"></span><h2>SHAPE_SIN3<a class="headerlink" href="#shape-sin3" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-sin3"></span><h2>SHAPE_SIN3<a class="headerlink" href="#shape-sin3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd symmetric moment.</p>
 <ul class="simple">
@@ -1047,7 +1049,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="shape-s-sin3">
-<span id="cgyro-shape-s-sin3"></span><h2>SHAPE_S_SIN3<a class="headerlink" href="#shape-s-sin3" title="Permalink to this headline"></a></h2>
+<span id="cgyro-shape-s-sin3"></span><h2>SHAPE_S_SIN3<a class="headerlink" href="#shape-s-sin3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd symmetric moment shear.</p>
 <ul class="simple">
@@ -1056,12 +1058,12 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="silent-flag">
-<span id="cgyro-silent-flag"></span><h2>SILENT_FLAG<a class="headerlink" href="#silent-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-silent-flag"></span><h2>SILENT_FLAG<a class="headerlink" href="#silent-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="s-delta">
-<span id="cgyro-s-delta"></span><h2>S_DELTA<a class="headerlink" href="#s-delta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-s-delta"></span><h2>S_DELTA<a class="headerlink" href="#s-delta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the average triangularity of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -1075,7 +1077,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="s-kappa">
-<span id="cgyro-s-kappa"></span><h2>S_KAPPA<a class="headerlink" href="#s-kappa" title="Permalink to this headline"></a></h2>
+<span id="cgyro-s-kappa"></span><h2>S_KAPPA<a class="headerlink" href="#s-kappa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the elongation of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -1089,7 +1091,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="s-zeta">
-<span id="cgyro-s-zeta"></span><h2>S_ZETA<a class="headerlink" href="#s-zeta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-s-zeta"></span><h2>S_ZETA<a class="headerlink" href="#s-zeta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the average squareness of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -1102,7 +1104,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="temp">
-<span id="cgyro-temp"></span><h2>TEMP_*<a class="headerlink" href="#temp" title="Permalink to this headline"></a></h2>
+<span id="cgyro-temp"></span><h2>TEMP_*<a class="headerlink" href="#temp" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale temperature.  First species temperature is TEMP_1, and so on.</p>
 <div class="math notranslate nohighlight">
@@ -1117,7 +1119,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="theta-plot">
-<span id="cgyro-theta-plot"></span><h2>THETA_PLOT<a class="headerlink" href="#theta-plot" title="Permalink to this headline"></a></h2>
+<span id="cgyro-theta-plot"></span><h2>THETA_PLOT<a class="headerlink" href="#theta-plot" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The number of poloidal points for output of large fluctuation moment arrays.</p>
 <p><strong>Commments</strong></p>
@@ -1128,17 +1130,17 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="udsymmetry-flag">
-<span id="cgyro-udsymmetry-flag"></span><h2>UDSYMMETRY_FLAG<a class="headerlink" href="#udsymmetry-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-udsymmetry-flag"></span><h2>UDSYMMETRY_FLAG<a class="headerlink" href="#udsymmetry-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="up-radial">
-<span id="cgyro-up-radial"></span><h2>UP_RADIAL<a class="headerlink" href="#up-radial" title="Permalink to this headline"></a></h2>
+<span id="cgyro-up-radial"></span><h2>UP_RADIAL<a class="headerlink" href="#up-radial" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="upwind-single-flag">
-<span id="cgyro-upwind-single-flag"></span><h2>UPWIND_SINGLE_FLAG<a class="headerlink" href="#upwind-single-flag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-upwind-single-flag"></span><h2>UPWIND_SINGLE_FLAG<a class="headerlink" href="#upwind-single-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Control the precision of upwind communication.</p>
 <p><strong>Choices</strong></p>
@@ -1153,7 +1155,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="velocity-order">
-<span id="cgyro-velocity-order"></span><h2>VELOCITY_ORDER<a class="headerlink" href="#velocity-order" title="Permalink to this headline"></a></h2>
+<span id="cgyro-velocity-order"></span><h2>VELOCITY_ORDER<a class="headerlink" href="#velocity-order" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Specify the ordering inside the velocity space</p>
 <p><strong>Choices</strong></p>
@@ -1170,7 +1172,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="z">
-<span id="cgyro-z"></span><h2>Z_*<a class="headerlink" href="#z" title="Permalink to this headline"></a></h2>
+<span id="cgyro-z"></span><h2>Z_*<a class="headerlink" href="#z" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species charge.  First species charge is Z_1, and so on.</p>
 <p><strong>Comments</strong></p>
@@ -1187,7 +1189,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="z-eff">
-<span id="cgyro-z-eff"></span><h2>Z_EFF<a class="headerlink" href="#z-eff" title="Permalink to this headline"></a></h2>
+<span id="cgyro-z-eff"></span><h2>Z_EFF<a class="headerlink" href="#z-eff" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>User-specified value for <span class="math notranslate nohighlight">\(Z_\mathrm{eff}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -1200,7 +1202,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="z-eff-method">
-<span id="cgyro-z-eff-method"></span><h2>Z_EFF_METHOD<a class="headerlink" href="#z-eff-method" title="Permalink to this headline"></a></h2>
+<span id="cgyro-z-eff-method"></span><h2>Z_EFF_METHOD<a class="headerlink" href="#z-eff-method" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Control how <span class="math notranslate nohighlight">\(Z_\mathrm{eff}\)</span> is computed.</p>
 <p><strong>Choices</strong></p>
@@ -1216,7 +1218,7 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="zeta">
-<span id="cgyro-zeta"></span><h2>ZETA<a class="headerlink" href="#zeta" title="Permalink to this headline"></a></h2>
+<span id="cgyro-zeta"></span><h2>ZETA<a class="headerlink" href="#zeta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Squareness, <span class="math notranslate nohighlight">\(\zeta\)</span>, of the flux surface.</p>
 <p><strong>Comments</strong></p>
@@ -1228,12 +1230,12 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <hr class="docutils" />
 </section>
 <section id="zf-test-mode">
-<span id="cgyro-zf-test-mode"></span><h2>ZF_TEST_MODE<a class="headerlink" href="#zf-test-mode" title="Permalink to this headline"></a></h2>
+<span id="cgyro-zf-test-mode"></span><h2>ZF_TEST_MODE<a class="headerlink" href="#zf-test-mode" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 </section>
 <section id="zmag">
-<span id="cgyro-zmag"></span><h2>ZMAG<a class="headerlink" href="#zmag" title="Permalink to this headline"></a></h2>
+<span id="cgyro-zmag"></span><h2>ZMAG<a class="headerlink" href="#zmag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <hr class="docutils" />
 <p>Return to <a class="reference internal" href="cgyro_table.html"><span class="doc">table of inputs</span></a></p>
diff --git a/docs/cgyro/cgyro_table.html b/docs/cgyro/cgyro_table.html
index 48df5d6..0e2fcb2 100644
--- a/docs/cgyro/cgyro_table.html
+++ b/docs/cgyro/cgyro_table.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>Tabular list for input.cgyro</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Tabular list for input.cgyro</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/cgyro_table.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -89,7 +91,7 @@
            <div itemprop="articleBody">
              
   <section id="tabular-list-for-input-cgyro">
-<h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-input-cgyro" title="Permalink to this headline"></a></h1>
+<h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-input-cgyro" title="Permalink to this heading"></a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="#tab-shape"><span class="std std-ref">Plasma shape/geometry</span></a></p></li>
 <li><p><a class="reference internal" href="#tab-advshape"><span class="std std-ref">Advanced shape parameters</span></a></p></li>
diff --git a/docs/cgyro/cgyro_titan.html b/docs/cgyro/cgyro_titan.html
index 6e94193..3666d88 100644
--- a/docs/cgyro/cgyro_titan.html
+++ b/docs/cgyro/cgyro_titan.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 OLCF Titan (deprecated)</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Running CGYRO on OLCF Titan (deprecated)</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/cgyro_titan.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -88,17 +90,17 @@
            <div itemprop="articleBody">
              
   <section id="running-cgyro-on-olcf-titan-deprecated">
-<h1>Running CGYRO on OLCF Titan (deprecated)<a class="headerlink" href="#running-cgyro-on-olcf-titan-deprecated" title="Permalink to this headline"></a></h1>
+<h1>Running CGYRO on OLCF Titan (deprecated)<a class="headerlink" href="#running-cgyro-on-olcf-titan-deprecated" title="Permalink to this heading"></a></h1>
 <p>ORNL Titan is one of the most popular GPU platforms on which to run CGYRO.
 This document provides some guidance on how to best make use of its resources</p>
 <section id="titan-capabilities">
-<h2>Titan capabilities<a class="headerlink" href="#titan-capabilities" title="Permalink to this headline"></a></h2>
+<h2>Titan capabilities<a class="headerlink" href="#titan-capabilities" title="Permalink to this heading"></a></h2>
 <p>The bulk of the Titan compute power comes from the approximately 18k nodes, each hosting a single AMD Opteron CPU and a NVIDIA K20X GPU.
 For our purposes, each Opteron provides 16 execution threads.
 Each node is also equiped with 32 GB of CPU RAM and 5GB of GPU RAM.</p>
 </section>
 <section id="titan-platform-file">
-<h2>Titan Platform File<a class="headerlink" href="#titan-platform-file" title="Permalink to this headline"></a></h2>
+<h2>Titan Platform File<a class="headerlink" href="#titan-platform-file" title="Permalink to this heading"></a></h2>
 <p>The recommended platform file is:</p>
 <blockquote>
 <div><ul class="simple">
@@ -107,7 +109,7 @@ <h2>Titan Platform File<a class="headerlink" href="#titan-platform-file" title="
 </div></blockquote>
 </section>
 <section id="memory-vs-speed-tradeoff-in-collisional-term">
-<h2>Memory vs speed tradeoff in collisional term<a class="headerlink" href="#memory-vs-speed-tradeoff-in-collisional-term" title="Permalink to this headline"></a></h2>
+<h2>Memory vs speed tradeoff in collisional term<a class="headerlink" href="#memory-vs-speed-tradeoff-in-collisional-term" title="Permalink to this heading"></a></h2>
 <p>Unless you are using the simplified collision operator, i.e. <strong>not COLLISION_MODEL=5</strong>,
 CGYRO will run that operator on CPU-only by default.
 This choice has been made due to the significant memory cost of the other operators,
@@ -122,14 +124,14 @@ <h2>Memory vs speed tradeoff in collisional term<a class="headerlink" href="#mem
 <p>The faster setup will require significantly more GPU memory. If your job fails with CUDA errors, try increasing the number of nodes being used.</p>
 </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 2.</p>
 <p>For really big runs, you can make use of more nodes by setting <strong>-nomp 4</strong> or even <strong>-nomp 8</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>
diff --git a/docs/cgyro/outputs.html b/docs/cgyro/outputs.html
index 616da86..8467dd2 100644
--- a/docs/cgyro/outputs.html
+++ b/docs/cgyro/outputs.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>CGYRO output files</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">CGYRO output files</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/outputs.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -89,7 +91,7 @@
            <div itemprop="articleBody">
              
   <section id="cgyro-output-files">
-<h1>CGYRO output files<a class="headerlink" href="#cgyro-output-files" title="Permalink to this headline"></a></h1>
+<h1>CGYRO output files<a class="headerlink" href="#cgyro-output-files" title="Permalink to this heading"></a></h1>
 <p>It is not <strong>not recommended</strong> to read these files directly.  Rather, we encourage the use
 of the CGYRO python data interface.</p>
 <table class="colwidths-given docutils align-default" id="id1">
@@ -214,7 +216,7 @@ <h1>CGYRO output files<a class="headerlink" href="#cgyro-output-files" title="Pe
 </tbody>
 </table>
 <section id="output-normalization">
-<h2>Output Normalization<a class="headerlink" href="#output-normalization" title="Permalink to this headline"></a></h2>
+<h2>Output Normalization<a class="headerlink" href="#output-normalization" title="Permalink to this heading"></a></h2>
 <p>Ion sound gyroradius</p>
 <div class="math notranslate nohighlight">
 \[\rho_{s,{\rm unit}} = \frac{c_s}{e B_{\rm unit}/(m_D c)}\]</div>
diff --git a/docs/cgyro/running_cases.html b/docs/cgyro/running_cases.html
index 02263c1..4803097 100644
--- a/docs/cgyro/running_cases.html
+++ b/docs/cgyro/running_cases.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 Cases</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Running Cases</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/cgyro/running_cases.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -88,9 +90,9 @@
            <div itemprop="articleBody">
              
   <section id="running-cases">
-<h1>Running Cases<a class="headerlink" href="#running-cases" title="Permalink to this headline"></a></h1>
+<h1>Running Cases<a class="headerlink" href="#running-cases" title="Permalink to this heading"></a></h1>
 <section id="quick-start-example">
-<h2>Quick-start example<a class="headerlink" href="#quick-start-example" title="Permalink to this headline"></a></h2>
+<h2>Quick-start example<a class="headerlink" href="#quick-start-example" title="Permalink to this heading"></a></h2>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cgyro -g reg08
 $ cd reg08
 $ cgyro -e .
@@ -102,7 +104,7 @@ <h2>Quick-start example<a class="headerlink" href="#quick-start-example" title="
 </figure>
 </section>
 <section id="command-line-usage">
-<h2>Command-line usage<a class="headerlink" href="#command-line-usage" title="Permalink to this headline"></a></h2>
+<h2>Command-line usage<a class="headerlink" href="#command-line-usage" title="Permalink to this heading"></a></h2>
 <p>The input files and configuration for numerous linear and nonlinear cases can
 be auto-generated using the <code class="docutils literal notranslate"><span class="pre">-g</span></code> flag.  Often, it is easiest to find a template case that is close to what you would like to run, and then modify it accordingly.  A list of all regression and template cases in generated by typing:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cgyro -g
@@ -119,7 +121,7 @@ <h2>Command-line usage<a class="headerlink" href="#command-line-usage" title="Pe
 <p>On the large systems at NERSC, ORNL and elsewhere, you will need to establish an <strong>interactive queue</strong> to execute the command above.  The result should be diagnostics printed to the screen plus a few output files.  Pay attention to the file <code class="docutils literal notranslate"><span class="pre">out.cgyro.mpi</span></code>. This shows the acceptable number of MPI tasks.</p>
 </section>
 <section id="batch-submission">
-<h2>Batch submission<a class="headerlink" href="#batch-submission" title="Permalink to this headline"></a></h2>
+<h2>Batch submission<a class="headerlink" href="#batch-submission" title="Permalink to this heading"></a></h2>
 <p>On established platforms, the burden of writing batch script files and setting core counts is managed by the <code class="docutils literal notranslate"><span class="pre">gacode_qsub</span></code> script.  To generate a <code class="docutils literal notranslate"><span class="pre">batch.src</span></code> file, you could type:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ gacode_qsub -e nl01 -n 512 -nomp 2 -queue regular -repo atom -w 0:09:00
 </pre></div>
diff --git a/docs/download.html b/docs/download.html
index f4cbf8b..d131b0f 100644
--- a/docs/download.html
+++ b/docs/download.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" />
@@ -82,8 +84,8 @@
         <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>Download and user agreement</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Download and user agreement</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/download.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -94,7 +96,7 @@
            <div itemprop="articleBody">
              
   <section id="download-and-user-agreement">
-<h1>Download and user agreement<a class="headerlink" href="#download-and-user-agreement" title="Permalink to this headline"></a></h1>
+<h1>Download and user agreement<a class="headerlink" href="#download-and-user-agreement" title="Permalink to this heading"></a></h1>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>GACODE User Agreement
  Initial version (2013.07.02) 
  Updated version (2018.11.06)
@@ -161,11 +163,11 @@ <h1>Download and user agreement<a class="headerlink" href="#download-and-user-ag
 </tbody>
 </table>
 <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>Sources are found in the <a class="reference external" href="http://github.com/gafusion">gacode repository</a> on GitHub.</p>
 </section>
 <section id="repository-access">
-<h2>Repository access<a class="headerlink" href="#repository-access" title="Permalink to this headline"></a></h2>
+<h2>Repository access<a class="headerlink" href="#repository-access" title="Permalink to this heading"></a></h2>
 <p>Get a (free) account at <a class="reference external" href="http://github.com">GitHub</a> and send your GitHub username to <strong>gacode-AT-fusion.gat.com</strong> with a request for user or developer access.</p>
 </section>
 </section>
diff --git a/docs/genindex.html b/docs/genindex.html
index 5a8cf0a..ca73424 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -15,7 +15,9 @@
         <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="#" />
@@ -75,8 +77,8 @@
         <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>Index</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Index</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
diff --git a/docs/geometry.html b/docs/geometry.html
index f3105f1..c48855a 100644
--- a/docs/geometry.html
+++ b/docs/geometry.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>
@@ -87,8 +89,8 @@
         <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>FLUX-SURFACE GEOMETRY</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">FLUX-SURFACE GEOMETRY</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/geometry.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -99,9 +101,9 @@
            <div itemprop="articleBody">
              
   <section id="flux-surface-geometry">
-<h1>FLUX-SURFACE GEOMETRY<a class="headerlink" href="#flux-surface-geometry" title="Permalink to this headline"></a></h1>
+<h1>FLUX-SURFACE GEOMETRY<a class="headerlink" href="#flux-surface-geometry" title="Permalink to this heading"></a></h1>
 <section id="coordinates">
-<h2>Coordinates<a class="headerlink" href="#coordinates" title="Permalink to this headline"></a></h2>
+<h2>Coordinates<a class="headerlink" href="#coordinates" title="Permalink to this heading"></a></h2>
 <p>GYRO/CGYRO/NEO use a right-handed (positively-oriented), field-aligned coordinate system
 <span class="math notranslate nohighlight">\((r,\theta,\alpha)\)</span> and the Clebsch field representation</p>
 <div class="math notranslate nohighlight">
@@ -115,7 +117,7 @@ <h2>Coordinates<a class="headerlink" href="#coordinates" title="Permalink to thi
 <p>The coordinate systems <span class="math notranslate nohighlight">\((R,Z,\varphi)\)</span> and <span class="math notranslate nohighlight">\((r,\theta,\varphi)\)</span> are positively oriented.</p>
 </section>
 <section id="bounding-box-method">
-<h2>Bounding-box method<a class="headerlink" href="#bounding-box-method" title="Permalink to this headline"></a></h2>
+<h2>Bounding-box method<a class="headerlink" href="#bounding-box-method" title="Permalink to this heading"></a></h2>
 <p>In the MXH parameterization <span id="id1">[<a class="reference internal" href="zreferences.html#id9" title="R. Arbon, J. Candy, and E.A. Belli. Rapidly-convergent flux-surface shape parameterization. Plasma Phys. Control. Fusion, 63:012001, 2020. doi:10.1088/1361-6587/abc63b.">ACB20</a>]</span>, we use the bounding-box method to define</p>
 <ul class="simple">
 <li><p><strong>minor radius</strong> <span class="math notranslate nohighlight">\(r\)</span></p></li>
@@ -131,7 +133,7 @@ <h2>Bounding-box method<a class="headerlink" href="#bounding-box-method" title="
 2 Z_0      = &amp; \max_\ell(Z) + \min_\ell(Z) \; .\end{split}\]</div>
 </section>
 <section id="effective-field">
-<h2>Effective field<a class="headerlink" href="#effective-field" title="Permalink to this headline"></a></h2>
+<h2>Effective field<a class="headerlink" href="#effective-field" title="Permalink to this heading"></a></h2>
 <p>The effective field strength, <span class="math notranslate nohighlight">\(B_{\rm {unit}}\)</span>, is defined as</p>
 <div class="math notranslate nohighlight">
 \[B_\mathrm{unit} = \frac{1}{r} \frac{d\chi _{t}}{dr} \; ,\]</div>
@@ -139,7 +141,7 @@ <h2>Effective field<a class="headerlink" href="#effective-field" title="Permalin
 roughly equivalent field that would be obtained if the flux surface was deformed to a circle.</p>
 </section>
 <section id="equilibria">
-<h2>Equilibria<a class="headerlink" href="#equilibria" title="Permalink to this headline"></a></h2>
+<h2>Equilibria<a class="headerlink" href="#equilibria" title="Permalink to this heading"></a></h2>
 <p>GYRO/CGYRO/NEO can be run using <strong>circular equilibrium</strong> or <strong>shaped Grad-Shafranov equilibrium</strong>.</p>
 <p><strong>(1) Circular equilibrium</strong></p>
 <p>The flux surfaces, which are <strong>not</strong> local G-S equilibria, have the form:</p>
@@ -172,7 +174,7 @@ <h2>Equilibria<a class="headerlink" href="#equilibria" title="Permalink to this
 </figure>
 </section>
 <section id="table-of-geometry-parameters">
-<h2>Table of geometry parameters<a class="headerlink" href="#table-of-geometry-parameters" title="Permalink to this headline"></a></h2>
+<h2>Table of geometry parameters<a class="headerlink" href="#table-of-geometry-parameters" title="Permalink to this heading"></a></h2>
 <table class="colwidths-given docutils align-default">
 <colgroup>
 <col style="width: 25%" />
@@ -328,7 +330,7 @@ <h2>Table of geometry parameters<a class="headerlink" href="#table-of-geometry-p
 <p>For further information about geometry and normalization conventions, consult the GYRO Technical Guide   <span id="id3">[<a class="reference internal" href="zreferences.html#id37" title="J. Candy and E. Belli. GYRO Technical Guide. General Atomics Technical Report, 2010.">CB10</a>]</span>.</p>
 </section>
 <section id="magnetic-field-orientation">
-<h2>Magnetic field orientation<a class="headerlink" href="#magnetic-field-orientation" title="Permalink to this headline"></a></h2>
+<h2>Magnetic field orientation<a class="headerlink" href="#magnetic-field-orientation" title="Permalink to this heading"></a></h2>
 <p>GACODE uses a right-handed (positively-oriented), field-aligned coordinate system <span class="math notranslate nohighlight">\((r,\theta,\varphi)\)</span>, whereas DIII-D uses a (positively-oriented) cylindrical system <span class="math notranslate nohighlight">\((R,\phi,Z)\)</span>.  Looking down on the tokamak from above, the orientation of the GACODE toroidal angle is clockwise, whereas the DIII-D toroidal angle is counter-clockwise:</p>
 <figure class="align-center">
 <a class="reference internal image-reference" href="_images/Orient_gacode.png"><img alt="flux surface" src="_images/Orient_gacode.png" style="width: 600.0px; height: 600.0px;" /></a>
diff --git a/docs/gyro.html b/docs/gyro.html
index ebd8076..fec343f 100644
--- a/docs/gyro.html
+++ b/docs/gyro.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" />
@@ -89,8 +91,8 @@
         <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>GYRO</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">GYRO</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/gyro.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -101,10 +103,10 @@
            <div itemprop="articleBody">
              
   <section id="gyro">
-<h1>GYRO<a class="headerlink" href="#gyro" title="Permalink to this headline"></a></h1>
+<h1>GYRO<a class="headerlink" href="#gyro" title="Permalink to this heading"></a></h1>
 <a class="reference internal image-reference" href="_images/supertorus-hi-2.jpg"><img alt="Classic GYRO torus" src="_images/supertorus-hi-2.jpg" style="width: 95%;" /></a>
 <section id="quick-links">
-<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this headline"></a></h2>
+<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this heading"></a></h2>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="gyro/gyro_table.html">Tabular list for input.gyro</a></li>
@@ -116,7 +118,7 @@ <h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to thi
 </div>
 </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>GYRO <span id="id1">[<a class="reference internal" href="zreferences.html#id37" title="J. Candy and E. Belli. GYRO Technical Guide. General Atomics Technical Report, 2010.">CB10</a>, <a class="reference internal" href="zreferences.html#id26" title="J. Candy and R.E. Waltz. Anomalous transport scaling in the DIII-D tokamak matched by supercomputer simulation. Phys. Rev. Lett., 91:045001, 2003. doi:10.1103/PhysRevLett.91.045001.">CW03a</a>, <a class="reference internal" href="zreferences.html#id25" title="J. Candy and R.E. Waltz. An Eulerian gyrokinetic-Maxwell solver. J. Comput. Phys., 186:545, 2003. doi:10.1016/S0021-9991(03)00079-2.">CW03b</a>, <a class="reference internal" href="zreferences.html#id27" title="J. Candy, R.E. Waltz, and W. Dorland. The local limit of global gyrokinetic simulations. Phys. Plasmas, 11:L25, 2004. doi:10.1063/1.1695358.">CWD04</a>]</span> is a legacy multi-species global electromagnetic gyrokinetic solver.  Thousands of nonlinear simulations with GYRO have informed the fusion community’s understanding of core plasma turbulence <span id="id2">[<a class="reference internal" href="zreferences.html#id51" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Gyrokinetic simulations of ion and impurity transport. Phys. Plasmas, 12:022305, 2005.">EMCW05</a>, <a class="reference internal" href="zreferences.html#id76" title="N.T. Howard, C. Holland, A.E. White, M. Greenwald, and J. Candy. Multi-scale gyrokinetic simulation of tokamak plasmas: enhanced heat loss due to cross-scale coupling of plasma turbulence. Nucl. Fusion, 56(1):014004, 2016. doi:10.1088/0029-5515/56/1/014004.">HHW+16</a>, <a class="reference internal" href="zreferences.html#id79" title="J.E. Kinsey, R.E. Waltz, and J. Candy. Nonlinear gyrokinetic turbulence simulations of E×B shear quenching of transport. Phys. Plasmas, 12:062302, 2005.">KWC05</a>, <a class="reference internal" href="zreferences.html#id80" title="J.E. Kinsey, R.E. Waltz, and J. Candy. The effect of safety factor and magnetic shear on turbulent transport in nonlinear gyrokinetic simulations. Phys. Plasmas, 13:022305, 2006.">KWC06</a>, <a class="reference internal" href="zreferences.html#id81" title="J.E. Kinsey, R.E. Waltz, and J. Candy. The effect of plasma shaping on turbulent transport and E×B shear quenching in nonlinear gyrokinetic simulations. Phys. Plasmas, 14:102306, 2007.">KWC07</a>]</span>
 and provided a <em>transport database</em> for the calibration of reduced transport models such as TGLF <span id="id3">[<a class="reference internal" href="zreferences.html#id96" title="G.M. Staebler, J.E. Kinsey, and R.E. Waltz. A theory-based transport model with comprehensive physics. Phys. Plasmas, 14:055909, 2007.">SKW07</a>]</span>.  GYRO was the first – and for many years the only – global electromagnetic solver.  It pioneered the development of numerical algorithms for the GK equations with kinetic electrons.  GYRO is formulated in real space and like all global solvers requires <em>ad hoc</em> absorbing-layer boundary conditions when simulating cases with profile variation. This approach is suitable for core turbulence simulations, which cover a large radial region and are dominated by low wavenumbers.  More recently, as the understanding of core transport has become increasingly complete, the cutting edge of research moved radially toward the pedestal region, where plasmas are characterized by larger collisionality and steeper pressure gradients that greatly modify the turbulent phenomena at play. This motivated the development, from scratch, of the <a class="reference internal" href="cgyro.html"><span class="doc">CGYRO</span></a> code <span id="id4">[<a class="reference internal" href="zreferences.html#id21" title="E.A. Belli and J. Candy. Implications of advanced collision operators for gyrokinetic simulation. Plasma Phys. Control. Fusion, 59:045005, 2017.">BC17</a>, <a class="reference internal" href="zreferences.html#id22" title="E.A. Belli and J. Candy. Impact of centrifugal drifts on ion turbulent transport. Phys. Plasmas, 25:032301, 2018.">BC18</a>, <a class="reference internal" href="zreferences.html#id42" title="J. Candy and E.A. Belli. Spectral treatment of gyrokinetic shear flow. J. Comput. Phys., 356:448, 2018. doi:10.1016/j.jcp.2017.12.020.">CB18</a>, <a class="reference internal" href="zreferences.html#id41" title="J. Candy, E.A. Belli, and R.V. Bravenec. A high-accuracy Eulerian gyrokinetic solver for collisional plasmas. J. Comput. Phys., 324:73, 2016. doi:10.1016/j.jcp.2016.07.039.">CBB16</a>]</span> to complement GYRO.</p>
 <p>For the interested reader we offer a <a class="reference internal" href="gyro/gyro_history.html"><span class="doc">brief history of gyrokinetic simulation</span></a>, including some idiosyncratic and possibly forgotten aspects of gyrokinetic research in the 2000s.  We also reproduce a <a class="reference internal" href="gyro/gyro_vv.html"><span class="doc">summary of GYRO verification and validation results</span></a> from the same era.</p>
diff --git a/docs/gyro/gyro_gallery.html b/docs/gyro/gyro_gallery.html
index de56a33..693a0b8 100644
--- a/docs/gyro/gyro_gallery.html
+++ b/docs/gyro/gyro_gallery.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>
         <script src="../_static/contentui.js"></script>
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@@ -89,9 +91,9 @@
         <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><a href="../gyro.html">GYRO</a> &raquo;</li>
-      <li>Gallery of classic GYRO images (circa 2003)</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../gyro.html">GYRO</a></li>
+      <li class="breadcrumb-item active">Gallery of classic GYRO images (circa 2003)</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/gyro/gyro_gallery.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -102,7 +104,7 @@
            <div itemprop="articleBody">
              
   <section id="gallery-of-classic-gyro-images-circa-2003">
-<h1>Gallery of classic GYRO images (circa 2003)<a class="headerlink" href="#gallery-of-classic-gyro-images-circa-2003" title="Permalink to this headline"></a></h1>
+<h1>Gallery of classic GYRO images (circa 2003)<a class="headerlink" href="#gallery-of-classic-gyro-images-circa-2003" title="Permalink to this heading"></a></h1>
 <figure class="align-center">
 <a class="reference internal image-reference" href="../_images/supertorus-hi-1.jpg"><img alt="High resolution torus, linear phase" src="../_images/supertorus-hi-1.jpg" style="width: 75%;" /></a>
 </figure>
diff --git a/docs/gyro/gyro_history.html b/docs/gyro/gyro_history.html
index 11fb3c5..e6962bb 100644
--- a/docs/gyro/gyro_history.html
+++ b/docs/gyro/gyro_history.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>
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@@ -97,9 +99,9 @@
         <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><a href="../gyro.html">GYRO</a> &raquo;</li>
-      <li>Gyrokinetic Simulation in the 2000s</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../gyro.html">GYRO</a></li>
+      <li class="breadcrumb-item active">Gyrokinetic Simulation in the 2000s</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/gyro/gyro_history.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -110,13 +112,13 @@
            <div itemprop="articleBody">
              
   <section id="gyrokinetic-simulation-in-the-2000s">
-<h1>Gyrokinetic Simulation in the 2000s<a class="headerlink" href="#gyrokinetic-simulation-in-the-2000s" title="Permalink to this headline"></a></h1>
+<h1>Gyrokinetic Simulation in the 2000s<a class="headerlink" href="#gyrokinetic-simulation-in-the-2000s" title="Permalink to this heading"></a></h1>
 <p><em>[This overview was written during the period 2006-2009]</em></p>
 <hr class="docutils" />
 <p>In the text below we describe the prehistory, history and present use of the GYRO code.  A broad spectrum of published code applications is summarized, and the key role played by GYRO within the US fusion program is clarified.  More historical details can be found in the Spring 2008 Issue of SciDAC review, whereas the
 <a class="reference external" href="https://github.com/gafusion/doc/blob/master/manuals/gyro/gyro_technical_manual.pdf">Technical Manual</a>  provides a detailed description of the underlying equations and discretization schemes.</p>
 <section id="prehistory">
-<h2>Prehistory<a class="headerlink" href="#prehistory" title="Permalink to this headline"></a></h2>
+<h2>Prehistory<a class="headerlink" href="#prehistory" title="Permalink to this heading"></a></h2>
 <p>The use of gyrokinetic codes at General Atomics began in 1994 with the acquisition of the linear gyrokinetic stability code GSTOTAL <span id="id1">[<a class="reference internal" href="../zreferences.html#id86" title="M. Kotschenreuther, G. Rewoldt, and W.M. Tang. Comparison of initial value and eigenvalue codes for kinetic toroidal plasma instabilities. Comput. Phys. Commun., 88:128, 1995. doi:10.1016/0010-4655(95)00035-E.">KRT95</a>]</span>.  GSTOTAL was an Eulerian initial-value code with trapped and passing particles (ions and electrons) as well as collisional and electromagnetic physics.  GSTOTAL represented an enormous technical advance in simulation capability, comparable in significance to Kotschenreuther’s prior invention of the well-known <span class="math notranslate nohighlight">\(\delta f\)</span> method <span id="id2">[<a class="reference internal" href="../zreferences.html#id85" title="M. Kotschenreuther. Invited talk 9I4. Bull. Am. Phys. Soc., 33:2107, 1988.">Kot88</a>]</span> for particle simulation. The time-advance scheme in GSTOTAL was <em>fully implicit</em> and allowed use of timesteps much larger than those imposed by the electron parallel Courant limit. Historically speaking, GSTOTAL was the first step toward a practical <em>nonlinear</em> gyrokinetic code.  With the addition of plasma shaping and finite-<span class="math notranslate nohighlight">\(\delta B\)</span> effects, GSTOTAL evolved into the linear stability code GKS.  GKS has been routinely used in DIII-D experimental studies for over a decade.  Combined with results from nonlinear flux-tube gyrofluid simulations <span id="id3">[<a class="reference internal" href="../zreferences.html#id115" title="R.E. Waltz, G.R. Kerbel, and J. Milovich. Toroidal gyro-landau fluid model turbulence simulations in a nonlinear ballooning mode representation with radial modes. Phys. Plasmas, 1:2229, 1994.">WKM94</a>, <a class="reference internal" href="../zreferences.html#id116" title="R.E. Waltz, G.R. Kerbel, J. Milovich, and G.W. Hammett. Advances in the simulation of toroidal gyro-landau fluid model turbulence. Phys. Plasmas, 2:2408, 1995.">WKMH95</a>]</span>, GKS was crucial in the development of GLF23 <span id="id4">[<a class="reference internal" href="../zreferences.html#id117" title="R.E. Waltz, G.M. Staebler, W. Dorland, G.W. Hammett, M. Kotschenreuther, and J.A. Konings. A gyro-landau fluid transport model. Phys. Plasmas, 4:2482, 1997.">WSD+97</a>]</span>, one of the most popular transport models worldwide.</p>
 <p>In what follows, we will draw a distinction between local and global simulations.  In this context, <em>local</em> means <em>flux-tube</em>.  Flux-tube simulations represent the <span class="math notranslate nohighlight">\(\rho_* \rightarrow 0\)</span> limit of global simulations, for which the transport scaling is purely gyroBohm <span id="id5">[<a class="reference internal" href="../zreferences.html#id27" title="J. Candy, R.E. Waltz, and W. Dorland. The local limit of global gyrokinetic simulations. Phys. Plasmas, 11:L25, 2004. doi:10.1063/1.1695358.">CWD04</a>]</span> <a class="footnote-reference brackets" href="#id79" id="id6">1</a>.   Here, <span class="math notranslate nohighlight">\(\rho_* = \rho_s/a\)</span> is the ratio of gyroradius to system size, with <span class="math notranslate nohighlight">\(\rho_s\)</span> the ion-sound Larmor radius, and <span class="math notranslate nohighlight">\(a\)</span> the plasma minor radius.</p>
 <p>Nonlinear flux-tube ‘’gyrofluid’’ simulations by Beer, Dorland, Hammett, Snyder, Waltz and others provided the key physics discoveries in the mid-1990s, years before the same phenomena were observed in gyrokinetic simulations.</p>
@@ -131,7 +133,7 @@ <h2>Prehistory<a class="headerlink" href="#prehistory" title="Permalink to this
 </div>
 </section>
 <section id="design-history">
-<h2>Design History<a class="headerlink" href="#design-history" title="Permalink to this headline"></a></h2>
+<h2>Design History<a class="headerlink" href="#design-history" title="Permalink to this heading"></a></h2>
 <p>Development of GYRO started in 1999.  The primary goal was to generalize GS2 by retaining profile-variation effects to allow, in principle, deviations from pure gyroBohm scaling.  The numerical methods for GYRO were initially patterned after GS2 wherever possible.  In the end, many significant departures from GS2 were required to meet the GYRO design target <em>and</em> to simultaneously increase computational efficiency.</p>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
@@ -144,22 +146,22 @@ <h2>Design History<a class="headerlink" href="#design-history" title="Permalink
 </div>
 </section>
 <section id="yearly-publication-synopsis">
-<h2>Yearly Publication Synopsis<a class="headerlink" href="#yearly-publication-synopsis" title="Permalink to this headline"></a></h2>
+<h2>Yearly Publication Synopsis<a class="headerlink" href="#yearly-publication-synopsis" title="Permalink to this heading"></a></h2>
 <section id="id20">
-<h3>2002<a class="headerlink" href="#id20" title="Permalink to this headline"></a></h3>
+<h3>2002<a class="headerlink" href="#id20" title="Permalink to this heading"></a></h3>
 <p>The first application of GYRO was to use the global capability with adiabatic electons to systematically examine the breaking of gyroBohm scaling (including what are now called, somewhat ambiguously, <em>nonlocal</em> or <em>turbulence spreading</em> effects) via profile variation <span id="id21">[<a class="reference internal" href="../zreferences.html#id120" title="R.E. Waltz, J. Candy, and M.N. Rosenbluth. Gyrokinetic turbulence simulation of profile shear stabilization and broken gyrobohm scaling. Phys. Plasmas, 9:1938, 2002.">WCR02</a>]</span>.</p>
 </section>
 <section id="id22">
-<h3>2003<a class="headerlink" href="#id22" title="Permalink to this headline"></a></h3>
+<h3>2003<a class="headerlink" href="#id22" title="Permalink to this heading"></a></h3>
 <p>GYRO numerical algorithms were documented <span id="id23">[<a class="reference internal" href="../zreferences.html#id25" title="J. Candy and R.E. Waltz. An Eulerian gyrokinetic-Maxwell solver. J. Comput. Phys., 186:545, 2003. doi:10.1016/S0021-9991(03)00079-2.">CW03b</a>]</span>, although publication was significantly delayed after the first submission was lost in transit.  A significant amount of linear and nonlinear benchmark data related to the Cyclone base case was given, as were parameter scans for nonlinear electromagnetic variants of the Cyclone case.  On the experimental side, simulations of DIII-D L-mode discharges were shown to match experimental power flow data within error bars <span id="id24">[<a class="reference internal" href="../zreferences.html#id26" title="J. Candy and R.E. Waltz. Anomalous transport scaling in the DIII-D tokamak matched by supercomputer simulation. Phys. Rev. Lett., 91:045001, 2003. doi:10.1103/PhysRevLett.91.045001.">CW03a</a>]</span> on the ion temperature gradient.  These simulations were physically realistic, and included finite-<span class="math notranslate nohighlight">\(\beta\)</span> effects, and collisional electron physics at real mass ratio, equilibrium <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> and profile shearing, as well as plasma shaping.</p>
 </section>
 <section id="id25">
-<h3>2004<a class="headerlink" href="#id25" title="Permalink to this headline"></a></h3>
+<h3>2004<a class="headerlink" href="#id25" title="Permalink to this heading"></a></h3>
 <p>Turbulent dynamos in the tokamak current-voltage relation <span id="id26">[<a class="reference internal" href="../zreferences.html#id59" title="F.L. Hinton, R.E. Waltz, and J. Candy. Effect of electromagnetic turbulence in the neoclassical Ohm's law. Phys. Plasmas, 11:2433, 2004.">HWC04</a>]</span> were studied, showing that the turbulent dynamo EMF drives large current density corrugations at low-order rational surfaces, but little net current.  In other work, we attempted to correct misunderstanding generated by a highly-publicized global <span class="math notranslate nohighlight">\(\rho_*\)</span>-scan <span id="id27">[<a class="reference internal" href="../zreferences.html#id89" title="Z. Lin, S. Ethier, T.S. Hahm, and W.M. Tang. Size scaling of turbulent transport in magnetically confined plasmas. Phys. Rev. Lett., 88:195004, 2002.">LEHT02</a>]</span> with highly artificial profiles.  The single scan appeared to suggest a universal range in <span class="math notranslate nohighlight">\(\rho_*\)</span> marking the transition from Bohm to gyroBohm scaling.  GYRO work established that the transition <strong>cannot</strong> be characterized by a universal curve; rather, the transition is highly dependent on the profile shape <span id="id28">[<a class="reference internal" href="../zreferences.html#id27" title="J. Candy, R.E. Waltz, and W. Dorland. The local limit of global gyrokinetic simulations. Phys. Plasmas, 11:L25, 2004. doi:10.1063/1.1695358.">CWD04</a>]</span> <a class="footnote-reference brackets" href="#id81" id="id29">3</a>.</p>
 <p>During this period, there were persistent claims from certain groups that transport is depressed near a <span class="math notranslate nohighlight">\(q_\mathrm{min}\)</span>-surface where there is a <em>gap</em> in singular surfaces <span id="id30">[<a class="reference internal" href="../zreferences.html#id84" title="Y. Kishimoto, J.-Y. Kim, W. Horton, T. Tajima, M.J. LeBrun, S.A. Dettrick, J.Q. Li, and S. Shirai. Discontinuity model for internal transport formation in reversed magnetic shear plasmas. Nucl. Fusion, 40:667, 2000.">KKH+00</a>]</span>.  Global GYRO simulations indicated that transport flows tends to vary monotonically across <span class="math notranslate nohighlight">\(q_\mathrm{min}\)</span> surfaces <span id="id31">[<a class="reference internal" href="../zreferences.html#id28" title="J. Candy, R.E. Waltz, and M.N. Rosenbluth. Smooothness of turbulent transport across a minimum-$q$ surface. Phys. Plasmas, 11:1879, 2004.">CWR04</a>]</span> (as expected from linear theory and flux-tube gyrofluid simulations <span id="id32">[<a class="reference internal" href="../zreferences.html#id115" title="R.E. Waltz, G.R. Kerbel, and J. Milovich. Toroidal gyro-landau fluid model turbulence simulations in a nonlinear ballooning mode representation with radial modes. Phys. Plasmas, 1:2229, 1994.">WKM94</a>, <a class="reference internal" href="../zreferences.html#id116" title="R.E. Waltz, G.R. Kerbel, J. Milovich, and G.W. Hammett. Advances in the simulation of toroidal gyro-landau fluid model turbulence. Phys. Plasmas, 2:2408, 1995.">WKMH95</a>]</span>) due to the appearance of nonresonant modes. These modes are absent in some simplified gyrofluid simulations which at first appeared to confirm the barrier hypothesis.</p>
 </section>
 <section id="id33">
-<h3>2005<a class="headerlink" href="#id33" title="Permalink to this headline"></a></h3>
+<h3>2005<a class="headerlink" href="#id33" title="Permalink to this heading"></a></h3>
 <p>The first systematic gyrokinetic study of particle transport and impurity dynamics was made with GYRO as thesis work for a UCSD graduate student.   In particular, temperature-gradient-induced particle pinches, thermal and energetic helium ash transport, differential flows in D-T plasmas, and collisional effects on particle pinches were examined <span id="id34">[<a class="reference internal" href="../zreferences.html#id51" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Gyrokinetic simulations of ion and impurity transport. Phys. Plasmas, 12:022305, 2005.">EMCW05</a>]</span>.  Scans in temperature and density gradients (moving from ITG- to TEM-dominated transport), <span class="math notranslate nohighlight">\(T_i/T_e\)</span>, <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> and parallel velocity shear <span id="id35">[<a class="reference internal" href="../zreferences.html#id79" title="J.E. Kinsey, R.E. Waltz, and J. Candy. Nonlinear gyrokinetic turbulence simulations of E×B shear quenching of transport. Phys. Plasmas, 12:062302, 2005.">KWC05</a>]</span> were also published.</p>
 <p>A detailed study of the beta dependence of electron and ion transport was made <span id="id36">[<a class="reference internal" href="../zreferences.html#id29" title="J. Candy. Beta scaling of transport in microturbulence simulations. Phys. Plasmas, 12:072307, 2005.">Can05</a>]</span>.  This latter work documents the so-called <em>beta runaway</em> phenomenon, which occurs at about half of the MHD crictical beta; as of Winter 2009, it remains an unsolved problem in gyrokinetics.</p>
 <p>Using a profile feedback scheme, simulations starting with DIII-D L-mode profiles successfully (and slightly) relaxed the experimental temperature and density so that simulated power flows matched experimental ones <span id="id37">[<a class="reference internal" href="../zreferences.html#id121" title="R.E. Waltz, J. Candy, F.L. Hinton, C. Estrada-Mila, and J.E. Kinsey. Advances in comprehensive simulations of transport in tokamaks. Nucl. Fusion, 45:741, 2005.">WCH+05</a>]</span>.  This sort of capability was an early landmark in the development of a more comprehensive steady-state gyrokinetic transport code.  GYRO simulations also yielded several examples of nonlocal transport <span id="id38">[<a class="reference internal" href="../zreferences.html#id123" title="R.E. Waltz. Rho-star scaling and physically realistic gyrokinetic simulations of transport in DIII-D. Fus. Sci. Tech., 48:1051, 2005.">Wal05</a>, <a class="reference internal" href="../zreferences.html#id122" title="R.E. Waltz and J. Candy. Heuristic theory of nonlocally broken gyrobohm scaling. Phys. Plasmas, 12:072303, 2005.">WC05</a>]</span>; in particular, turbulence <em>draining</em> from unstable to less unstable (or stable) regions.  At this time, the detailed radial structure of nonlinear profile perturbations was also explored: persistent (i.e., time-averaged) structure tied to rational surfaces <span id="id39">[<a class="reference internal" href="../zreferences.html#id29" title="J. Candy. Beta scaling of transport in microturbulence simulations. Phys. Plasmas, 12:072307, 2005.">Can05</a>, <a class="reference internal" href="../zreferences.html#id121" title="R.E. Waltz, J. Candy, F.L. Hinton, C. Estrada-Mila, and J.E. Kinsey. Advances in comprehensive simulations of transport in tokamaks. Nucl. Fusion, 45:741, 2005.">WCH+05</a>]</span> was found when electrons are kinetic.  These <em>corrugation</em> structures are electrostatic in nature, and most pronounced for lower-order surfaces</p>
@@ -171,12 +173,12 @@ <h3>2005<a class="headerlink" href="#id33" title="Permalink to this headline">
 <p>The width of these structures is on the order of a few ion gyroradii.</p>
 </section>
 <section id="id40">
-<h3>2006<a class="headerlink" href="#id40" title="Permalink to this headline"></a></h3>
+<h3>2006<a class="headerlink" href="#id40" title="Permalink to this heading"></a></h3>
 <p>GYRO results showed that ITG/TEM turbulence could induce the transport of energetic fusion alpha particles <span id="id41">[<a class="reference internal" href="../zreferences.html#id53" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Turbulent transport of alpha particles and helium ash in reactor plasmas. Phys. Plasmas, 13:112303, 2006.">EMCW06b</a>]</span>.  Systematic safety factor, magnetic shear, and MHD alpha parameter scans <span id="id42">[<a class="reference internal" href="../zreferences.html#id80" title="J.E. Kinsey, R.E. Waltz, and J. Candy. The effect of safety factor and magnetic shear on turbulent transport in nonlinear gyrokinetic simulations. Phys. Plasmas, 13:022305, 2006.">KWC06</a>]</span> were carried out.  Theory and simulations of gyrokinetic turbulent heating <span id="id43">[<a class="reference internal" href="../zreferences.html#id60" title="F.L. Hinton and R.E. Waltz. Gyrokinetic turbulent heating. Phys. Plasmas, 13:102301, 2006.">HW06</a>]</span> were published.  GYRO simulations which perfectly project profiles from dimensionally similar DIII-D discharges verified that the L-modes did indeed have Bohm scaling, and that the experimentally-inferred gyroBohm scaling in some H-modes was actually due to experimental profile <em>dissimilarity</em> <span id="id44">[<a class="reference internal" href="../zreferences.html#id124" title="R.E. Waltz, J. Candy, and C.C. Petty. Projected profile similarity in gyrokinetic simulations of Bohm and gyroBohm scaled DIII-D L and H modes. Phys. Plasmas, 13:072304, 2006.">WCP06</a>]</span>.   The predicted <em>profile corrugations</em> in the electron temperature gradient were observed in <span class="math notranslate nohighlight">\(q_\mathrm{min} = 2\)</span> DIII-D discharges, and the attending <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shear layer is believed to be the trigger for low-power reversed shear ITB formation <span id="id45">[<a class="reference internal" href="../zreferences.html#id125" title="R.E. Waltz, M.E. Austin, K.H. Burrell, and J. Candy. Gyrokinetic simulations of off-axis minimum-q profile corrugations. Phys. Plasmas, 12:052301, 2006.">WABC06</a>]</span>.  Density peaking via a particle pinch was demonstrated for a DIII-D L-mode plasma <span id="id46">[<a class="reference internal" href="../zreferences.html#id52" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Density peaking and turbulent pinch in DIII-D discharges. Phys. Plasmas, 13:074505, 2006.">EMCW06a</a>]</span>.</p>
 <p>In studies relating to the foundation of gyrokinetic theory, the connection between velocity-space resolution, entropy production and conservation, and numerical dissipation was rigorously demonstrated <span id="id47">[<a class="reference internal" href="../zreferences.html#id30" title="J. Candy and R.E. Waltz. Velocity-space resolution, entropy production and upwind dissipation in Eulerian gyrokinetic simulations. Phys. Plasmas, 13:032310, 2006.">CW06</a>]</span>, and the parallel nonlinearity was shown to be asymptotically subdominant (as required by the gyrokinetic ordering) to have a negligible effect on energy transport for experimentally-relevant discharges <span id="id48">[<a class="reference internal" href="../zreferences.html#id31" title="J. Candy, R.E. Waltz, S.E. Parker, and Y. Chen. Relevance of the parallel nonlinearity in gyrokinetic simulations of tokamak plasmas. Phys. Plasmas, 13:074501, 2006.">CWPC06</a>]</span>.</p>
 </section>
 <section id="id49">
-<h3>2007<a class="headerlink" href="#id49" title="Permalink to this headline"></a></h3>
+<h3>2007<a class="headerlink" href="#id49" title="Permalink to this heading"></a></h3>
 <p>The capability to simultaneously treat electron and ion gyroaverages, and thus to perform fully-coupled, multi-scale ITG-ETG simulations, was added to GYRO <span id="id50">[<a class="reference internal" href="../zreferences.html#id34" title="J. Candy, R.E. Waltz, M.R. Fahey, and C. Holland. Plasma microturbulence simulation of instabilities at highly disparate scales. J. Phys: Conf. Series, 78:012008, 2007.">CWFH07a</a>]</span>.  The results of these simulations allowed us to make significant progress on the problem of electron-scale transport using coupled ITG/TEM-ETG turbulence at a reduced ion-to-electron mass ratio.  We were able to</p>
 <ul class="simple">
 <li><p>identify the failure of the popular adiabatic ion model of ETG transport <span id="id51">[<a class="reference internal" href="../zreferences.html#id33" title="J. Candy, R.E. Waltz, M.R. Fahey, and C. Holland. The effect of ion-scale dynamics on electron-temperature-gradient turbulence. Plasma Phys. Control. Fusion, 49:1209, 2007.">CWFH07b</a>]</span>,</p></li>
@@ -190,7 +192,7 @@ <h3>2007<a class="headerlink" href="#id49" title="Permalink to this headline">
 <p>The first systematic studies of gyrokinetic momentum transport <span id="id57">[<a class="reference internal" href="../zreferences.html#id127" title="R.E. Waltz, G.M. Staebler, J. Candy, and F.L. Hinton. Gyrokinetic theory and simulation of angular momentum transport. Phys. Plasmas, 14:122507, 2007.">WSCH07</a>]</span>, including the effects of the angular momentum pinch from <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shear as well as the coriolis pinch, were published, and the effect of plasma shape on <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shear quenching and transport was studied <span id="id58">[<a class="reference internal" href="../zreferences.html#id81" title="J.E. Kinsey, R.E. Waltz, and J. Candy. The effect of plasma shaping on turbulent transport and E×B shear quenching in nonlinear gyrokinetic simulations. Phys. Plasmas, 14:102306, 2007.">KWC07</a>]</span>.</p>
 </section>
 <section id="id59">
-<h3>2008<a class="headerlink" href="#id59" title="Permalink to this headline"></a></h3>
+<h3>2008<a class="headerlink" href="#id59" title="Permalink to this heading"></a></h3>
 <p>The next step in the validation of GYRO was also begun, with the development and application of synthetic BES and CECE diagnostics to allow direct comparisons of GYRO fluctuation predictions against DIII-D core turbulence measurements.  The initial results have been presented at a number of conferences and published in multiple journals <span id="id60">[<a class="reference internal" href="../zreferences.html#id62" title="C. Holland, J. Candy, R.E Waltz, A.E. White, G.R. McKee, M.W. Shafer, L. Schmitz, and G.R Tynan. Validating simulations of core tokamak turbulence: current status and future directions. J. Phys: Conf. Series, 125:012043, 2008.">HCW+08</a>, <a class="reference internal" href="../zreferences.html#id133" title="A.E. White, L. Schmitz, G.R. McKee, C. Holland, W.A. Peebles, T.A. Carter, M.W. Shafer, M.E. Austin, K.H. Burrell, J. Candy, and others. Measurements of core electron temperature and density fluctuations in DIII-D and comparison to nonlinear gyrokinetic simulations. Phys. Plasmas, 15(5):056116, 2008.">WSM+08</a>]</span>.  The initial study focused upon modeling a steady, MHD-free L-mode DIII-D discharge, with the primary conclusions that:</p>
 <ol class="arabic simple">
 <li><p>Using local, fixed-gradient simulations, GYRO could match the <em>experimental</em> (as calculated via a ONETWO power balance analysis) energy flows within experimental gradient uncertainties for <span class="math notranslate nohighlight">\(r/a &lt; 0.6\)</span> (where <span class="math notranslate nohighlight">\(r/a\)</span> denotes normalized toroidal flux), but systematically underpredicted the energy flow at larger radii.</p></li>
@@ -201,34 +203,34 @@ <h3>2008<a class="headerlink" href="#id59" title="Permalink to this headline">
 <p>Significant progress on <strong>neoclassical</strong> and <strong>steady-state transport physics</strong> was also made; these lines of research have a separate wiki.</p>
 </section>
 <section id="id63">
-<h3>2009<a class="headerlink" href="#id63" title="Permalink to this headline"></a></h3>
+<h3>2009<a class="headerlink" href="#id63" title="Permalink to this heading"></a></h3>
 <p>Researchers from MIT were able to demonstrate good agreement between GYRO and C-Mod experiment via synthetic PCI diagnostics <span id="id64">[<a class="reference internal" href="../zreferences.html#id90" title="L. Lin, M. Porkolab, E.M. Edlund, J.C. Rost, C.L. Fiore, M. Greenwald, Y. Lin, D.R. Mikkelsen, N. Tsujii, and S J. Wukitch. Studies of turbulence and transport in Alcator C-Mod H-mode plasmas with phase contrast imaging and comparisons with GYRO. Phys. Plasmas, 16:012502, 2009.">LPE+09</a>]</span>.</p>
 </section>
 </section>
 <section id="a-computational-science-and-user-perspective">
-<h2>A Computational Science and User Perspective<a class="headerlink" href="#a-computational-science-and-user-perspective" title="Permalink to this headline"></a></h2>
+<h2>A Computational Science and User Perspective<a class="headerlink" href="#a-computational-science-and-user-perspective" title="Permalink to this heading"></a></h2>
 <p>GYRO owes it’s computational efficiency in part to the strong support from the ORNL Center for Computational Science (CCS).  GYRO runs well on a wide range of small clusters to large supercomputers.  One can move between platforms seamlessly by setting a <strong>single environment variable</strong>.  GYRO was among the earliest applications ported to the Cray X1 and XT3 at ORNL.  The code is modular and the layout is carefully organized.  There are few uses of esoteric language features.  Initial X1 optimizations to take advantage of multistreaming and vectorization were quite successful for all but the collision operator.  A later effort to improve the performance on the collision operator yielded a factor-of-ten improvement on the X1, with an average 10% improvement on IBM and commodity systems.  Recent PERC data is available which analyzes GYRO performance on various HPC systems <span id="id65">[<a class="reference internal" href="../zreferences.html#id134" title="P. Worley, J. Candy, L. Carrington, K. Huck, T. Kaiser, G. Mahinthakumar, A. Maloney, S. Moore, D. Reed, P. Roth, H. Shan, S. Shende, A. Snavely, S. Sreepathi, F. Wolf, and Y. Zhang. Performance analysis of gyro: a tool evaluation. In Proceedings of the 2005 SciDAC Conference, San Francisco, CA, June 26-30. 2005.">WCC+05</a>]</span> using the IPM, KOJAK, SvPablo, TAU and PMaC modeling tool suite.  Additional GYRO performance data on various systems (including the Cray X1, XD1 and XT3) has been presented by Vetter <span id="id66">[<a class="reference internal" href="../zreferences.html#id109" title="J.S. Vetter, S. Alam, Jr. T.H. Dunigan, M.R. Fahey, P.C. Roth, and P. Worley. Early evaluation of the cray xt3 at ornl. In Proceedings of the 47th Cray User Group Conference, Knoxville, TN, May 16-19. 2005.">VATHD+05</a>]</span>, Worley <span id="id67">[<a class="reference internal" href="../zreferences.html#id135" title="P. Worley, S. Alam, Jr. T.H. Dunigan, M.R. Fahey, and J.S. Vetter. Comparative analysis of interprocess communication on the x1, xd1, and xt3. In Proceedings of the 47th Cray User Group Conference, Knoxville, TN, May 16-19. 2005.">WATHD+05</a>]</span> and Fahey <span id="id68">[<a class="reference internal" href="../zreferences.html#id54" title="M.R. Fahey and J. Candy. GYRO: A 5-D gyrokinetic-Maxwell solver. In ACM/IEEE Proceedings of SC2004: High Performance Computing, Networking and Storage (Pittsburgh, PA). 2004.">FC04</a>]</span>.  GYRO is presently so reliable that it is routinely used by ORNL staff to diagnose <em>system hardware and software issues</em>.  For example, chassis interconnect problems on the XD1, filesystem slowdown in the XT3, and memory management issues on the SGI Altix.</p>
 <p>From the point of view of <em>utility</em>, the Eulerian codes GS2 and GYRO are set apart from all other codes in the US program in that they have a large (and growing) non-developer users group.  Numerous painstaking simulations of DIII-D, JET, JT60, and NSTX discharges have been made.  R. Bravenec and C. Holland have developed synthetic diagnostic tools to analyze GYRO data.</p>
 <p>In addition to many Cyclone-based scans, we maintain a <a class="reference download internal" download="" href="../_downloads/3881d4fcf0de4ae62c476c508fc379e1/gyro-database.pdf"><code class="xref download docutils literal notranslate"><span class="pre">transport</span> <span class="pre">database</span></code></a> containing over 300 well-resolved flux tube simulations based on the GA standard case parameters <span id="id69">[<a class="reference internal" href="../zreferences.html#id117" title="R.E. Waltz, G.M. Staebler, W. Dorland, G.W. Hammett, M. Kotschenreuther, and J.A. Konings. A gyro-landau fluid transport model. Phys. Plasmas, 4:2482, 1997.">WSD+97</a>]</span>.  Nearly all of these give particle and energy transport coefficients for both electrons and ions.  Some also include momentum transport.   Additional scans are continuously being added to the database.  In our view, compiling a database of simulations is a key practical end-product of nonlinear gyrokinetic simulations.  This database provides the benchmarks and validation for the GA advanced gyrofluid transport model TGLF <span id="id70">[<a class="reference internal" href="../zreferences.html#id95" title="G.M. Staebler, J.E. Kinsey, and R.E. Waltz. Gyro-Landau fluid equations for trapped and passing particles. Phys. Plasmas, 12:102508, 2005.">SKW05</a>, <a class="reference internal" href="../zreferences.html#id96" title="G.M. Staebler, J.E. Kinsey, and R.E. Waltz. A theory-based transport model with comprehensive physics. Phys. Plasmas, 14:055909, 2007.">SKW07</a>]</span>.</p>
 </section>
 <section id="urban-legends">
-<h2>Urban Legends<a class="headerlink" href="#urban-legends" title="Permalink to this headline"></a></h2>
+<h2>Urban Legends<a class="headerlink" href="#urban-legends" title="Permalink to this heading"></a></h2>
 <p>The Eulerian codes GS2 and GYRO have had to confront a number
 of <a class="reference external" href="http://en.wikipedia.org/wiki/Urban_legend">urban legends</a> mostly in the form of unpublished/unsubstantiated claims circulating within the fusion theory community. These seem to originate from researchers having no first-hand experience with either Eulerian schemes or local simulations.  We number these for future reference.</p>
 <section id="ul1-the-local-gyrobohm-limit-of-global-codes-differs-from-local-codes">
-<h3>UL1: The local gyroBohm limit of global codes differs from local codes<a class="headerlink" href="#ul1-the-local-gyrobohm-limit-of-global-codes-differs-from-local-codes" title="Permalink to this headline"></a></h3>
+<h3>UL1: The local gyroBohm limit of global codes differs from local codes<a class="headerlink" href="#ul1-the-local-gyrobohm-limit-of-global-codes-differs-from-local-codes" title="Permalink to this heading"></a></h3>
 <p>This cannot be true.  As <span class="math notranslate nohighlight">\(\rho_*\)</span> vanishes, the transport obtained from a global code reaches a limiting value at a given radial location.  This limiting value (i.e., the gyroBohm scaled limit) is identical to the local simulation result.  This not only provides the physical meaning of a local simulation, but is an important test of validity for local and global codes alike.  GYRO has passed this test repeatedly <span id="id72">[<a class="reference internal" href="../zreferences.html#id27" title="J. Candy, R.E. Waltz, and W. Dorland. The local limit of global gyrokinetic simulations. Phys. Plasmas, 11:L25, 2004. doi:10.1063/1.1695358.">CWD04</a>, <a class="reference internal" href="../zreferences.html#id120" title="R.E. Waltz, J. Candy, and M.N. Rosenbluth. Gyrokinetic turbulence simulation of profile shear stabilization and broken gyrobohm scaling. Phys. Plasmas, 9:1938, 2002.">WCR02</a>]</span>.</p>
 </section>
 <section id="ul2-full-torus-simulations-are-necessary-to-correctly-compute-the-local-transport">
-<h3>UL2: Full torus simulations are necessary to correctly compute the local transport<a class="headerlink" href="#ul2-full-torus-simulations-are-necessary-to-correctly-compute-the-local-transport" title="Permalink to this headline"></a></h3>
+<h3>UL2: Full torus simulations are necessary to correctly compute the local transport<a class="headerlink" href="#ul2-full-torus-simulations-are-necessary-to-correctly-compute-the-local-transport" title="Permalink to this heading"></a></h3>
 <p>DIII-D full-physics simulations which span 1/6th of a torus, 1/3rd of a torus, 1/2 of a torus, and a full torus give transport diffusivities which differ only by few percent <span id="id73">[<a class="reference internal" href="../zreferences.html#id121" title="R.E. Waltz, J. Candy, F.L. Hinton, C. Estrada-Mila, and J.E. Kinsey. Advances in comprehensive simulations of transport in tokamaks. Nucl. Fusion, 45:741, 2005.">WCH+05</a>]</span>. In fact, full-torus simulations are generally wasteful of computer resources.  Global codes which are limited to full torus operation could obtain significantly more accurate results by simulating only a fraction of a torus but operating with a higher number of particles per cell and/or spatial resolution.</p>
 </section>
 <section id="ul3-eulerian-codes-have-inadequate-velocity-space-resolution">
-<h3>UL3: Eulerian codes have inadequate velocity-space resolution<a class="headerlink" href="#ul3-eulerian-codes-have-inadequate-velocity-space-resolution" title="Permalink to this headline"></a></h3>
+<h3>UL3: Eulerian codes have inadequate velocity-space resolution<a class="headerlink" href="#ul3-eulerian-codes-have-inadequate-velocity-space-resolution" title="Permalink to this heading"></a></h3>
 <p>The truth is in fact quite the opposite.  Published GYRO simulations are always checked for adequate grid convergence by the standard method of grid refinement.  GYRO has a particularly efficient velocity-space discretization scheme which suffers no accuracy loss even when the distribution is nearly discontinuous across the trapped-passing boundary.  We typically use 128 velocity gridpoints per real-space cell.  This is roughly equivalent to 128 particles per cell (PPC) in terms of points where the distribution function is known.  We emphasize that this was, until recently, <strong>significantly more</strong> than that typically used in PIC simulations <a class="footnote-reference brackets" href="#id83" id="id74">4</a>.  We have verified that no significant fine-scale structure in the distribution is being ignored or ‘’coarse-grained’’.  Recent GYRO work <span id="id75">[<a class="reference internal" href="../zreferences.html#id30" title="J. Candy and R.E. Waltz. Velocity-space resolution, entropy production and upwind dissipation in Eulerian gyrokinetic simulations. Phys. Plasmas, 13:032310, 2006.">CW06</a>]</span> demonstrates a detailed steady-state balance between production of fluctuations and (numerical) dissipation, thus resolving the <em>entropy paradox</em> in a manner consistent with the picture developed by Krommes <span id="id76">[<a class="reference internal" href="../zreferences.html#id88" title="J.A. Krommes. Thermostatted $\delta f$. Phys. Plasmas, 6:1477, 1999.">Kro99</a>, <a class="reference internal" href="../zreferences.html#id87" title="J.A. Krommes and G. Hu. The role of dissipation in the theory and simulations of homogeneous plasma turbulence, and resolution of the entropy paradox. Phys. Plasmas, 1:3211, 1994.">KH94</a>]</span>.  The numerical dissipation is also shown to be so small that it does not affect the observed transport.</p>
 </section>
 <section id="ul4-the-parallel-nonlinearity-can-have-a-dramatic-effect-on-the-transport">
-<h3>UL4: The parallel nonlinearity can have a dramatic effect on the transport<a class="headerlink" href="#ul4-the-parallel-nonlinearity-can-have-a-dramatic-effect-on-the-transport" title="Permalink to this headline"></a></h3>
+<h3>UL4: The parallel nonlinearity can have a dramatic effect on the transport<a class="headerlink" href="#ul4-the-parallel-nonlinearity-can-have-a-dramatic-effect-on-the-transport" title="Permalink to this heading"></a></h3>
 <p>This is false for realistic core tokamak parameters.  The so-called parallel nonlinearity (a velocity-space nonlinearity which is formally one order smaller in <span class="math notranslate nohighlight">\(\rho_*\)</span> than other terms in the gyrokinetic equations) is only one of several small terms commonly neglected in the standard operation of gyrokinetic codes.  GYRO has shown <span id="id77">[<a class="reference internal" href="../zreferences.html#id31" title="J. Candy, R.E. Waltz, S.E. Parker, and Y. Chen. Relevance of the parallel nonlinearity in gyrokinetic simulations of tokamak plasmas. Phys. Plasmas, 13:074501, 2006.">CWPC06</a>]</span> that the parallel nonlinearity has no statistically significant effect on the diagnosed transport when <cite>rho_* &lt; 0.01</cite>. Moreover, the parallel nonlinearity has nothing whatsoever to do with the entropy paradox or with producing steady-states of turbulence.  To be clear the parallel nonlinearity (related to the nonlinear Landau damping and to wave-particle trapping) is the physical origin of a small turbulent heating source. GYRO is the first code to diagnostically calculate this heating <span id="id78">[<a class="reference internal" href="../zreferences.html#id60" title="F.L. Hinton and R.E. Waltz. Gyrokinetic turbulent heating. Phys. Plasmas, 13:102301, 2006.">HW06</a>]</span>.</p>
 <dl class="footnote brackets">
 <dt class="label" id="id79"><span class="brackets"><a class="fn-backref" href="#id6">1</a></span></dt>
diff --git a/docs/gyro/gyro_list.html b/docs/gyro/gyro_list.html
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   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
-          <li><a href="../gyro.html">GYRO</a> &raquo;</li>
-      <li>Alphabetical list for input.gyro</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../gyro.html">GYRO</a></li>
+      <li class="breadcrumb-item active">Alphabetical list for input.gyro</li>
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@@ -106,9 +108,9 @@
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   <section id="alphabetical-list-for-input-gyro">
-<h1>Alphabetical list for input.gyro<a class="headerlink" href="#alphabetical-list-for-input-gyro" title="Permalink to this headline"></a></h1>
+<h1>Alphabetical list for input.gyro<a class="headerlink" href="#alphabetical-list-for-input-gyro" title="Permalink to this heading"></a></h1>
 <section id="amp-phi-n">
-<span id="gyro-amp-phi-n"></span><h2>AMP_PHI_N<a class="headerlink" href="#amp-phi-n" title="Permalink to this headline"></a></h2>
+<span id="gyro-amp-phi-n"></span><h2>AMP_PHI_N<a class="headerlink" href="#amp-phi-n" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Initial amplitude of finite-<span class="math notranslate nohighlight">\(n\)</span> modes.</p>
 <p><strong>Comments</strong></p>
diff --git a/docs/gyro/gyro_table.html b/docs/gyro/gyro_table.html
index df0426f..cd006d2 100644
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-      <li>Tabular list for input.gyro</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../gyro.html">GYRO</a></li>
+      <li class="breadcrumb-item active">Tabular list for input.gyro</li>
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@@ -102,7 +104,7 @@
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-<h1>Tabular list for input.gyro<a class="headerlink" href="#tabular-list-for-input-gyro" title="Permalink to this headline"></a></h1>
+<h1>Tabular list for input.gyro<a class="headerlink" href="#tabular-list-for-input-gyro" title="Permalink to this heading"></a></h1>
 <table class="colwidths-given docutils align-default" id="id1">
 <caption><span class="caption-text"><strong>Control parameters</strong></span><a class="headerlink" href="#id1" title="Permalink to this table"></a></caption>
 <colgroup>
diff --git a/docs/gyro/gyro_vv.html b/docs/gyro/gyro_vv.html
index ab19304..a5a0fb4 100644
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+++ b/docs/gyro/gyro_vv.html
@@ -16,7 +16,9 @@
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
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-          <li><a href="../gyro.html">GYRO</a> &raquo;</li>
-      <li>GYRO verification and validation (pre 2010)</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../gyro.html">GYRO</a></li>
+      <li class="breadcrumb-item active">GYRO verification and validation (pre 2010)</li>
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@@ -107,13 +109,13 @@
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   <section id="gyro-verification-and-validation-pre-2010">
-<h1>GYRO verification and validation (pre 2010)<a class="headerlink" href="#gyro-verification-and-validation-pre-2010" title="Permalink to this headline"></a></h1>
+<h1>GYRO verification and validation (pre 2010)<a class="headerlink" href="#gyro-verification-and-validation-pre-2010" title="Permalink to this heading"></a></h1>
 <p><em>[This research summary was written in 2010]</em></p>
 <hr class="docutils" />
 <section id="verification-studies">
-<h2>Verification Studies<a class="headerlink" href="#verification-studies" title="Permalink to this headline"></a></h2>
+<h2>Verification Studies<a class="headerlink" href="#verification-studies" title="Permalink to this heading"></a></h2>
 <section id="cyclone-base-case-with-adiabatic-electrons-2001">
-<h3>Cyclone Base Case with Adiabatic Electrons (2001)<a class="headerlink" href="#cyclone-base-case-with-adiabatic-electrons-2001" title="Permalink to this headline"></a></h3>
+<h3>Cyclone Base Case with Adiabatic Electrons (2001)<a class="headerlink" href="#cyclone-base-case-with-adiabatic-electrons-2001" title="Permalink to this heading"></a></h3>
 <p>A complete <span class="math notranslate nohighlight">\(R/L_T\)</span> scan for the Cyclone Base Case with adiabatic electron
 was published in <span id="id1">[<a class="reference internal" href="../zreferences.html#id25" title="J. Candy and R.E. Waltz. An Eulerian gyrokinetic-Maxwell solver. J. Comput. Phys., 186:545, 2003. doi:10.1016/S0021-9991(03)00079-2.">CW03b</a>]</span>.  We reproduce below Fig. 11 from that publication:</p>
 <figure class="align-center">
@@ -122,7 +124,7 @@ <h3>Cyclone Base Case with Adiabatic Electrons (2001)<a class="headerlink" href=
 <p><strong>Figure 1:</strong> <span class="math notranslate nohighlight">\(\chi_i\)</span> versus <span class="math notranslate nohighlight">\(R/L_T\)</span> scan for the Cyclone Base Case, compared with results from the LLNL and Univ. of Colorado gyrokinetic PIC codes.</p>
 </section>
 <section id="local-limit-of-global-simulations-2004">
-<h3>Local limit of Global Simulations (2004)<a class="headerlink" href="#local-limit-of-global-simulations-2004" title="Permalink to this headline"></a></h3>
+<h3>Local limit of Global Simulations (2004)<a class="headerlink" href="#local-limit-of-global-simulations-2004" title="Permalink to this heading"></a></h3>
 <p>After the publication of this work, a community-wide benchmark exercise was carried out between codes with local capability (GYRO and GS2) and a global code (GTC).  The difficulties encountered by the global code in attempting to reproduce the local limit in <span class="math notranslate nohighlight">\(s-\alpha\)</span> geometry was addressed in <span id="id2">[<a class="reference internal" href="../zreferences.html#id27" title="J. Candy, R.E. Waltz, and W. Dorland. The local limit of global gyrokinetic simulations. Phys. Plasmas, 11:L25, 2004. doi:10.1063/1.1695358.">CWD04</a>]</span>, where it was demonstrated that the local limit can be achieved in a truly global simulation.  We reproduce below Fig. 3 of that paper:</p>
 <figure class="align-center">
 <a class="reference internal image-reference" href="../_images/candy_pop2004_fig3.png"><img alt="candy_pop2004_fig3" src="../_images/candy_pop2004_fig3.png" style="width: 75%;" /></a>
@@ -130,7 +132,7 @@ <h3>Local limit of Global Simulations (2004)<a class="headerlink" href="#local-l
 <p><strong>Figure 2:</strong> Curves show radial profile of <span class="math notranslate nohighlight">\(\chi_i\)</span> averaged over the time inteval <span class="math notranslate nohighlight">\(400 \le (c_s/a) t \le 900\)</span>, as computed by GYRO.  Solid dots show results of three separate GS2 flux-tube simulations.</p>
 </section>
 <section id="gyrokinetic-simulation-of-impurities-2004">
-<h3>Gyrokinetic Simulation of Impurities (2004)<a class="headerlink" href="#gyrokinetic-simulation-of-impurities-2004" title="Permalink to this headline"></a></h3>
+<h3>Gyrokinetic Simulation of Impurities (2004)<a class="headerlink" href="#gyrokinetic-simulation-of-impurities-2004" title="Permalink to this heading"></a></h3>
 <p>Prior to 2004, basically all simulation work was done with pure plasmas.  As part of a Ph.D. thesis (Estrada-Mila), a paper on the topic of transport in impure plasmas <span id="id3">[<a class="reference internal" href="../zreferences.html#id51" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Gyrokinetic simulations of ion and impurity transport. Phys. Plasmas, 12:022305, 2005.">EMCW05</a>]</span> was published.  This work contained crucial benchmarks with the GS2 code.  Figure 1 from that paper is reproduced below:</p>
 <figure class="align-center">
 <a class="reference internal image-reference" href="../_images/estrada_pop2005_fig1.png"><img alt="estrada_pop2005_fig1" src="../_images/estrada_pop2005_fig1.png" style="width: 75%;" /></a>
@@ -138,7 +140,7 @@ <h3>Gyrokinetic Simulation of Impurities (2004)<a class="headerlink" href="#gyro
 <p><strong>Figure 3:</strong> Adiabatic electron comparison of growth rates for the GYRO (solid line) and GS2 (black dot) codes.  Also shown are published results by Dong <span id="id4">[<a class="reference internal" href="../zreferences.html#id48" title="J.Q. Dong and W. Horton. Study of impurity mode and ion temperature gradient mode in toroidal plasmas. Phys. Plasmas, 2:3412, 1995.">DH95</a>]</span> (dotted line) which neglect trapping.  Plot (a) shows the growth rate as functions of <span class="math notranslate nohighlight">\(k_\theta \rho_s\)</span>. Plot (b) shows the effect of carbon concentration, <span class="math notranslate nohighlight">\(f_C = z_C n_C/n_e\)</span>, for <span class="math notranslate nohighlight">\(k_\theta \rho_s = 1/\sqrt{2}\)</span> and <span class="math notranslate nohighlight">\(s=1\)</span>.  All other parameters are the same in both plots.  Agreement between GYRO and GS2 is extremely good.</p>
 </section>
 <section id="electron-temperature-gradient-turbulence-2006">
-<h3>Electron Temperature Gradient Turbulence (2006)<a class="headerlink" href="#electron-temperature-gradient-turbulence-2006" title="Permalink to this headline"></a></h3>
+<h3>Electron Temperature Gradient Turbulence (2006)<a class="headerlink" href="#electron-temperature-gradient-turbulence-2006" title="Permalink to this heading"></a></h3>
 <p>Motivated by incorrect published results from a global code, a large community-wide benchmark exercise was carried out including the most advanced European gyrokinetic code, GENE.  The results were published in a paper <span id="id5">[<a class="reference internal" href="../zreferences.html#id92" title="W.M. Nevins, J. Candy, S. Cowley, T. Dannert, A. Dimits, W. Dorland, C. Estrada-Mila, G.W. Hammett, F. Jenko, M.J. Pueschel, and D.E. Shumaker. Characterizing electron temperature gradient turbulence via numerical simulation. Phys. Plasmas, 13:122306, 2006.">NCC+06</a>]</span> that clarified difficulties associated with simulations of ETG turbulence, and a new low-shear operating point was designed so that benchmark case was physically well-behaved.  Remarkable intercode agreement was obtained</p>
 <figure class="align-center">
 <a class="reference internal image-reference" href="../_images/nevins_pop2006_fig8.png"><img alt="nevins_pop2006_fig8" src="../_images/nevins_pop2006_fig8.png" style="width: 75%;" /></a>
@@ -148,7 +150,7 @@ <h3>Electron Temperature Gradient Turbulence (2006)<a class="headerlink" href="#
 <p>Later, the exercise was successfully achieved by the GEM code.  The GTC group refused to participate.</p>
 </section>
 <section id="energetic-particle-transport-coefficients-2009">
-<h3>Energetic particle transport coefficients (2009)<a class="headerlink" href="#energetic-particle-transport-coefficients-2009" title="Permalink to this headline"></a></h3>
+<h3>Energetic particle transport coefficients (2009)<a class="headerlink" href="#energetic-particle-transport-coefficients-2009" title="Permalink to this heading"></a></h3>
 <p>Following up on initial work by Estrada-Mila <span id="id6">[<a class="reference internal" href="../zreferences.html#id52" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Density peaking and turbulent pinch in DIII-D discharges. Phys. Plasmas, 13:074505, 2006.">EMCW06a</a>]</span>, Angioni <span id="id7">[<a class="reference internal" href="../zreferences.html#id7" title="C. Angioni, A.G. Peeters, G.V. Pereverzev, A. Bottino, J. Candy, R. Dux, E. Fable, T. Hein, and R.E. Waltz. Gyrokinetic simulations of impurity, He ash and α particle transport and consequences on ITER transport modelling. Nucl. Fusion, 49:055013, 2009.">APP+09</a>]</span> carried out detailed GS2-GYRO comparsions of alpha particle quasilinear transport coefficients.  This comparison tests, among other things, the multi-scale accuracy of the gyro-averaging operators for electrons and ions.  Below we reproduce Fig. 5 of that paper:</p>
 <figure class="align-center">
 <a class="reference internal image-reference" href="../_images/angioni_nf2009_fig5.png"><img alt="angioni_nf2009_fig5" src="../_images/angioni_nf2009_fig5.png" style="width: 75%;" /></a>
@@ -156,7 +158,7 @@ <h3>Energetic particle transport coefficients (2009)<a class="headerlink" href="
 <p><strong>Figure 5:</strong> Diffusion, thermodiffusion and pure convection coefficients for <span class="math notranslate nohighlight">\(\alpha\)</span> particles in the case of a Maxwellian unperturbed distribution function, computed by linear GYRO (open squares), and linear GS2 (full circles). The codes are found in perfect agreement. The same quantities computed by GS2 in the case of an equilibrium slowing down distribution function are also plotted for comparison (full squares).  For the particle thermodiffusion coefficient <span class="math notranslate nohighlight">\(C_{T\alpha}\)</span> as well as for the diagonal heat conduction coefficient <span class="math notranslate nohighlight">\(\chi_{T\alpha}/\chi_{n\alpha}\)</span> both the actual curve obtained with a Maxwellian distribution (dashed line), as well as the same curve but rescaled by the factor <span class="math notranslate nohighlight">\(d {\rm ln} T_\alpha/d {\rm ln} T_e\)</span> (solid line), have been plotted. The latter curve allows a direct comparison with the corresponding coefficients obtained in the case of a slowing down distribution function.</p>
 </section>
 <section id="compressional-electromagnetic-perturbations-2010">
-<h3>Compressional Electromagnetic Perturbations (2010)<a class="headerlink" href="#compressional-electromagnetic-perturbations-2010" title="Permalink to this headline"></a></h3>
+<h3>Compressional Electromagnetic Perturbations (2010)<a class="headerlink" href="#compressional-electromagnetic-perturbations-2010" title="Permalink to this heading"></a></h3>
 <p>Recently, compressional electromagnetic capability, <span class="math notranslate nohighlight">\(\delta B_\lVert\)</span> was added to GYRO and linear benchmarks were carried out against GS2 – the only other nonlinear code with the same capability:</p>
 <figure class="align-center">
 <a class="reference internal image-reference" href="../_images/belli_pop2010_fig1.png"><img alt="belli_pop2010_fig1" src="../_images/belli_pop2010_fig1.png" style="width: 75%;" /></a>
@@ -166,9 +168,9 @@ <h3>Compressional Electromagnetic Perturbations (2010)<a class="headerlink" href
 </section>
 <hr class="docutils" />
 <section id="gyro-validation-abstracts">
-<h2>GYRO Validation Abstracts<a class="headerlink" href="#gyro-validation-abstracts" title="Permalink to this headline"></a></h2>
+<h2>GYRO Validation Abstracts<a class="headerlink" href="#gyro-validation-abstracts" title="Permalink to this heading"></a></h2>
 <section id="comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data">
-<h3>Comparison of GYRO synthetic diagnostic results with DIII-D BES and CER data<a class="headerlink" href="#comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data" title="Permalink to this headline"></a></h3>
+<h3>Comparison of GYRO synthetic diagnostic results with DIII-D BES and CER data<a class="headerlink" href="#comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data" title="Permalink to this heading"></a></h3>
 <p><strong>Contact</strong> – C. Holland</p>
 <p><strong>Abstract</strong> –
 The implementation of synthetic diagnostics that model physical beam emission spectroscopy and correlation electron cyclotron emission diagnostics is presented. Initial results from their applications to local gyrokinetic simulations of two locations in a DIII-D L-mode discharge performed with the GYRO code are also discussed.   At both locations, the attenuation of the GYRO-predicted fluctuations due to the spatial averaging imposed by the diagnostics’ spot sizes is significant, and its incorporation via the use of synthetic diagnostics is shown to be essential for quantitative comparisons such as these.</p>
@@ -177,7 +179,7 @@ <h3>Comparison of GYRO synthetic diagnostic results with DIII-D BES and CER data
 <p><strong>Resources</strong> – <a class="reference external" href="http://link.aip.org/link/?PHPAEN/16/052301/1">Phys. Plasmas, May 2009</a></p>
 </section>
 <section id="comparison-of-gyro-synthetic-diagnostic-results-with-c-mod-pci-data">
-<h3>Comparison of GYRO synthetic diagnostic results with C-Mod PCI data<a class="headerlink" href="#comparison-of-gyro-synthetic-diagnostic-results-with-c-mod-pci-data" title="Permalink to this headline"></a></h3>
+<h3>Comparison of GYRO synthetic diagnostic results with C-Mod PCI data<a class="headerlink" href="#comparison-of-gyro-synthetic-diagnostic-results-with-c-mod-pci-data" title="Permalink to this heading"></a></h3>
 <p><strong>Contact</strong> – L. Lin</p>
 <p><strong>Abstract</strong> –
 Data is taken from ohmic plasmas in the Alcator C-Mod tokamak using phase contrast imaging (PCI) diagnostic, with experiments carried out over the range of densities covering the ‘neo-Alcator’ to the ‘saturated ohmic’ regime.  This was compared with GYRO simulations using a synthetic PCI diagnostic method.</p>
@@ -186,7 +188,7 @@ <h3>Comparison of GYRO synthetic diagnostic results with C-Mod PCI data<a class=
 <p><strong>Resources</strong> – <a class="reference external" href="http://dx.doi.org/10.1088/0741-3335/51/6/065006">Plasma Phys. Control. Fus., June 2009</a></p>
 </section>
 <section id="comparison-of-gyro-simulations-with-fast-sweeping-and-doppler-reflectometer-data-in-tore-supra">
-<h3>Comparison of GYRO simulations with fast-sweeping and Doppler reflectometer data in Tore Supra<a class="headerlink" href="#comparison-of-gyro-simulations-with-fast-sweeping-and-doppler-reflectometer-data-in-tore-supra" title="Permalink to this headline"></a></h3>
+<h3>Comparison of GYRO simulations with fast-sweeping and Doppler reflectometer data in Tore Supra<a class="headerlink" href="#comparison-of-gyro-simulations-with-fast-sweeping-and-doppler-reflectometer-data-in-tore-supra" title="Permalink to this heading"></a></h3>
 <p><strong>Contact</strong> – A. Casati</p>
 <p><strong>Abstract</strong> –
 Turbulence measurements in TORE SUPRA tokamak plasmas have been quantitatively compared to predictions by nonlinear gyrokinetic simulations. The GYRO results simultaneously match within experimental uncertainty (a) the magnitude of effective heat diffusivity, (b) rms values of density fluctuations, and (c) wave-number spectra in both the directions perpendicular to the magnetic field. Moreover, the GYRO nonlinear simulations help to revise as an instrumental effect the apparent experimental evidence of strong turbulence anisotropy at spatial scales of the order of ion-sound Larmor radius.</p>
@@ -195,7 +197,7 @@ <h3>Comparison of GYRO simulations with fast-sweeping and Doppler reflectometer
 <p><strong>Resources</strong> – <a class="reference external" href="http://link.aps.org/doi/10.1103/PhysRevLett.102.165005">Phys. Rev. Lett., February 2009</a></p>
 </section>
 <section id="anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation">
-<h3>Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation<a class="headerlink" href="#anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation" title="Permalink to this headline"></a></h3>
+<h3>Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation<a class="headerlink" href="#anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation" title="Permalink to this heading"></a></h3>
 <p><strong>Contact</strong> – J. Candy</p>
 <p><strong>Abstract</strong> –
 The measured transport levels and apparent Bohm-like scaling observed in the DIII-D tokamak was reproduced with in experimental error bars using a series a GYRO simulations and sensitivity studies.</p>
diff --git a/docs/index.html b/docs/index.html
index 9e4ee49..7fb05d1 100644
--- a/docs/index.html
+++ b/docs/index.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" />
@@ -77,8 +79,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="#" class="icon icon-home"></a> &raquo;</li>
-      <li>The General Atomics GACODE Suite</li>
+      <li><a href="#" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">The General Atomics GACODE Suite</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -89,7 +91,7 @@
            <div itemprop="articleBody">
              
   <section id="the-general-atomics-gacode-suite">
-<h1>The General Atomics GACODE Suite<a class="headerlink" href="#the-general-atomics-gacode-suite" title="Permalink to this headline"></a></h1>
+<h1>The General Atomics GACODE Suite<a class="headerlink" href="#the-general-atomics-gacode-suite" title="Permalink to this heading"></a></h1>
 <figure class="align-center">
 <a class="reference internal image-reference" href="_images/marshall_code.png"><img alt="Marshall Rosenbluth (early 1980s)" src="_images/marshall_code.png" style="width: 90%;" /></a>
 </figure>
@@ -97,19 +99,19 @@ <h1>The General Atomics GACODE Suite<a class="headerlink" href="#the-general-ato
 at <a class="reference external" href="http://www.ga.com/magnetic-fusion">General Atomics</a>, and distributed through
 the <a class="reference external" href="https://github.com/gafusion/gacode/">GACODE source code repository</a> at GitHub.</p>
 <section id="running-gacode">
-<h2>Running GACODE<a class="headerlink" href="#running-gacode" title="Permalink to this headline"></a></h2>
+<h2>Running GACODE<a class="headerlink" href="#running-gacode" title="Permalink to this heading"></a></h2>
 <p>There are numerous <a class="reference internal" href="setup.html"><span class="doc">public installations</span></a> of GACODE (via <a class="reference external" href="https://scidac.github.io/atom">AToM</a> or local maintainers).  You can also <a class="reference internal" href="build.html"><span class="doc">install and build</span></a> the GACODE suite from sources to run on your desktop or laptop.</p>
 </section>
 <section id="geometry">
-<h2>Geometry<a class="headerlink" href="#geometry" title="Permalink to this headline"></a></h2>
+<h2>Geometry<a class="headerlink" href="#geometry" title="Permalink to this heading"></a></h2>
 <p>A description of the unified method used to describe <a class="reference internal" href="geometry.html"><span class="doc">flux-surface geometry</span></a>.</p>
 </section>
 <section id="plasma-rotation">
-<h2>Plasma rotation<a class="headerlink" href="#plasma-rotation" title="Permalink to this headline"></a></h2>
+<h2>Plasma rotation<a class="headerlink" href="#plasma-rotation" title="Permalink to this heading"></a></h2>
 <p>Some notes about <a class="reference internal" href="rotation.html"><span class="doc">plasma rotation</span></a>.</p>
 </section>
 <section id="experimental-profiles">
-<h2>Experimental profiles<a class="headerlink" href="#experimental-profiles" title="Permalink to this headline"></a></h2>
+<h2>Experimental profiles<a class="headerlink" href="#experimental-profiles" title="Permalink to this heading"></a></h2>
 <p>GACODE software works with the <a class="reference internal" href="input_gacode.html#input-gacode"><span class="std std-ref">input.gacode</span></a> format.</p>
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">Software</span></p>
diff --git a/docs/input_gacode.html b/docs/input_gacode.html
index aed9a7a..7d6adb6 100644
--- a/docs/input_gacode.html
+++ b/docs/input_gacode.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>
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     <script src="_static/js/theme.js"></script>
@@ -82,8 +84,8 @@
         <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>input.gacode</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">input.gacode</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/input_gacode.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -94,13 +96,13 @@
            <div itemprop="articleBody">
              
   <section id="input-gacode">
-<span id="id1"></span><h1>input.gacode<a class="headerlink" href="#input-gacode" title="Permalink to this headline"></a></h1>
+<span id="id1"></span><h1>input.gacode<a class="headerlink" href="#input-gacode" title="Permalink to this heading"></a></h1>
 <p>To see what a sample <a class="reference internal" href="#"><span class="doc">input.gacode</span></a> looks like, at the command line type</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ cgyro -g reg14 <span class="p">;</span> cat reg14/input.gacode
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$<span class="w"> </span>cgyro<span class="w"> </span>-g<span class="w"> </span>reg14<span class="w"> </span><span class="p">;</span><span class="w"> </span>cat<span class="w"> </span>reg14/input.gacode
 </pre></div>
 </div>
 <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>The file <a class="reference internal" href="#"><span class="doc">input.gacode</span></a> contains the entire dataset required for specification of experimental profiles. All such profiles are specified on an nexp-point grid.  The information included is sufficient to carry out simulations of strongly-shaped up-down asymmetric (i.e., arbitrary) equilibria using the new <a class="reference internal" href="geometry.html"><span class="doc">MXH equilibrium parameters</span></a> <span id="id2">[<a class="reference internal" href="zreferences.html#id9" title="R. Arbon, J. Candy, and E.A. Belli. Rapidly-convergent flux-surface shape parameterization. Plasma Phys. Control. Fusion, 63:012001, 2020. doi:10.1088/1361-6587/abc63b.">ACB20</a>]</span>.</p>
 <p>Profile ordering in <a class="reference internal" href="#"><span class="doc">input.gacode</span></a> is arbitrary and comment lines (starting with <code class="docutils literal notranslate"><span class="pre">#</span></code> in the first column) can be added for convenience.  These comment lines are ignored by the parser.  To generate <a class="reference internal" href="#"><span class="doc">input.gacode</span></a>, please use the <code class="docutils literal notranslate"><span class="pre">profiles_gen</span></code> command-line tool.</p>
 <table class="colwidths-given docutils align-default" id="id3">
diff --git a/docs/license.html b/docs/license.html
index 554fee0..8243a7a 100644
--- a/docs/license.html
+++ b/docs/license.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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@@ -78,8 +80,8 @@
         <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>GACODE License</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">GACODE License</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/license.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -90,7 +92,7 @@
            <div itemprop="articleBody">
              
   <section id="gacode-license">
-<h1>GACODE License<a class="headerlink" href="#gacode-license" title="Permalink to this headline"></a></h1>
+<h1>GACODE License<a class="headerlink" href="#gacode-license" title="Permalink to this heading"></a></h1>
 <p>Copyright 2018, “Turbulence and Transport Group” &lt;<a class="reference external" href="mailto:gacode&#37;&#52;&#48;fusion&#46;gat&#46;com">gacode<span>&#64;</span>fusion<span>&#46;</span>gat<span>&#46;</span>com</a>&gt;</p>
 <p>Permission is hereby granted, free of charge, to any person obtaining a copy of this software
 and associated documentation files (the “Software”), to deal in the Software without restriction,
diff --git a/docs/misc.html b/docs/misc.html
index 6eb2dbc..3e01aaf 100644
--- a/docs/misc.html
+++ b/docs/misc.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>
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@@ -82,8 +84,8 @@
         <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>Miscellaneous</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Miscellaneous</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/misc.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -94,7 +96,7 @@
            <div itemprop="articleBody">
              
   <section id="miscellaneous">
-<h1>Miscellaneous<a class="headerlink" href="#miscellaneous" title="Permalink to this headline"></a></h1>
+<h1>Miscellaneous<a class="headerlink" href="#miscellaneous" title="Permalink to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="shortfall.html">DIII-D L-mode shortfall</a></li>
diff --git a/docs/neo.html b/docs/neo.html
index 09b2ae3..ac64926 100644
--- a/docs/neo.html
+++ b/docs/neo.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>
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@@ -90,8 +92,8 @@
         <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>NEO</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">NEO</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/neo.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -102,9 +104,9 @@
            <div itemprop="articleBody">
              
   <section id="neo">
-<h1>NEO<a class="headerlink" href="#neo" title="Permalink to this headline"></a></h1>
+<h1>NEO<a class="headerlink" href="#neo" title="Permalink to this heading"></a></h1>
 <section id="quick-links">
-<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this headline"></a></h2>
+<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this heading"></a></h2>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="neo/neo_table.html">Parameters for input.neo</a></li>
@@ -116,7 +118,7 @@ <h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to thi
 <p>The equations solved in NEO complement those solved in gyrokinetic codes such as GYRO and CGYRO insofar as together they represent the complete first-order deviation of the plasma from a local Maxwellian.</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>
 <p>The primary NEO input file is <a class="reference internal" href="neo/neo_table.html"><span class="doc">input.neo</span></a>.  Profile data can be optionally captured from  <a class="reference internal" href="input_gacode.html"><span class="doc">input.gacode</span></a>.</p>
 <p>NEO can also be run using a subroutine interface. In this case, inputs and outputs are contained in a monolithic module file named neo_interface. The interface parameter name is formed by prepending neo_ and appending _in to the name of the corresponding input.neo parameter.</p>
 <div class="highlight-fortran notranslate"><div class="highlight"><pre><span></span><span class="k">use </span><span class="n">neo_interface</span>
@@ -128,11 +130,11 @@ <h2>Data input<a class="headerlink" href="#data-input" title="Permalink to this
 </div>
 </section>
 <section id="data-output">
-<h2>Data output<a class="headerlink" href="#data-output" title="Permalink to this headline"></a></h2>
+<h2>Data output<a class="headerlink" href="#data-output" title="Permalink to this heading"></a></h2>
 <p>A description of the NEO output files and output subroutine parameters is <a class="reference internal" href="neo/outputs.html"><span class="doc">here</span></a>.</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>
 <p>When run in local profile mode, the NEO normalizing length <span class="math notranslate nohighlight">\(a\)</span>, normalizing mass <span class="math notranslate nohighlight">\(m_{\rm norm}\)</span>, normalizing density <span class="math notranslate nohighlight">\(n_{\rm norm}\)</span>, normalizing temperature <span class="math notranslate nohighlight">\(T_{\rm norm}\)</span>, and normalizing velocity <span class="math notranslate nohighlight">\({\rm v}_{\rm norm} = \sqrt{T_{\rm norm}/m_{\rm norm}}\)</span> are arbitrary, since the input.neo parameters are set with respect to these and the output parameters are defined with respect to these. For experimental profiles, the normalizations are set as follows:</p>
 <table class="colwidths-given docutils align-default">
 <colgroup>
diff --git a/docs/neo/neo_list.html b/docs/neo/neo_list.html
index 572e97c..a667579 100644
--- a/docs/neo/neo_list.html
+++ b/docs/neo/neo_list.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>
@@ -162,9 +164,9 @@
         <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><a href="../neo.html">NEO</a> &raquo;</li>
-      <li>Alphabetical list for input.neo</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../neo.html">NEO</a></li>
+      <li class="breadcrumb-item active">Alphabetical list for input.neo</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/neo/neo_list.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -175,9 +177,9 @@
            <div itemprop="articleBody">
              
   <section id="alphabetical-list-for-input-neo">
-<h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-list-for-input-neo" title="Permalink to this headline"></a></h1>
+<h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-list-for-input-neo" title="Permalink to this heading"></a></h1>
 <section id="aniso-model">
-<span id="neo-aniso-model"></span><h2>ANISO_MODEL_*<a class="headerlink" href="#aniso-model" title="Permalink to this headline"></a></h2>
+<span id="neo-aniso-model"></span><h2>ANISO_MODEL_*<a class="headerlink" href="#aniso-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to treat a species with an anisotropic temperature model.</p>
 <p><strong>Choices</strong></p>
@@ -201,7 +203,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="beta-star">
-<span id="neo-beta-star"></span><h2>BETA_STAR<a class="headerlink" href="#beta-star" title="Permalink to this headline"></a></h2>
+<span id="neo-beta-star"></span><h2>BETA_STAR<a class="headerlink" href="#beta-star" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized effective pressure gradient:</p>
 <div class="math notranslate nohighlight">
@@ -217,7 +219,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="btccw">
-<span id="neo-btccw"></span><h2>BTCCW<a class="headerlink" href="#btccw" title="Permalink to this headline"></a></h2>
+<span id="neo-btccw"></span><h2>BTCCW<a class="headerlink" href="#btccw" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the orientation of the toroidal magnetic field <span class="math notranslate nohighlight">\(B_t\)</span> relative to the toroidal angle <span class="math notranslate nohighlight">\(\varphi\)</span>.</p>
 <p><strong>Choices</strong></p>
@@ -234,7 +236,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="collision-model">
-<span id="neo-collision-model"></span><h2>COLLISION_MODEL<a class="headerlink" href="#collision-model" title="Permalink to this headline"></a></h2>
+<span id="neo-collision-model"></span><h2>COLLISION_MODEL<a class="headerlink" href="#collision-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the collision operator model.</p>
 <p><strong>Choices</strong></p>
@@ -252,7 +254,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="delta">
-<span id="neo-delta"></span><h2>DELTA<a class="headerlink" href="#delta" title="Permalink to this headline"></a></h2>
+<span id="neo-delta"></span><h2>DELTA<a class="headerlink" href="#delta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Average triangularity, <span class="math notranslate nohighlight">\(\delta\)</span>, of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -267,7 +269,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dens">
-<span id="neo-dens"></span><h2>DENS_*<a class="headerlink" href="#dens" title="Permalink to this headline"></a></h2>
+<span id="neo-dens"></span><h2>DENS_*<a class="headerlink" href="#dens" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale density:</p>
 <div class="math notranslate nohighlight">
@@ -283,7 +285,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dlnndr">
-<span id="neo-dlnndr"></span><h2>DLNNDR_*<a class="headerlink" href="#dlnndr" title="Permalink to this headline"></a></h2>
+<span id="neo-dlnndr"></span><h2>DLNNDR_*<a class="headerlink" href="#dlnndr" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale density gradient scale length:</p>
 <div class="math notranslate nohighlight">
@@ -299,7 +301,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dlnndre-ade">
-<span id="neo-dlnndre-ade"></span><h2>DLNNDRE_ADE<a class="headerlink" href="#dlnndre-ade" title="Permalink to this headline"></a></h2>
+<span id="neo-dlnndre-ade"></span><h2>DLNNDRE_ADE<a class="headerlink" href="#dlnndre-ade" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale density gradient scale length of the electrons for the case of adiabatic electrons:</p>
 <div class="math notranslate nohighlight">
@@ -314,7 +316,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dlntdr">
-<span id="neo-dlntdr"></span><h2>DLNTDR_*<a class="headerlink" href="#dlntdr" title="Permalink to this headline"></a></h2>
+<span id="neo-dlntdr"></span><h2>DLNTDR_*<a class="headerlink" href="#dlntdr" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale temperature gradient scale length:</p>
 <div class="math notranslate nohighlight">
@@ -329,7 +331,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dlntdr-para">
-<span id="neo-dlntdr-para"></span><h2>DLNTDR_PARA_*<a class="headerlink" href="#dlntdr-para" title="Permalink to this headline"></a></h2>
+<span id="neo-dlntdr-para"></span><h2>DLNTDR_PARA_*<a class="headerlink" href="#dlntdr-para" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale parallel temperature gradient scale length:</p>
 <div class="math notranslate nohighlight">
@@ -344,7 +346,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dlntdr-perp">
-<span id="neo-dlntdr-perp"></span><h2>DLNTDR_PERP_*<a class="headerlink" href="#dlntdr-perp" title="Permalink to this headline"></a></h2>
+<span id="neo-dlntdr-perp"></span><h2>DLNTDR_PERP_*<a class="headerlink" href="#dlntdr-perp" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale perpendicular temperature gradient scale length:</p>
 <div class="math notranslate nohighlight">
@@ -359,7 +361,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dlntdre-ade">
-<span id="neo-dlntdre-ade"></span><h2>DLNTDRE_ADE<a class="headerlink" href="#dlntdre-ade" title="Permalink to this headline"></a></h2>
+<span id="neo-dlntdre-ade"></span><h2>DLNTDRE_ADE<a class="headerlink" href="#dlntdre-ade" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale temperature gradient scale length of the electrons for the case of adiabatic electrons:</p>
 <div class="math notranslate nohighlight">
@@ -374,7 +376,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="dphi0dr">
-<span id="neo-dphi0dr"></span><h2>DPHI0DR<a class="headerlink" href="#dphi0dr" title="Permalink to this headline"></a></h2>
+<span id="neo-dphi0dr"></span><h2>DPHI0DR<a class="headerlink" href="#dphi0dr" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale radial electric field:</p>
 <div class="math notranslate nohighlight">
@@ -391,7 +393,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="epar0">
-<span id="neo-epar0"></span><h2>EPAR0<a class="headerlink" href="#epar0" title="Permalink to this headline"></a></h2>
+<span id="neo-epar0"></span><h2>EPAR0<a class="headerlink" href="#epar0" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale inductive electric field:</p>
 <div class="math notranslate nohighlight">
@@ -410,7 +412,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="epar0-spitzer">
-<span id="neo-epar0-spitzer"></span><h2>EPAR0_SPITZER<a class="headerlink" href="#epar0-spitzer" title="Permalink to this headline"></a></h2>
+<span id="neo-epar0-spitzer"></span><h2>EPAR0_SPITZER<a class="headerlink" href="#epar0-spitzer" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale inductive electric field for use in the Spitzer problem:</p>
 <div class="math notranslate nohighlight">
@@ -424,7 +426,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="equilibrium-model">
-<span id="neo-equilibrium-model"></span><h2>EQUILIBRIUM_MODEL<a class="headerlink" href="#equilibrium-model" title="Permalink to this headline"></a></h2>
+<span id="neo-equilibrium-model"></span><h2>EQUILIBRIUM_MODEL<a class="headerlink" href="#equilibrium-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the geometric equilibrium model.</p>
 <p><strong>Choices</strong></p>
@@ -444,7 +446,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="geo-ny">
-<span id="neo-geo-ny"></span><h2>GEO_NY<a class="headerlink" href="#geo-ny" title="Permalink to this headline"></a></h2>
+<span id="neo-geo-ny"></span><h2>GEO_NY<a class="headerlink" href="#geo-ny" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of Fourier coefficients for general Grad-Shafranov equilibrium.</p>
 <p><strong>Comments</strong></p>
@@ -457,7 +459,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="geo-yin">
-<span id="neo-geo-yin"></span><h2>GEO_YIN<a class="headerlink" href="#geo-yin" title="Permalink to this headline"></a></h2>
+<span id="neo-geo-yin"></span><h2>GEO_YIN<a class="headerlink" href="#geo-yin" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Array of dimension (8,0:32) with the normalized Fourier coefficients <span class="math notranslate nohighlight">\(\{a\_R,b\_R,a\_Z,b\_Z\}/a\)</span> and their radial derivatives <span class="math notranslate nohighlight">\(\{a\_Rp,b\_Rp,a\_Zp,b\_Zp\}\)</span> for general Grad-Shafranov equilibrium.</p>
 <p><strong>Comments</strong></p>
@@ -470,7 +472,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="ipccw">
-<span id="neo-ipccw"></span><h2>IPCCW<a class="headerlink" href="#ipccw" title="Permalink to this headline"></a></h2>
+<span id="neo-ipccw"></span><h2>IPCCW<a class="headerlink" href="#ipccw" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the orientation of the plasma current (and thus the poloidal magnetic field <span class="math notranslate nohighlight">\(B_p\)</span>) relative to the toroidal angle <span class="math notranslate nohighlight">\(\varphi\)</span>.</p>
 <p><strong>Choices</strong></p>
@@ -487,7 +489,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="kappa">
-<span id="neo-kappa"></span><h2>KAPPA<a class="headerlink" href="#kappa" title="Permalink to this headline"></a></h2>
+<span id="neo-kappa"></span><h2>KAPPA<a class="headerlink" href="#kappa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Elongation, <span class="math notranslate nohighlight">\(\kappa\)</span>, of the flux surface.</p>
 <p><strong>Comments</strong></p>
@@ -499,7 +501,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="mass">
-<span id="neo-mass"></span><h2>MASS_*<a class="headerlink" href="#mass" title="Permalink to this headline"></a></h2>
+<span id="neo-mass"></span><h2>MASS_*<a class="headerlink" href="#mass" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized mass:</p>
 <div class="math notranslate nohighlight">
@@ -514,7 +516,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="n-energy">
-<span id="neo-n-energy"></span><h2>N_ENERGY<a class="headerlink" href="#n-energy" title="Permalink to this headline"></a></h2>
+<span id="neo-n-energy"></span><h2>N_ENERGY<a class="headerlink" href="#n-energy" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The number of energy polynomials -  1 in the computational domain (<span class="math notranslate nohighlight">\(n_{\varepsilon,\rm total}\)</span> = N_ENERGY+1).</p>
 <p><strong>Comments</strong></p>
@@ -527,7 +529,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="n-radial">
-<span id="neo-n-radial"></span><h2>N_RADIAL<a class="headerlink" href="#n-radial" title="Permalink to this headline"></a></h2>
+<span id="neo-n-radial"></span><h2>N_RADIAL<a class="headerlink" href="#n-radial" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The number of radial gridpoints, <span class="math notranslate nohighlight">\(n_r\)</span> in the computational domain.</p>
 <p><strong>Comments</strong></p>
@@ -541,7 +543,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="n-species">
-<span id="neo-n-species"></span><h2>N_SPECIES<a class="headerlink" href="#n-species" title="Permalink to this headline"></a></h2>
+<span id="neo-n-species"></span><h2>N_SPECIES<a class="headerlink" href="#n-species" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The number of kinetic species.</p>
 <p><strong>Comments</strong></p>
@@ -567,7 +569,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="n-theta">
-<span id="neo-n-theta"></span><h2>N_THETA<a class="headerlink" href="#n-theta" title="Permalink to this headline"></a></h2>
+<span id="neo-n-theta"></span><h2>N_THETA<a class="headerlink" href="#n-theta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The number of theta gridpoints, <span class="math notranslate nohighlight">\(n_\theta\)</span> in the computational domain.</p>
 <p><strong>Comments</strong></p>
@@ -580,7 +582,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="n-xi">
-<span id="neo-n-xi"></span><h2>N_XI<a class="headerlink" href="#n-xi" title="Permalink to this headline"></a></h2>
+<span id="neo-n-xi"></span><h2>N_XI<a class="headerlink" href="#n-xi" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The number of xi polynomials -  1 in the computational domain (<span class="math notranslate nohighlight">\(n_{\xi,\rm total}\)</span> = N_XI+1).</p>
 <p><strong>Comments</strong></p>
@@ -593,7 +595,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="ne-ade">
-<span id="neo-ne-ade"></span><h2>NE_ADE<a class="headerlink" href="#ne-ade" title="Permalink to this headline"></a></h2>
+<span id="neo-ne-ade"></span><h2>NE_ADE<a class="headerlink" href="#ne-ade" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale density of the electrons for the case of adiabatic electrons:</p>
 <div class="math notranslate nohighlight">
@@ -607,7 +609,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="nu-1">
-<span id="neo-nu-1"></span><h2>NU_1<a class="headerlink" href="#nu-1" title="Permalink to this headline"></a></h2>
+<span id="neo-nu-1"></span><h2>NU_1<a class="headerlink" href="#nu-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized collision frequency of the first kinetic species:</p>
 <div class="math notranslate nohighlight">
@@ -625,7 +627,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="omega-rot">
-<span id="neo-omega-rot"></span><h2>OMEGA_ROT<a class="headerlink" href="#omega-rot" title="Permalink to this headline"></a></h2>
+<span id="neo-omega-rot"></span><h2>OMEGA_ROT<a class="headerlink" href="#omega-rot" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized toroidal angular frequency:</p>
 <div class="math notranslate nohighlight">
@@ -640,7 +642,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="omega-rot-deriv">
-<span id="neo-omega-rot-deriv"></span><h2>OMEGA_ROT_DERIV<a class="headerlink" href="#omega-rot-deriv" title="Permalink to this headline"></a></h2>
+<span id="neo-omega-rot-deriv"></span><h2>OMEGA_ROT_DERIV<a class="headerlink" href="#omega-rot-deriv" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized toroidal rotation shear:</p>
 <div class="math notranslate nohighlight">
@@ -655,7 +657,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="profile-dlnndr-scale">
-<span id="neo-profile-dlnndr-scale"></span><h2>PROFILE_DLNNDR_*_SCALE<a class="headerlink" href="#profile-dlnndr-scale" title="Permalink to this headline"></a></h2>
+<span id="neo-profile-dlnndr-scale"></span><h2>PROFILE_DLNNDR_*_SCALE<a class="headerlink" href="#profile-dlnndr-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Scaling factor for the normalized equilibrium-scale density gradient scale length in profile mode:</p>
 <div class="math notranslate nohighlight">
@@ -670,7 +672,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="profile-dlntdr-scale">
-<span id="neo-profile-dlntdr-scale"></span><h2>PROFILE_DLNTDR_*_SCALE<a class="headerlink" href="#profile-dlntdr-scale" title="Permalink to this headline"></a></h2>
+<span id="neo-profile-dlntdr-scale"></span><h2>PROFILE_DLNTDR_*_SCALE<a class="headerlink" href="#profile-dlntdr-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Scaling factor for the normalized equilibrium-scale temperature gradient scale length in profile mode:</p>
 <div class="math notranslate nohighlight">
@@ -685,7 +687,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="profile-equilibrium-model">
-<span id="neo-profile-equilibrium-model"></span><h2>PROFILE_EQUILIBRIUM_MODEL<a class="headerlink" href="#profile-equilibrium-model" title="Permalink to this headline"></a></h2>
+<span id="neo-profile-equilibrium-model"></span><h2>PROFILE_EQUILIBRIUM_MODEL<a class="headerlink" href="#profile-equilibrium-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects the geometric equilibrium model for experimental profiles.</p>
 <p><strong>Choices</strong></p>
@@ -702,7 +704,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="profile-erad0-model">
-<span id="neo-profile-erad0-model"></span><h2>PROFILE_ERAD0_MODEL<a class="headerlink" href="#profile-erad0-model" title="Permalink to this headline"></a></h2>
+<span id="neo-profile-erad0-model"></span><h2>PROFILE_ERAD0_MODEL<a class="headerlink" href="#profile-erad0-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to include <span class="math notranslate nohighlight">\(E_r^{(0)}\)</span> for experimental profiles.</p>
 <p><strong>Choices</strong></p>
@@ -719,7 +721,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="profile-model">
-<span id="neo-profile-model"></span><h2>PROFILE_MODEL<a class="headerlink" href="#profile-model" title="Permalink to this headline"></a></h2>
+<span id="neo-profile-model"></span><h2>PROFILE_MODEL<a class="headerlink" href="#profile-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects how the radial profile is defined.</p>
 <p><strong>Choices</strong></p>
@@ -748,7 +750,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="q">
-<span id="neo-q"></span><h2>Q<a class="headerlink" href="#q" title="Permalink to this headline"></a></h2>
+<span id="neo-q"></span><h2>Q<a class="headerlink" href="#q" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Magnitude of the safety factor, <span class="math notranslate nohighlight">\(|q|\)</span>, of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -762,7 +764,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="rho-star">
-<span id="neo-rho-star"></span><h2>RHO_STAR<a class="headerlink" href="#rho-star" title="Permalink to this headline"></a></h2>
+<span id="neo-rho-star"></span><h2>RHO_STAR<a class="headerlink" href="#rho-star" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio of the Larmor radius of the normalizing species to the normalizing length scale:</p>
 <div class="math notranslate nohighlight">
@@ -776,7 +778,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="rmaj-over-a">
-<span id="neo-rmaj-over-a"></span><h2>RMAJ_OVER_A<a class="headerlink" href="#rmaj-over-a" title="Permalink to this headline"></a></h2>
+<span id="neo-rmaj-over-a"></span><h2>RMAJ_OVER_A<a class="headerlink" href="#rmaj-over-a" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio of the flux-surface-center major radius, <span class="math notranslate nohighlight">\(R_0\)</span>, to the normalizing length scale:math:<cite>a</cite>.</p>
 <p><strong>Comments</strong></p>
@@ -787,7 +789,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="rmin-over-a">
-<span id="neo-rmin-over-a"></span><h2>RMIN_OVER_A<a class="headerlink" href="#rmin-over-a" title="Permalink to this headline"></a></h2>
+<span id="neo-rmin-over-a"></span><h2>RMIN_OVER_A<a class="headerlink" href="#rmin-over-a" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio of the midplane minor radius <span class="math notranslate nohighlight">\(r\)</span> to the normalizing length scale:math:<cite>a</cite>.</p>
 <p><strong>Comments</strong></p>
@@ -798,7 +800,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="rmin-over-a-2">
-<span id="neo-rmin-over-a-2"></span><h2>RMIN_OVER_A_2<a class="headerlink" href="#rmin-over-a-2" title="Permalink to this headline"></a></h2>
+<span id="neo-rmin-over-a-2"></span><h2>RMIN_OVER_A_2<a class="headerlink" href="#rmin-over-a-2" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio of the midplane minor radius <span class="math notranslate nohighlight">\(r\)</span> to the normalizing length scale:math:<cite>a</cite>.</p>
 <p><strong>Comments</strong></p>
@@ -810,7 +812,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="rotation-model">
-<span id="neo-rotation-model"></span><h2>ROTATION_MODEL<a class="headerlink" href="#rotation-model" title="Permalink to this headline"></a></h2>
+<span id="neo-rotation-model"></span><h2>ROTATION_MODEL<a class="headerlink" href="#rotation-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to solve the DKE in the diamagnetic ordering limit or in the sonic toroidal rotation ordering limit.</p>
 <p><strong>Choices</strong></p>
@@ -829,7 +831,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="s-delta">
-<span id="neo-s-delta"></span><h2>S_DELTA<a class="headerlink" href="#s-delta" title="Permalink to this headline"></a></h2>
+<span id="neo-s-delta"></span><h2>S_DELTA<a class="headerlink" href="#s-delta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the average triangularity of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -843,7 +845,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="s-kappa">
-<span id="neo-s-kappa"></span><h2>S_KAPPA<a class="headerlink" href="#s-kappa" title="Permalink to this headline"></a></h2>
+<span id="neo-s-kappa"></span><h2>S_KAPPA<a class="headerlink" href="#s-kappa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the elongation of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -857,7 +859,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="s-zeta">
-<span id="neo-s-zeta"></span><h2>S_ZETA<a class="headerlink" href="#s-zeta" title="Permalink to this headline"></a></h2>
+<span id="neo-s-zeta"></span><h2>S_ZETA<a class="headerlink" href="#s-zeta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the squareness of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -871,7 +873,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="s-zmag">
-<span id="neo-s-zmag"></span><h2>S_ZMAG<a class="headerlink" href="#s-zmag" title="Permalink to this headline"></a></h2>
+<span id="neo-s-zmag"></span><h2>S_ZMAG<a class="headerlink" href="#s-zmag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Measure of the rate of change of the elevation of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -885,7 +887,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shear">
-<span id="neo-shear"></span><h2>SHEAR<a class="headerlink" href="#shear" title="Permalink to this headline"></a></h2>
+<span id="neo-shear"></span><h2>SHEAR<a class="headerlink" href="#shear" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Magnetic shear, <span class="math notranslate nohighlight">\(s\)</span>, of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -900,7 +902,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shift">
-<span id="neo-shift"></span><h2>SHIFT<a class="headerlink" href="#shift" title="Permalink to this headline"></a></h2>
+<span id="neo-shift"></span><h2>SHIFT<a class="headerlink" href="#shift" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Shafranov shift, <span class="math notranslate nohighlight">\(\Delta\)</span>, of the flux surface:</p>
 <div class="math notranslate nohighlight">
@@ -914,7 +916,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-cos0">
-<span id="neo-shape-cos0"></span><h2>SHAPE_COS0<a class="headerlink" href="#shape-cos0" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-cos0"></span><h2>SHAPE_COS0<a class="headerlink" href="#shape-cos0" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>0th antisymmetric moment.</p>
 <ul class="simple">
@@ -923,7 +925,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos0">
-<span id="neo-shape-s-cos0"></span><h2>SHAPE_S_COS0<a class="headerlink" href="#shape-s-cos0" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-s-cos0"></span><h2>SHAPE_S_COS0<a class="headerlink" href="#shape-s-cos0" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>0th antisymmetric moment shear.</p>
 <ul class="simple">
@@ -932,7 +934,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-cos1">
-<span id="neo-shape-cos1"></span><h2>SHAPE_COS1<a class="headerlink" href="#shape-cos1" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-cos1"></span><h2>SHAPE_COS1<a class="headerlink" href="#shape-cos1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>1st antisymmetric moment.</p>
 <ul class="simple">
@@ -941,7 +943,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos1">
-<span id="neo-shape-s-cos1"></span><h2>SHAPE_S_COS1<a class="headerlink" href="#shape-s-cos1" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-s-cos1"></span><h2>SHAPE_S_COS1<a class="headerlink" href="#shape-s-cos1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>1th antisymmetric moment shear.</p>
 <ul class="simple">
@@ -950,7 +952,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-cos2">
-<span id="neo-shape-cos2"></span><h2>SHAPE_COS2<a class="headerlink" href="#shape-cos2" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-cos2"></span><h2>SHAPE_COS2<a class="headerlink" href="#shape-cos2" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>2nd antisymmetric moment.</p>
 <ul class="simple">
@@ -959,7 +961,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos2">
-<span id="neo-shape-s-cos2"></span><h2>SHAPE_S_COS2<a class="headerlink" href="#shape-s-cos2" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-s-cos2"></span><h2>SHAPE_S_COS2<a class="headerlink" href="#shape-s-cos2" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>2th antisymmetric moment shear.</p>
 <ul class="simple">
@@ -968,7 +970,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-cos3">
-<span id="neo-shape-cos3"></span><h2>SHAPE_COS3<a class="headerlink" href="#shape-cos3" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-cos3"></span><h2>SHAPE_COS3<a class="headerlink" href="#shape-cos3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd antisymmetric moment.</p>
 <ul class="simple">
@@ -977,7 +979,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-s-cos3">
-<span id="neo-shape-s-cos3"></span><h2>SHAPE_S_COS3<a class="headerlink" href="#shape-s-cos3" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-s-cos3"></span><h2>SHAPE_S_COS3<a class="headerlink" href="#shape-s-cos3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd antisymmetric moment.</p>
 <ul class="simple">
@@ -986,7 +988,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-sin3">
-<span id="neo-shape-sin3"></span><h2>SHAPE_SIN3<a class="headerlink" href="#shape-sin3" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-sin3"></span><h2>SHAPE_SIN3<a class="headerlink" href="#shape-sin3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd symmetric moment.</p>
 <ul class="simple">
@@ -995,7 +997,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="shape-s-sin3">
-<span id="neo-shape-s-sin3"></span><h2>SHAPE_S_SIN3<a class="headerlink" href="#shape-s-sin3" title="Permalink to this headline"></a></h2>
+<span id="neo-shape-s-sin3"></span><h2>SHAPE_S_SIN3<a class="headerlink" href="#shape-s-sin3" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>3rd symmetric moment shear.</p>
 <ul class="simple">
@@ -1004,7 +1006,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="silent-flag">
-<span id="neo-silent-flag"></span><h2>SILENT_FLAG<a class="headerlink" href="#silent-flag" title="Permalink to this headline"></a></h2>
+<span id="neo-silent-flag"></span><h2>SILENT_FLAG<a class="headerlink" href="#silent-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects how much data to print out.</p>
 <p><strong>Choices</strong></p>
@@ -1019,7 +1021,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="sim-model">
-<span id="neo-sim-model"></span><h2>SIM_MODEL<a class="headerlink" href="#sim-model" title="Permalink to this headline"></a></h2>
+<span id="neo-sim-model"></span><h2>SIM_MODEL<a class="headerlink" href="#sim-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to determine the neoclassical transport from analytic theory or from numerical solution of the DKE.</p>
 <p><strong>Choices</strong></p>
@@ -1037,7 +1039,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="spitzer-model">
-<span id="neo-spitzer-model"></span><h2>SPITZER_MODEL<a class="headerlink" href="#spitzer-model" title="Permalink to this headline"></a></h2>
+<span id="neo-spitzer-model"></span><h2>SPITZER_MODEL<a class="headerlink" href="#spitzer-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to solve the standard neoclassical transport problem or the Spitzer problem.</p>
 <p><strong>Choices</strong></p>
@@ -1055,7 +1057,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="te-ade">
-<span id="neo-te-ade"></span><h2>TE_ADE<a class="headerlink" href="#te-ade" title="Permalink to this headline"></a></h2>
+<span id="neo-te-ade"></span><h2>TE_ADE<a class="headerlink" href="#te-ade" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale temperature of the electrons for the case of adiabatic electrons:</p>
 <div class="math notranslate nohighlight">
@@ -1069,7 +1071,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="temp">
-<span id="neo-temp"></span><h2>TEMP_*<a class="headerlink" href="#temp" title="Permalink to this headline"></a></h2>
+<span id="neo-temp"></span><h2>TEMP_*<a class="headerlink" href="#temp" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale temperature:</p>
 <div class="math notranslate nohighlight">
@@ -1084,7 +1086,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="temp-para">
-<span id="neo-temp-para"></span><h2>TEMP_PARA_*<a class="headerlink" href="#temp-para" title="Permalink to this headline"></a></h2>
+<span id="neo-temp-para"></span><h2>TEMP_PARA_*<a class="headerlink" href="#temp-para" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale parallel temperature:</p>
 <div class="math notranslate nohighlight">
@@ -1099,7 +1101,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="temp-perp">
-<span id="neo-temp-perp"></span><h2>TEMP_PERP_*<a class="headerlink" href="#temp-perp" title="Permalink to this headline"></a></h2>
+<span id="neo-temp-perp"></span><h2>TEMP_PERP_*<a class="headerlink" href="#temp-perp" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale perpendicular temperature:</p>
 <div class="math notranslate nohighlight">
@@ -1114,7 +1116,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="threed-model">
-<span id="neo-threed-model"></span><h2>THREED_MODEL<a class="headerlink" href="#threed-model" title="Permalink to this headline"></a></h2>
+<span id="neo-threed-model"></span><h2>THREED_MODEL<a class="headerlink" href="#threed-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to solve the DKE in toroidally axisymmetric limit (2D) or with nonaxisymmetric effects (3D).</p>
 <p><strong>Choices</strong></p>
@@ -1136,7 +1138,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="threed-exb-model">
-<span id="neo-threed-exb-model"></span><h2>THREED_EXB_MODEL<a class="headerlink" href="#threed-exb-model" title="Permalink to this headline"></a></h2>
+<span id="neo-threed-exb-model"></span><h2>THREED_EXB_MODEL<a class="headerlink" href="#threed-exb-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter which selects whether to include the higher-order <span class="math notranslate nohighlight">\({\bf E} \times {\bf B}\)</span> drift velocity in the DKE with nonaxisymmetric effects (3D).</p>
 <p><strong>Choices</strong></p>
@@ -1156,7 +1158,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="threed-exb-dphi0dr">
-<span id="neo-threed-exb-dphi0dr"></span><h2>THREED_EXB_DPHI0DR<a class="headerlink" href="#threed-exb-dphi0dr" title="Permalink to this headline"></a></h2>
+<span id="neo-threed-exb-dphi0dr"></span><h2>THREED_EXB_DPHI0DR<a class="headerlink" href="#threed-exb-dphi0dr" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The normalized equilibrium-scale radial electric field in the higher-order <span class="math notranslate nohighlight">\({\bf E} \times {\bf B}\)</span> drift velocity:</p>
 <div class="math notranslate nohighlight">
@@ -1173,7 +1175,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="z">
-<span id="neo-z"></span><h2>Z_*<a class="headerlink" href="#z" title="Permalink to this headline"></a></h2>
+<span id="neo-z"></span><h2>Z_*<a class="headerlink" href="#z" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The species’ charge.</p>
 <p><strong>Commments</strong></p>
@@ -1185,7 +1187,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="zeta">
-<span id="neo-zeta"></span><h2>ZETA<a class="headerlink" href="#zeta" title="Permalink to this headline"></a></h2>
+<span id="neo-zeta"></span><h2>ZETA<a class="headerlink" href="#zeta" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Squareness, <span class="math notranslate nohighlight">\(\zeta\)</span>, of the flux surface.</p>
 <p><strong>Comments</strong></p>
@@ -1197,7 +1199,7 @@ <h1>Alphabetical list for input.neo<a class="headerlink" href="#alphabetical-lis
 <hr class="docutils" />
 </section>
 <section id="zmag-over-a">
-<span id="neo-zmag-over-a"></span><h2>ZMAG_OVER_A<a class="headerlink" href="#zmag-over-a" title="Permalink to this headline"></a></h2>
+<span id="neo-zmag-over-a"></span><h2>ZMAG_OVER_A<a class="headerlink" href="#zmag-over-a" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>The ratio of the elevation of the flux surface, <span class="math notranslate nohighlight">\(Z_0\)</span>, to the normalizing length scale <span class="math notranslate nohighlight">\(a\)</span>.</p>
 <p><strong>Comments</strong></p>
diff --git a/docs/neo/neo_table.html b/docs/neo/neo_table.html
index b24b713..f73978a 100644
--- a/docs/neo/neo_table.html
+++ b/docs/neo/neo_table.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>
@@ -93,9 +95,9 @@
         <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><a href="../neo.html">NEO</a> &raquo;</li>
-      <li>Parameters for input.neo</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../neo.html">NEO</a></li>
+      <li class="breadcrumb-item active">Parameters for input.neo</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/neo/neo_table.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -106,7 +108,7 @@
            <div itemprop="articleBody">
              
   <section id="parameters-for-input-neo">
-<h1>Parameters for input.neo<a class="headerlink" href="#parameters-for-input-neo" title="Permalink to this headline"></a></h1>
+<h1>Parameters for input.neo<a class="headerlink" href="#parameters-for-input-neo" title="Permalink to this heading"></a></h1>
 <p>Some features of <strong>input.neo</strong> to note:</p>
 <ul class="simple">
 <li><p>Parameters not specified in input.neo are filled in by default. Default values are shown in the parameter definitions.</p></li>
@@ -460,7 +462,7 @@ <h1>Parameters for input.neo<a class="headerlink" href="#parameters-for-input-ne
 </tbody>
 </table>
 <section id="extra-subroutine-interface-parameters">
-<h2>Extra subroutine interface parameters<a class="headerlink" href="#extra-subroutine-interface-parameters" title="Permalink to this headline"></a></h2>
+<h2>Extra subroutine interface parameters<a class="headerlink" href="#extra-subroutine-interface-parameters" title="Permalink to this heading"></a></h2>
 <p>These parameters are available only via the subroutine interface, i.e. not in <strong>input.neo</strong>.</p>
 <table class="colwidths-given docutils align-default">
 <colgroup>
diff --git a/docs/neo/outputs.html b/docs/neo/outputs.html
index a2e3c3b..ea5316d 100644
--- a/docs/neo/outputs.html
+++ b/docs/neo/outputs.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>
@@ -97,9 +99,9 @@
         <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><a href="../neo.html">NEO</a> &raquo;</li>
-      <li>NEO Output Files</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../neo.html">NEO</a></li>
+      <li class="breadcrumb-item active">NEO Output Files</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/neo/outputs.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -110,11 +112,11 @@
            <div itemprop="articleBody">
              
   <section id="neo-output-files">
-<h1>NEO Output Files<a class="headerlink" href="#neo-output-files" title="Permalink to this headline"></a></h1>
+<h1>NEO Output Files<a class="headerlink" href="#neo-output-files" title="Permalink to this heading"></a></h1>
 <p>NEO output files are produced only if <a class="reference internal" href="neo_list.html#neo-silent-flag"><span class="std std-ref">SILENT_FLAG</span></a> = 0.</p>
 <p>All NEO runtime information is written to out.neo.run.</p>
 <section id="standard-output-files">
-<h2>Standard output files<a class="headerlink" href="#standard-output-files" title="Permalink to this headline"></a></h2>
+<h2>Standard output files<a class="headerlink" href="#standard-output-files" title="Permalink to this heading"></a></h2>
 <table class="colwidths-given docutils align-default">
 <colgroup>
 <col style="width: 40%" />
@@ -163,7 +165,7 @@ <h2>Standard output files<a class="headerlink" href="#standard-output-files" tit
 </table>
 </section>
 <section id="experimental-profiles-output-files">
-<h2>Experimental profiles output files<a class="headerlink" href="#experimental-profiles-output-files" title="Permalink to this headline"></a></h2>
+<h2>Experimental profiles output files<a class="headerlink" href="#experimental-profiles-output-files" title="Permalink to this heading"></a></h2>
 <p>Produced only if <a class="reference internal" href="neo_list.html#neo-profile-model"><span class="std std-ref">PROFILE_MODEL</span></a> = 2.</p>
 <table class="colwidths-given docutils align-default">
 <colgroup>
@@ -186,7 +188,7 @@ <h2>Experimental profiles output files<a class="headerlink" href="#experimental-
 </table>
 </section>
 <section id="rotation-output-files">
-<h2>Rotation output files<a class="headerlink" href="#rotation-output-files" title="Permalink to this headline"></a></h2>
+<h2>Rotation output files<a class="headerlink" href="#rotation-output-files" title="Permalink to this heading"></a></h2>
 <p>Produced only if <a class="reference internal" href="neo_list.html#neo-rotation-model"><span class="std std-ref">ROTATION_MODEL</span></a> = 2.</p>
 <table class="colwidths-given docutils align-default">
 <colgroup>
@@ -206,7 +208,7 @@ <h2>Rotation output files<a class="headerlink" href="#rotation-output-files" tit
 </table>
 </section>
 <section id="subroutine-output">
-<h2>Subroutine output<a class="headerlink" href="#subroutine-output" title="Permalink to this headline"></a></h2>
+<h2>Subroutine output<a class="headerlink" href="#subroutine-output" title="Permalink to this heading"></a></h2>
 <p>When neo is run in subroutine mode, the outputs are contained in a monolithic file named neo_interface.  The NEO subroutine output parameters are as follows:</p>
 <table class="colwidths-given docutils align-default">
 <colgroup>
@@ -326,9 +328,9 @@ <h2>Subroutine output<a class="headerlink" href="#subroutine-output" title="Perm
 </section>
 <hr class="docutils" />
 <section id="detailed-description-of-neo-output-files">
-<h2>Detailed description of NEO output files<a class="headerlink" href="#detailed-description-of-neo-output-files" title="Permalink to this headline"></a></h2>
+<h2>Detailed description of NEO output files<a class="headerlink" href="#detailed-description-of-neo-output-files" title="Permalink to this heading"></a></h2>
 <section id="out-neo-equil">
-<span id="neo-out-neo-equil"></span><h3>out.neo.equil<a class="headerlink" href="#out-neo-equil" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-equil"></span><h3>out.neo.equil<a class="headerlink" href="#out-neo-equil" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Equilibrium/geometry input data</p>
 <p><strong>Format</strong></p>
@@ -357,7 +359,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-exp-norm">
-<span id="neo-out-neo-exp-norm"></span><h3>out.neo.exp_norm<a class="headerlink" href="#out-neo-exp-norm" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-exp-norm"></span><h3>out.neo.exp_norm<a class="headerlink" href="#out-neo-exp-norm" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Normalizing experimental parameters (in units)</p>
 <p><strong>Format</strong></p>
@@ -378,7 +380,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-f">
-<span id="neo-out-neo-f"></span><h3>out.neo.f<a class="headerlink" href="#out-neo-f" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-f"></span><h3>out.neo.f<a class="headerlink" href="#out-neo-f" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>First-order distribution function solution (dimensionless), specifically vector of <span class="math notranslate nohighlight">\(\hat{g}_{a,ie,ix,it}\)</span> (first-order non-adiabatic distribution function for each species <span class="math notranslate nohighlight">\(a\)</span>), where</p>
 <div class="math notranslate nohighlight">
@@ -392,7 +394,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-grid">
-<span id="neo-out-neo-grid"></span><h3>out.neo.grid<a class="headerlink" href="#out-neo-grid" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-grid"></span><h3>out.neo.grid<a class="headerlink" href="#out-neo-grid" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Numerical grid parameters</p>
 <p><strong>Format</strong></p>
@@ -412,7 +414,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-phi">
-<span id="neo-out-neo-phi"></span><h3>out.neo.phi<a class="headerlink" href="#out-neo-phi" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-phi"></span><h3>out.neo.phi<a class="headerlink" href="#out-neo-phi" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical first-order electrostatic potential (normalized) vs. <span class="math notranslate nohighlight">\(\theta\)</span></p>
 <p><strong>Format</strong></p>
@@ -427,7 +429,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-rotation">
-<span id="neo-out-neo-rotation"></span><h3>out.neo.rotation<a class="headerlink" href="#out-neo-rotation" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-rotation"></span><h3>out.neo.rotation<a class="headerlink" href="#out-neo-rotation" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Strong rotation poloidal asymmetry parameters (normalized)</p>
 <p>Define:</p>
@@ -467,7 +469,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-theory">
-<span id="neo-out-neo-theory"></span><h3>out.neo.theory<a class="headerlink" href="#out-neo-theory" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-theory"></span><h3>out.neo.theory<a class="headerlink" href="#out-neo-theory" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical transport coefficients from analytic theory (normalized)</p>
 <ul class="simple">
@@ -520,7 +522,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-theory-nclass">
-<span id="neo-out-neo-theory-nclass"></span><h3>out.neo.theory_nclass<a class="headerlink" href="#out-neo-theory-nclass" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-theory-nclass"></span><h3>out.neo.theory_nclass<a class="headerlink" href="#out-neo-theory-nclass" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical transport coefficients from the NCLASS code (normalized)</p>
 <ul class="simple">
@@ -549,7 +551,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-transport">
-<span id="neo-out-neo-transport"></span><h3>out.neo.transport<a class="headerlink" href="#out-neo-transport" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-transport"></span><h3>out.neo.transport<a class="headerlink" href="#out-neo-transport" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical transport coefficients from DKE solve (normalized)</p>
 <p><strong>Format</strong></p>
@@ -579,7 +581,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-transport-exp">
-<span id="neo-out-neo-transport-exp"></span><h3>out.neo.transport_exp<a class="headerlink" href="#out-neo-transport-exp" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-transport-exp"></span><h3>out.neo.transport_exp<a class="headerlink" href="#out-neo-transport-exp" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical transport coefficients from DKE solve (in units)</p>
 <p><strong>Format</strong></p>
@@ -609,7 +611,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-transport-flux">
-<span id="neo-out-neo-transport-flux"></span><h3>out.neo.transport_flux<a class="headerlink" href="#out-neo-transport-flux" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-transport-flux"></span><h3>out.neo.transport_flux<a class="headerlink" href="#out-neo-transport-flux" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical fluxes in GB units from DKE solve</p>
 <p>Define:</p>
@@ -640,7 +642,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-transport-gv">
-<span id="neo-out-neo-transport-gv"></span><h3>out.neo.transport_gv<a class="headerlink" href="#out-neo-transport-gv" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-transport-gv"></span><h3>out.neo.transport_gv<a class="headerlink" href="#out-neo-transport-gv" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Neoclassical fluxes from gyroviscosity (normalized)</p>
 <ul class="simple">
@@ -666,7 +668,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-vel">
-<span id="neo-out-neo-vel"></span><h3>out.neo.vel<a class="headerlink" href="#out-neo-vel" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-vel"></span><h3>out.neo.vel<a class="headerlink" href="#out-neo-vel" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Poloidal variation of first-order flows (normalized)</p>
 <p><strong>Format</strong></p>
@@ -682,7 +684,7 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 <hr class="docutils" />
 </section>
 <section id="out-neo-vel-fourier">
-<span id="neo-out-neo-vel-fourier"></span><h3>out.neo.vel_fourier<a class="headerlink" href="#out-neo-vel-fourier" title="Permalink to this headline"></a></h3>
+<span id="neo-out-neo-vel-fourier"></span><h3>out.neo.vel_fourier<a class="headerlink" href="#out-neo-vel-fourier" title="Permalink to this heading"></a></h3>
 <p><strong>Description</strong></p>
 <p>Poloidal variation of first-order flows (normalized) in Fourier series components</p>
 <div class="math notranslate nohighlight">
diff --git a/docs/prgen.html b/docs/prgen.html
index 8aafb65..48b4069 100644
--- a/docs/prgen.html
+++ b/docs/prgen.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" />
@@ -81,8 +83,8 @@
         <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>profiles_gen</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">profiles_gen</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/prgen.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -93,9 +95,9 @@
            <div itemprop="articleBody">
              
   <section id="profiles-gen">
-<h1>profiles_gen<a class="headerlink" href="#profiles-gen" title="Permalink to this headline"></a></h1>
+<h1>profiles_gen<a class="headerlink" href="#profiles-gen" title="Permalink to this heading"></a></h1>
 <section id="history-and-overview">
-<h2>History and Overview<a class="headerlink" href="#history-and-overview" title="Permalink to this headline"></a></h2>
+<h2>History and Overview<a class="headerlink" href="#history-and-overview" title="Permalink to this heading"></a></h2>
 <p>[DRAFT]</p>
 <p>The initial motivation for profiles_gen (circa 2005) was to separate the source code required to read and process ONETWO profile data from the main GYRO code base. The rationale was that reading plasma profile and geometry data to calculate suitable inputs for gyrokinetic simulation was not the job of a gyrokinetic code. In the early days, global gyrokinetic simulation was done with artificial/model profiles, and only GYRO was attempting to use bonafide experimental inputs. So in the summer of 2005 it was decided to split the GYRO experimental profile handling into a new tool called iterdb_read. This morphed into the tool iterdb2gyro, which finally became profiles_gen in 2010. The conceptual motivation for profiles_gen was to provide a barrier between the challenges of experimental profile data formats and the standard (typically dimensionless) inputs for gyrokinetic (GYRO) and neoclassical (NEO) simulation. Also, in the pre-2010 period, it became clear that there was a need to standardize and improve geometry input, as ONETWO geometry data was of limited quality. This led to the idea of separating the profile date (typically from ONETWO or TRANSP) from the equilibrium shape data (from EFIT). By 2009 (?), the ability to specify both a “profile statefile” and an EFIT “gfile” was established. The output from profiles_gen creates a unique form for use with the other GACODE transport codes.</p>
 </section>
diff --git a/docs/rotation.html b/docs/rotation.html
index 37f3702..bf6b062 100644
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@@ -16,7 +16,9 @@
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@@ -88,8 +90,8 @@
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   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>PLASMA ROTATION</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
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@@ -100,27 +102,27 @@
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   <section id="plasma-rotation">
-<h1>PLASMA ROTATION<a class="headerlink" href="#plasma-rotation" title="Permalink to this headline"></a></h1>
+<h1>PLASMA ROTATION<a class="headerlink" href="#plasma-rotation" title="Permalink to this heading"></a></h1>
 <section id="physical-considerations">
-<h2>Physical considerations<a class="headerlink" href="#physical-considerations" title="Permalink to this headline"></a></h2>
+<h2>Physical considerations<a class="headerlink" href="#physical-considerations" title="Permalink to this heading"></a></h2>
 <p>Sonic rotation can arise in tokamaks from torque due to neutral beam injection.  It is believed to play an important role in the suppression of turbulence and the formation of transport barriers through <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shear.  In addition, it produces a strong centrifugal force that pushes ions toroidally outward, causing them to redistribute nonuniformly around a flux surface.  As a result of quasi-neutrality, a poloidally-varying electrostatic potential is generated by the electrons to balance the density asymmetry.  This generates <strong>centrifugal drifts</strong> in addition to the usual <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> rotation, Coriolis drift, and parallel velocity shear. Because of their complexity, these centrifugal effects, which are second-order in the main ion Mach number, are ignored in most neoclassical and gyrokinetic codes.  Inclusion of full sonic rotation effects is particularly critical for studying transport of heavy impurities <span id="id1">[<a class="reference internal" href="zreferences.html#id13" title="E.A. Belli and J. Candy. Kinetic calculation of neoclassical transport including self-consistent electron and impurity dynamics. Plasma Phys. Control. Fusion, 50:095010, 2008. doi:10.1088/0741-3335/50/9/095010.">BC08</a>]</span>, as the influence of the centrifugal force is amplified by their large mass.</p>
 </section>
 <section id="sonic-rotation-formalism">
-<h2>Sonic rotation formalism<a class="headerlink" href="#sonic-rotation-formalism" title="Permalink to this headline"></a></h2>
+<h2>Sonic rotation formalism<a class="headerlink" href="#sonic-rotation-formalism" title="Permalink to this heading"></a></h2>
 <p>The rigorous derivation of the gyrokinetic equations for sonic rotation was carried out by Sugama <span id="id2">[<a class="reference internal" href="zreferences.html#id104" title="H. Sugama and W. Horton. Nonlinear electromagnetic gyrokinetic equation for plasmas with large mean flows. Phys. Plasmas, 5:2560, 1998.">SH98</a>]</span>.  Sugama followed the underlying rotation formulation of Hinton and Wong <span id="id3">[<a class="reference internal" href="zreferences.html#id58" title="F.L. Hinton and S.K. Wong. Neoclassical ion transport in rotating axisymmetric plasmas. Phys. Fluids, 28:3082, 1985. doi:10.1063/1.865350.">HW85</a>]</span>, who showed that in an axisymmetric system the zeroth-order flow velocity is</p>
 <div class="math notranslate nohighlight">
 \[\mathbf{U}_0 = \omega_0(\psi) R^2 \nabla \varphi \; .\]</div>
 <p>It is this scalar flux-function, <span class="math notranslate nohighlight">\(\omega_0\)</span>, that is the true free (input) function in both neoclassical and gyrokinetic theory.  Here, <span class="math notranslate nohighlight">\(\psi\)</span> is the poloidal flux.</p>
 </section>
 <section id="the-rotation-profile">
-<h2>The rotation profile<a class="headerlink" href="#the-rotation-profile" title="Permalink to this headline"></a></h2>
+<h2>The rotation profile<a class="headerlink" href="#the-rotation-profile" title="Permalink to this heading"></a></h2>
 <p>The relevant profile that gives a <em>complete specification of rotation</em> is the angular frequency <span class="math notranslate nohighlight">\(\omega_0(r)\)</span>, which in defined consistently throughout GACODE as</p>
 <div class="math notranslate nohighlight">
 \[\omega_0(r) \longrightarrow \frac{c E_r }{R B_p} \; .\]</div>
 <p>Thus, if the <span class="math notranslate nohighlight">\(E_r\)</span> is known from a priori analysis (say, through velocity measurements and force balance), then <span class="math notranslate nohighlight">\(\omega_0\)</span> is given by the formula above.  This equality is subtle (hence the reason for the arrow rather than an equality) and is clarified in detail in the last section.</p>
 </section>
 <section id="input-parameters">
-<h2>Input parameters<a class="headerlink" href="#input-parameters" title="Permalink to this headline"></a></h2>
+<h2>Input parameters<a class="headerlink" href="#input-parameters" title="Permalink to this heading"></a></h2>
 <p>CGYRO and NEO implement <em>full sonic rotation</em> (GYRO implements only a reduced model) according to the formulation of Hinton and Wong <span id="id4">[<a class="reference internal" href="zreferences.html#id58" title="F.L. Hinton and S.K. Wong. Neoclassical ion transport in rotating axisymmetric plasmas. Phys. Fluids, 28:3082, 1985. doi:10.1063/1.865350.">HW85</a>]</span>.  Neoclassically, the induced poloidally-varying electrostatic potential leads to the formation of potential wells.  In the banana regime these increase the effective trapped particle fraction, and in the Pfirsh-Schlüter regime increase the effective toroidal curvature.  In both instances, this may lead to enhanced neoclassical transport.  The code inputs are given in the tables below.</p>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
@@ -178,7 +180,7 @@ <h2>Input parameters<a class="headerlink" href="#input-parameters" title="Permal
 </table>
 </section>
 <section id="theoretical-basis-for-sonic-rotation">
-<h2>Theoretical basis for sonic rotation<a class="headerlink" href="#theoretical-basis-for-sonic-rotation" title="Permalink to this headline"></a></h2>
+<h2>Theoretical basis for sonic rotation<a class="headerlink" href="#theoretical-basis-for-sonic-rotation" title="Permalink to this heading"></a></h2>
 <p>In presence of rapid rotation, where the flow speed <span class="math notranslate nohighlight">\(U\)</span> is allowed to be of the order of the ion thermal speed, the Lorentz
 force term in the the Fokker-Planck equation (see <span id="id5">[<a class="reference internal" href="zreferences.html#id58" title="F.L. Hinton and S.K. Wong. Neoclassical ion transport in rotating axisymmetric plasmas. Phys. Fluids, 28:3082, 1985. doi:10.1063/1.865350.">HW85</a>]</span>)</p>
 <div class="math notranslate nohighlight">
@@ -205,7 +207,7 @@ <h2>Theoretical basis for sonic rotation<a class="headerlink" href="#theoretical
 <p>It is important to note that <span class="math notranslate nohighlight">\(\Phi_{-1}\)</span> is a <strong>flux function</strong>, whereas higher orders are not constant on a flux surface.</p>
 </section>
 <section id="connection-to-experimental-data">
-<h2>Connection to experimental data<a class="headerlink" href="#connection-to-experimental-data" title="Permalink to this headline"></a></h2>
+<h2>Connection to experimental data<a class="headerlink" href="#connection-to-experimental-data" title="Permalink to this heading"></a></h2>
 <p>We remark that <span class="math notranslate nohighlight">\(\omega_{0}\)</span> is a <strong>theoretical quantity</strong> that cannot be measured in the experiment.  This is similar
 to the observation that the experimentally-measured temperature <span class="math notranslate nohighlight">\(T_i\)</span> is really the sum of an <em>equilibrium temperature</em> and a small <em>fluctuating temperature</em> driven by turbulence: <span class="math notranslate nohighlight">\(T_i = T_{i0} + T_{i1}\)</span>.  If the drift ordering is valid, then we are justified in approximating the equilibrium temperature <span class="math notranslate nohighlight">\(T_{i0}\)</span> by the measured temperature <span class="math notranslate nohighlight">\(T_i\)</span>.
 For the rotation frequency, similar considerations hold.  We note that the theory shows that the potential always appears in the combination</p>
@@ -218,7 +220,7 @@ <h2>Connection to experimental data<a class="headerlink" href="#connection-to-ex
 Alternatively, in the diamagnetic rotation limit, we set <span class="math notranslate nohighlight">\(\omega_0 = 0\)</span> with the rotation contained in <span class="math notranslate nohighlight">\(\omega_1\)</span>.  The present theory works consistently in both cases.  Finally, the toroidal velocities <span class="math notranslate nohighlight">\(U_{\varphi,0} + U_{\varphi,1}\)</span> are treated in the same way.</p>
 </section>
 <section id="consistency-with-force-balance">
-<h2>Consistency with force balance<a class="headerlink" href="#consistency-with-force-balance" title="Permalink to this headline"></a></h2>
+<h2>Consistency with force balance<a class="headerlink" href="#consistency-with-force-balance" title="Permalink to this heading"></a></h2>
 <p>In experimental analyses the <em>radial force balance</em> relation is often used</p>
 <div class="math notranslate nohighlight">
 \[E_r = \frac{R B_p}{n_a z_a e} \frac{d p_a}{d\psi} + \frac{U_\varphi}{c} B_p - \frac{U_\theta}{c} B_t \; .\]</div>
diff --git a/docs/search.html b/docs/search.html
index 80279cd..3c855ff 100644
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@@ -78,8 +80,8 @@
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:16,particl:[7,13,18,22,24,26,28,29,31,32,34,39,42],particular:[13,19],particularli:[13,26],pascal:18,pass:[13,30,32,42],pass_grid:28,past:1,patholog:13,pattern:13,pci:13,peak:[13,30,42],pedest:[1,11,38,41],peebl:42,peeter:42,per:[13,31,32,38],perc:13,percent:13,pereverzev:42,perfect:16,perfectli:[13,30],perform:[13,16,28,39,41,42],perhap:27,period:[13,22,25],perlmutt:[17,41],perlmutter_gpu:27,permiss:19,permit:19,perp:[4,22],perpendicular:[16,22,23,41],persist:13,person:19,perturb:[4,13],petascal:42,petti:42,pfirsh:26,pg3eq:[13,16],ph:16,phase:[16,29,31,32,42],phenomena:[1,11,13],phenomenon:13,phi:[3,4,7,10,14,18,26,31,32],phi_0:[22,24,26],phi_1:[24,26],phi_:[22,24,26],phy:[16,24,42],physic:[2,7,9,13,16,28,30,39,41,42],physrevlett:42,pi:[4,10,18,22],pi_1:32,pi_2:32,pi_:[7,24,32],pi_a:[7,34],pi_e:32,pic:[13,16],pick:[3,6,30],pictur:13,pinch:[13,42],pinsker:42,pioneer:[1,11],pip:41,pitch:[4,5,22,24,28],pittsburgh:42,pivot:39,place:29,plai:[1,11,13,16,26,29],planck:[21,26,42],plank:22,plasma:[1,4,11,13,16,18,21,22,24,25,28,29,39,42],platform:[0,8,13,27,41],pleas:[12,18],plot:[8,16,17,28,41],plu:[5,8],pmac:13,pmatrix:38,point:[4,13,16,18,28,38,39],poisson:21,pol:10,polflux:18,poloid:[4,5,10,13,18,22,23,24,26,30,32,41,42],polynomi:[4,22,23,24,30,32],pop:30,popul:42,popular:[1,3,6,13,38],porkolab:42,port:13,portion:[9,19],posit:[4,10,22],possibl:[3,6,11,13,28,38],potenti:[4,13,22,24,26,30],power:[3,6,13,16,18,38,39,40],ppc:13,ppcf:24,pppl:41,practic:[13,21,26,34],pre:[11,25],precis:[4,5],predecessor:29,predict:[13,16,28,29,42],prefer:[30,38],prepend:21,prerequisit:17,presenc:[13,26],present:[9,12,13,16,17,19,22,24,26,41],preset:30,pressur:[1,4,5,11,18,22,23,30,32],prevent:[30,32],previou:[13,26],primari:[13,21,28,33],primarili:1,prime:[22,34,38],principl:13,print:[4,8,22],print_step:[2,5],prior:[13,16],priori:26,probabl:[13,39],problem:[3,4,13,22,23,38],proce:27,proceed:42,process:[3,6,25,39],produc:[13,24,26],product:[3,6,13,42],profil:[1,4,5,9,10,11,13,16,18,21,22,25,29,33,38,39,42],profile_dlnndr_1_scal:22,profile_dlnndr_2_scal:22,profile_dlnndr_3_scal:22,profile_dlnndr_:23,profile_dlntdr_1_scal:22,profile_dlntdr_2_scal:22,profile_dlntdr_3_scal:22,profile_dlntdr_:23,profile_equilibrium_model:[10,23],profile_erad0_model:23,profile_model:[5,23,24],profiles_gen:[2,17,18,41],profiles_gen_plot:41,program:13,progress:13,project:[0,4,13,21,27,42],pronounc:13,propag:16,proper:[10,19],properli:[10,13],properti:[4,42],provid:[1,3,6,11,13,19,25,28],pseudospectr:4,psfc:41,psi:[2,10,18,22,26,34],psi_:10,pst:41,ptot:18,publish:[9,13,16,19],pueschel:42,pull:[9,19],pure:[13,16,26],purg:27,purpos:[1,3,4,6,9,19],push:26,put:38,pygacod:41,python:[1,7,17],q:[2,5,10,13,18,23,24,26,30,32,34,38,42],q_1:32,q_2:32,q_:[7,13,24,32,37,38,39],q_a:[7,34],q_e:[16,32,37,38],q_i:[37,38],q_loc:32,q_prime_loc:32,q_sa:32,qa:[30,32],qbeam:[18,37],qbeami:[18,37],qbrem:[18,37],qcxi:[18,37],qei:[18,37],qfuse:[18,37],qfusi:[18,37],qhat:38,qion:[18,37],qioni:[18,37],ql:[29,31,32],ql_flux_spectrum:32,qline:[18,37],qmom:18,qohm:[18,37],qpar_beam:18,qpar_wal:18,qrfe:[18,37],qrfi:[18,37],qs:4,qsync:[18,37],quad:[26,34,38],quadratur:[30,32],qualit:28,qualiti:25,quantit:16,quantiti:[1,10,16,21,22,24,26,38],quasi:[22,26],quasilinear:[16,29,30,32],quasineutr:[2,4,5,39],quasineutral_flag:5,quench:[13,29,30,32,42],queri:0,question:[13,17,28],queue:8,quick:17,quit:13,r:[0,2,4,10,12,13,16,18,21,22,24,26,30,32,34,38,42],r_0:[4,10,18,22,24,26],r_1:38,r_2:38,r_3:38,r_:[30,32,38],r_j:[24,38],rad:[18,34,37],radial:[1,4,5,11,13,16,22,23,24,26,33,38,39,42],radian:18,radiat:[18,34,39],radii:[13,39],radiu:[1,2,4,5,10,13,16,18,21,22,23,24,29,30,32,39,42],ram:[3,6],rang:[13,16,21,22],rangl:[26,34],rank:[4,7,30,32],rapid:26,rapidli:[38,42],rate:[4,5,13,16,22,26,28,30,32,34],rather:[7,13,26,38,39],ratio:[4,13,21,22,24,29,39],ration:13,rational:25,raw:4,rb_:[30,32],rbf:28,rc:0,rc_:[30,32],re:22,reach:13,reaction:39,reactor:[37,39,42],read:[4,7,22,25,28,34,39],readabl:7,reader:11,real:[1,11,13,41],realist:[13,42],realiti:10,realli:[3,6,26],reason:[3,6,26],recent:[11,13,16,28,29,30],recipi:9,recombin:18,recommend:[2,3,4,6,7,30],rectangular:24,red:16,redistribut:26,reduc:[1,4,5,11,13,14,26,38],reduct:13,reed:42,ref:[22,38],refer:[4,13,17,19,24,28],refin:[13,30],reflect:10,refus:16,reg08:8,reg14:18,regardless:22,regim:[1,13,16,26],region:[1,11,13,29],regress:[0,8],regular:8,rel:[4,16,22,30],relat:[3,6,13,24,26,34],relax:[13,38,39,40],relev:[13,26,42],reliabl:13,remain:[13,30],remark:[16,26,29],renorm:39,repeatedli:13,repo:[8,27],report:[28,42],repositori:[0,17],repres:[13,21,26],represent:[10,34,42],reproduc:[11,13,16,30],repsect:30,request:[9,19],requir:[0,1,4,6,9,11,13,18,22,25,26,27,29,34,42],rescal:16,research:[1,11,13,16,28],reset:4,residu:[13,38,39,40],resolut:[4,22,39,41,42],resolv:[13,30],resourc:[3,6,13,16,28],respect:[4,21,22,26,30,32],respond:30,respons:[29,42],restart:[4,5,39,40,41],restart_step:5,restrict:[9,13,19,26,38],result:[3,4,6,8,9,11,13,17,19,26,29,30,38,42],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List","CGYRO Workshop 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\ No newline at end of file
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"quick-start-example"]], "Command-line usage": [[8, "command-line-usage"]], "Batch submission": [[8, "batch-submission"]], "Download and user agreement": [[9, "download-and-user-agreement"]], "Appropriate References": [[9, "id6"], [42, "id138"]], "Source code": [[9, "source-code"]], "Repository access": [[9, "repository-access"]], "FLUX-SURFACE GEOMETRY": [[10, "flux-surface-geometry"]], "Coordinates": [[10, "coordinates"]], "Bounding-box method": [[10, "bounding-box-method"]], "Effective field": [[10, "effective-field"]], "Equilibria": [[10, "equilibria"]], "Table of geometry parameters": [[10, "table-of-geometry-parameters"]], "Magnetic field orientation": [[10, "magnetic-field-orientation"]], "GYRO": [[11, "gyro"]], "Quick links": [[11, "quick-links"], [21, "quick-links"], [29, "quick-links"], [33, "quick-links"]], "Gallery of classic GYRO images (circa 2003)": [[12, "gallery-of-classic-gyro-images-circa-2003"]], "Gyrokinetic Simulation in the 2000s": [[13, "gyrokinetic-simulation-in-the-2000s"]], "Prehistory": [[13, "prehistory"]], "Design History": [[13, "design-history"]], "Yearly Publication Synopsis": [[13, "yearly-publication-synopsis"]], "2002": [[13, "id20"]], "2003": [[13, "id22"]], "2004": [[13, "id25"]], "2005": [[13, "id33"]], "2006": [[13, "id40"]], "2007": [[13, "id49"]], "2008": [[13, "id59"]], "2009": [[13, "id63"]], "A Computational Science and User Perspective": [[13, "a-computational-science-and-user-perspective"]], "Urban Legends": [[13, "urban-legends"]], "UL1: The local gyroBohm limit of global codes differs from local codes": [[13, "ul1-the-local-gyrobohm-limit-of-global-codes-differs-from-local-codes"]], "UL2: Full torus simulations are necessary to correctly compute the local transport": [[13, "ul2-full-torus-simulations-are-necessary-to-correctly-compute-the-local-transport"]], "UL3: Eulerian codes have inadequate velocity-space resolution": [[13, "ul3-eulerian-codes-have-inadequate-velocity-space-resolution"]], "UL4: The parallel nonlinearity can have a dramatic effect on the transport": [[13, "ul4-the-parallel-nonlinearity-can-have-a-dramatic-effect-on-the-transport"]], "Alphabetical list for input.gyro": [[14, "alphabetical-list-for-input-gyro"]], "AMP_PHI_N": [[14, "amp-phi-n"]], "Tabular list for input.gyro": [[15, "tabular-list-for-input-gyro"]], "GYRO verification and validation (pre 2010)": [[16, "gyro-verification-and-validation-pre-2010"]], "Verification Studies": [[16, "verification-studies"]], "Cyclone Base Case with Adiabatic Electrons (2001)": [[16, "cyclone-base-case-with-adiabatic-electrons-2001"]], "Local limit of Global Simulations (2004)": [[16, "local-limit-of-global-simulations-2004"]], "Gyrokinetic Simulation of Impurities (2004)": [[16, "gyrokinetic-simulation-of-impurities-2004"]], "Electron Temperature Gradient Turbulence (2006)": [[16, "electron-temperature-gradient-turbulence-2006"]], "Energetic particle transport coefficients (2009)": [[16, "energetic-particle-transport-coefficients-2009"]], "Compressional Electromagnetic Perturbations (2010)": [[16, "compressional-electromagnetic-perturbations-2010"]], "GYRO Validation Abstracts": [[16, "gyro-validation-abstracts"]], "Comparison of GYRO synthetic diagnostic results with DIII-D BES and CER data": [[16, "comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data"]], "Comparison of GYRO synthetic diagnostic results with C-Mod PCI data": [[16, "comparison-of-gyro-synthetic-diagnostic-results-with-c-mod-pci-data"]], "Comparison of GYRO simulations with fast-sweeping and Doppler reflectometer data in Tore Supra": [[16, "comparison-of-gyro-simulations-with-fast-sweeping-and-doppler-reflectometer-data-in-tore-supra"]], "Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation": [[16, "anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation"]], "The General Atomics GACODE Suite": [[17, "the-general-atomics-gacode-suite"]], "Running GACODE": [[17, "running-gacode"]], "Geometry": [[17, "geometry"]], "Plasma rotation": [[17, "plasma-rotation"]], "Experimental profiles": [[17, "experimental-profiles"]], "Software": [[17, null]], "Codes": [[17, null]], "Physics": [[17, null]], "input.gacode": [[18, "input-gacode"]], "File structure": [[18, "id3"]], "GACODE License": [[19, "gacode-license"]], "Miscellaneous": [[20, "miscellaneous"]], "NEO": [[21, "neo"]], "Data output": [[21, "data-output"]], "Alphabetical list for input.neo": [[22, "alphabetical-list-for-input-neo"]], "ANISO_MODEL_*": [[22, "aniso-model"]], "BETA_STAR": [[22, "beta-star"]], "DLNNDRE_ADE": [[22, "dlnndre-ade"]], "DLNTDR_PARA_*": [[22, "dlntdr-para"]], "DLNTDR_PERP_*": [[22, "dlntdr-perp"]], "DLNTDRE_ADE": [[22, "dlntdre-ade"]], "DPHI0DR": [[22, "dphi0dr"]], "EPAR0": [[22, "epar0"]], "EPAR0_SPITZER": [[22, "epar0-spitzer"]], "GEO_NY": [[22, "geo-ny"]], "GEO_YIN": [[22, "geo-yin"]], "NE_ADE": [[22, 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[[23, "id1"]], "Plasma equilibrium/geometry": [[23, "id2"]], "General models": [[23, "id3"]], "Profile models": [[23, "id4"]], "Nonaxisymmetric effects": [[23, "id6"]], "Species-dependent parameters": [[23, "id7"]], "Extra subroutine interface parameters": [[23, "extra-subroutine-interface-parameters"]], "NEO Output Files": [[24, "neo-output-files"]], "Standard output files": [[24, "standard-output-files"]], "Experimental profiles output files": [[24, "experimental-profiles-output-files"]], "Rotation output files": [[24, "rotation-output-files"]], "Subroutine output": [[24, "subroutine-output"]], "Detailed description of NEO output files": [[24, "detailed-description-of-neo-output-files"]], "out.neo.equil": [[24, "out-neo-equil"]], "out.neo.exp_norm": [[24, "out-neo-exp-norm"]], "out.neo.f": [[24, "out-neo-f"]], "out.neo.grid": [[24, "out-neo-grid"]], "out.neo.phi": [[24, "out-neo-phi"]], "out.neo.rotation": [[24, "out-neo-rotation"]], "out.neo.theory": [[24, "out-neo-theory"]], "out.neo.theory_nclass": [[24, "out-neo-theory-nclass"]], "out.neo.transport": [[24, "out-neo-transport"]], "out.neo.transport_exp": [[24, "out-neo-transport-exp"]], "out.neo.transport_flux": [[24, "out-neo-transport-flux"]], "out.neo.transport_gv": [[24, "out-neo-transport-gv"]], "out.neo.vel": [[24, "out-neo-vel"]], "out.neo.vel_fourier": [[24, "out-neo-vel-fourier"]], "profiles_gen": [[25, "profiles-gen"]], "History and Overview": [[25, "history-and-overview"]], "PLASMA ROTATION": [[26, "plasma-rotation"]], "Physical considerations": [[26, "physical-considerations"]], "Sonic rotation formalism": [[26, "sonic-rotation-formalism"]], "The rotation profile": [[26, "the-rotation-profile"]], "Input parameters": [[26, "input-parameters"]], "Theoretical basis for sonic rotation": [[26, "theoretical-basis-for-sonic-rotation"]], "Connection to experimental data": [[26, "connection-to-experimental-data"]], "Consistency with force balance": [[26, "consistency-with-force-balance"]], "Environment setup": [[27, "environment-setup"]], "NERSC CORI": [[27, "nersc-cori"]], "NERSC PERLMUTTER (GPU)": [[27, "nersc-perlmutter-gpu"]], "GA IRIS": [[27, "ga-iris"]], "DIII-D L-mode shortfall": [[28, "diii-d-l-mode-shortfall"]], "Key publications and presentations": [[28, "key-publications-and-presentations"]], "EXPERIMENTAL profiles": [[28, "experimental-profiles"]], "GYRO results": [[28, "gyro-results"]], "GKW results (added 25-jan-2013)": [[28, "gkw-results-added-25-jan-2013"]], "Cross-code benchmarking results": [[28, "cross-code-benchmarking-results"]], "Acknowledgments": [[28, "acknowledgments"]], "TGLF": [[29, "tglf"]], "References: TGLF validation against experimental data": [[29, "id4"]], "Alphabetical list for input.tglf": [[30, "alphabetical-list-for-input-tglf"]], "ADIABATIC_ELEC": [[30, "adiabatic-elec"]], "ALPHA_E": [[30, "alpha-e"]], "ALPHA_ZF": [[30, "alpha-zf"]], "ALPHA_MACH": [[30, "alpha-mach"]], "ALPHA_P": [[30, "alpha-p"]], "ALPHA_QUENCH": [[30, "alpha-quench"]], "ALPHA_SA": [[30, "alpha-sa"]], "AS_1": [[30, "as-1"]], "BETAE": [[30, "betae"]], "B_MODEL_SA": [[30, "b-model-sa"]], "DEBYE": [[30, "debye"]], "DEBYE_FACTOR": [[30, "debye-factor"]], "DELTA_LOC": [[30, "delta-loc"]], "DRMAJDX_LOC": [[30, "drmajdx-loc"]], "DRMINDX_LOC": [[30, "drmindx-loc"]], "DZMAJDX_LOC": [[30, "dzmajdx-loc"]], "ETG_FACTOR": [[30, "etg-factor"]], "FILTER": [[30, "filter"]], "FIND_WIDTH": [[30, "find-width"]], "FT_MODEL_SA": [[30, "ft-model-sa"]], "GCHAT": [[30, "gchat"]], "GEOMETRY_FLAG": [[30, "geometry-flag"]], "GHAT": [[30, "ghat"]], "GRADB_FACTOR": [[30, "gradb-factor"]], "IBRANCH": [[30, "ibranch"]], "IFLUX": [[30, "iflux"]], "KAPPA_LOC": [[30, "kappa-loc"]], "KX0_LOC": [[30, "kx0-loc"]], "KYGRID_MODEL": [[30, "kygrid-model"]], "LINSKER_FACTOR": [[30, "linsker-factor"]], "MASS_1": [[30, "mass-1"]], "NBASIS_MAX": [[30, "nbasis-max"]], "NBASIS_MIN": [[30, "nbasis-min"]], "NEW_EIKONAL": [[30, "new-eikonal"]], "NKY": [[30, "nky"]], "NMODES": [[30, "nmodes"]], "NS": [[30, "ns"]], "NWIDTH": [[30, "nwidth"]], "NXGRID": [[30, "nxgrid"]], "PARK": [[30, "park"]], "P_PRIME_LOC": [[30, "p-prime-loc"]], "Q_LOC": [[30, "q-loc"]], "Q_PRIME_LOC": [[30, "q-prime-loc"]], "Q_SA": [[30, "q-sa"]], "RLNS_1": [[30, "rlns-1"]], "RLTS_1": [[30, "rlts-1"]], "RMAJ_LOC": [[30, "rmaj-loc"]], "RMAJ_SA": [[30, "rmaj-sa"]], "RMIN_LOC": [[30, "rmin-loc"]], "RMIN_SA": [[30, "rmin-sa"]], "SAT_RULE": [[30, "sat-rule"]], "SHAT_SA": [[30, "shat-sa"]], "SIGN_BT": [[30, "sign-bt"]], "SIGN_IT": [[30, "sign-it"]], "S_DELTA_LOC": [[30, "s-delta-loc"]], "S_KAPPA_LOC": [[30, "s-kappa-loc"]], "S_ZETA_LOC": [[30, "s-zeta-loc"]], "TAUS_1": [[30, "taus-1"]], "THETA0_SA": [[30, "theta0-sa"]], "THETA_TRAPPED": [[30, "theta-trapped"]], "UNITS": [[30, "units"]], "USE_BISECTION": [[30, "use-bisection"]], "USE_BPAR": [[30, "use-bpar"]], "USE_BPER": [[30, "use-bper"]], "USE_INBOARD_DETRAPPED": [[30, "use-inboard-detrapped"]], "USE_MHD_RULE": [[30, "use-mhd-rule"]], "USE_TRANSPORT_MODEL": [[30, "use-transport-model"]], "VEXB": [[30, "vexb"]], "VEXB_SHEAR": [[30, "vexb-shear"]], "VPAR_1": [[30, "vpar-1"]], "VPAR_MODEL": [[30, "vpar-model"]], "VPAR_SHEAR_1": [[30, "vpar-shear-1"]], "VPAR_SHEAR_MODEL": [[30, "vpar-shear-model"]], "WD_ZERO": [[30, "wd-zero"]], "WIDTH": [[30, "width"]], "WIDTH_MIN": [[30, "width-min"]], "WRITE_WAVEFUNCTION_FLAG": [[30, "write-wavefunction-flag"]], "XNUE": [[30, "xnue"]], "XNU_FACTOR": [[30, "xnu-factor"]], "XNU_MODEL": [[30, "xnu-model"]], "XWELL_SA": [[30, "xwell-sa"]], "ZEFF": [[30, "zeff"]], "ZETA_LOC": [[30, "zeta-loc"]], "ZMAJ_LOC": [[30, "zmaj-loc"]], "ZS_1": [[30, "zs-1"]], "Alphabetical list for out.tglf files": [[31, "alphabetical-list-for-out-tglf-files"]], "density_spectrum": [[31, "density-spectrum"]], "eigenvalue_spectrum": [[31, "eigenvalue-spectrum"]], "field_spectrum": [[31, "field-spectrum"]], "intensity_spectrum": [[31, "intensity-spectrum"]], "nsts_crossphase_spectrum": [[31, "nsts-crossphase-spectrum"]], "QL_flux_spectrum": [[31, "ql-flux-spectrum"]], "sat_geo_spectrum": [[31, "sat-geo-spectrum"]], "scalar_saturation_parameters": [[31, "scalar-saturation-parameters"]], "spectral_shift": [[31, "spectral-shift"]], "sum_flux_spectrum": [[31, "sum-flux-spectrum"]], "temperature_spectrum": [[31, "temperature-spectrum"]], "Table of inputs and outputs": [[32, "table-of-inputs-and-outputs"]], "Control": [[32, "id1"]], "Species Vectors": [[32, "id2"]], "Gaussian width parameters": [[32, "id3"]], "Miller geometry parameters": [[32, "id4"]], "s-alpha geometry parameters": [[32, "id5"]], "Change-at-your-own-risk parameters": [[32, "id6"]], "TGLF output parameters": [[32, "id7"]], "TGLF output files": [[32, "id8"]], "TGYRO": [[33, "tgyro"]], "Data output, python interface, and plotting": [[33, "data-output-python-interface-and-plotting"]], "Transport equations and solution": [[33, "transport-equations-and-solution"]], "Equations solved in TGYRO": [[34, "equations-solved-in-tgyro"]], "Density Transport": [[34, "density-transport"]], "Density fluxes and sources": [[34, "id2"]], "Energy Transport": [[34, "energy-transport"]], "Energy fluxes and sources": [[34, "id3"]], "Momentum Transport": [[34, "momentum-transport"]], "Momentum fluxes and sources": [[34, "id4"]], "Connection of Fluxes to Powers": [[34, "connection-of-fluxes-to-powers"]], "OUTPUT": [[35, "output"]], "PLOT": [[36, "plot"]], "Scenarios and connection to energy sources": [[37, "scenarios-and-connection-to-energy-sources"]], "TGYRO solver algorithm": [[38, "tgyro-solver-algorithm"]], "Formulation": [[38, "formulation"]], "Some comments regarding units": [[38, "some-comments-regarding-units"]], "Solution strategy": [[38, "solution-strategy"]], "Formulation on a discrete grid": [[38, "formulation-on-a-discrete-grid"]], "Computation of the Jacobian": [[38, "computation-of-the-jacobian"]], "input.tgyro Alphabetical List": [[39, "input-tgyro-alphabetical-list"]], "LOC_BETAE_SCALE": [[39, "loc-betae-scale"]], "TGYRO_DEN_METHOD*": [[39, "tgyro-den-method"]], "LOC_DX": [[39, "loc-dx"]], "LOC_DX_MAX": [[39, "loc-dx-max"]], "LOC_ER_FEEDBACK_FLAG": [[39, "loc-er-feedback-flag"]], "LOC_EVOLVE_GRAD_ONLY_FLAG": [[39, "loc-evolve-grad-only-flag"]], "LOC_HE_FEEDBACK_FLAG": [[39, "loc-he-feedback-flag"]], "TGYRO_ITERATION_METHOD": [[39, "tgyro-iteration-method"]], "LOC_LOCK_PROFILE_FLAG": [[39, "loc-lock-profile-flag"]], "TGYRO_MODE": [[39, "tgyro-mode"]], "TGYRO_NEO_METHOD": [[39, "tgyro-neo-method"]], "TGYRO_RELAX_ITERATIONS": [[39, "tgyro-relax-iterations"]], "LOC_RELAX": [[39, "loc-relax"]], "LOC_RESIDUAL_METHOD": [[39, "loc-residual-method"]], "LOC_RESTART_FLAG": [[39, "loc-restart-flag"]], "LOC_SCENARIO": [[39, "loc-scenario"]], "TGYRO_THERM_FLAG*": [[39, "tgyro-therm-flag"]], "LOC_TE_FEEDBACK_FLAG": [[39, "loc-te-feedback-flag"]], "LOC_TI_FEEDBACK_FLAG": [[39, "loc-ti-feedback-flag"]], "TGYRO_WRITE_PROFILES_FLAG": [[39, "tgyro-write-profiles-flag"]], "input.tgyro Tabular List": [[40, "input-tgyro-tabular-list"]], "High-level control": [[40, "id1"]], "Iteration control": [[40, "id2"]], "Profile Feedback Control": [[40, "id3"]], "Physics Control": [[40, "id4"]], "Species Parameters": [[40, "id5"]], "CGYRO Workshop 2022": [[41, "cgyro-workshop-2022"]], "AGENDA": [[41, "agenda"]], "References": [[42, "references"]]}, "indexentries": {}})
\ No newline at end of file
diff --git a/docs/setup.html b/docs/setup.html
index 6213ba3..4a3ee69 100644
--- a/docs/setup.html
+++ b/docs/setup.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>Environment setup</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Environment setup</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/setup.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -95,10 +97,10 @@
            <div itemprop="articleBody">
              
   <section id="environment-setup">
-<h1>Environment setup<a class="headerlink" href="#environment-setup" title="Permalink to this headline"></a></h1>
+<h1>Environment setup<a class="headerlink" href="#environment-setup" title="Permalink to this heading"></a></h1>
 <p>Below we give information about the environment setup required to run GACODE tools on maintained platforms.  One this step is complete, proceed to instructions on running cases <a class="reference internal" href="cgyro/running_cases.html"><span class="doc">CGYRO</span></a>, <a class="reference internal" href="neo.html"><span class="doc">NEO</span></a>, <a class="reference internal" href="tgyro.html"><span class="doc">TGYRO</span></a>, and so on.</p>
 <section id="nersc-cori">
-<h2>NERSC CORI<a class="headerlink" href="#nersc-cori" title="Permalink to this headline"></a></h2>
+<h2>NERSC CORI<a class="headerlink" href="#nersc-cori" title="Permalink to this heading"></a></h2>
 <p>Add the following lines to <code class="docutils literal notranslate"><span class="pre">.bashrc</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export GACODE_PLATFORM=CORI_KNL_HT2_MKL
 export GACODE_ROOT=/global/cfs/cdirs/atom/atom-install-cori/gacode-source-mkl
@@ -106,13 +108,13 @@ <h2>NERSC CORI<a class="headerlink" href="#nersc-cori" title="Permalink to this
 . ${GACODE_ROOT}/platform/env/env.$GACODE_PLATFORM
 </pre></div>
 </div>
-<p>Sample job layout (1 node, 32 MPI, 4 OpenMP):</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ gacode_qsub -code cgyro -n 32 -nomp 4 -repo atom -w 15
+<p>Sample job layout (1 node, 32 MPI, 4 OpenMP, 59 min wall-clock time):</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ gacode_qsub -code cgyro -n 32 -nomp 4 -repo atom -w 00:59:00
 </pre></div>
 </div>
 </section>
 <section id="nersc-perlmutter-gpu">
-<h2>NERSC PERLMUTTER (GPU)<a class="headerlink" href="#nersc-perlmutter-gpu" title="Permalink to this headline"></a></h2>
+<h2>NERSC PERLMUTTER (GPU)<a class="headerlink" href="#nersc-perlmutter-gpu" title="Permalink to this heading"></a></h2>
 <p>Add the following lines to <code class="docutils literal notranslate"><span class="pre">.bashrc</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export GACODE_PLATFORM=PERLMUTTER_GPU
 export GACODE_ROOT=/global/cfs/cdirs/atom/atom-install-perlmutter/gacode-gpu
@@ -120,13 +122,13 @@ <h2>NERSC PERLMUTTER (GPU)<a class="headerlink" href="#nersc-perlmutter-gpu" tit
 . ${GACODE_ROOT}/platform/env/env.$GACODE_PLATFORM
 </pre></div>
 </div>
-<p>Sample job layout (1 node, 4 GPU, 16 MPI, 8 OpenMP):</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ gacode_qsub -code cgyro -n 16 -nomp 8 -repo atom_g -w 15
+<p>Sample job layout (1 node, 4 GPU, 16 MPI, 8 OpenMP, 59 min wall-clock time):</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ gacode_qsub -code cgyro -n 16 -nomp 8 -repo atom_g -w 00:59:00
 </pre></div>
 </div>
 </section>
 <section id="ga-iris">
-<h2>GA IRIS<a class="headerlink" href="#ga-iris" title="Permalink to this headline"></a></h2>
+<h2>GA IRIS<a class="headerlink" href="#ga-iris" title="Permalink to this heading"></a></h2>
 <p>To run in a <strong>dedicated GACODE environment</strong>, add these lines to <code class="docutils literal notranslate"><span class="pre">.bashrc</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export GACODE_PLATFORM=IRIS
 export GACODE_ROOT=/fusion/projects/theory/gacode
diff --git a/docs/shortfall.html b/docs/shortfall.html
index 81a0ad2..1ff1290 100644
--- a/docs/shortfall.html
+++ b/docs/shortfall.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>
@@ -92,9 +94,9 @@
         <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><a href="misc.html">Miscellaneous</a> &raquo;</li>
-      <li>DIII-D L-mode shortfall</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="misc.html">Miscellaneous</a></li>
+      <li class="breadcrumb-item active">DIII-D L-mode shortfall</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/shortfall.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -105,13 +107,13 @@
            <div itemprop="articleBody">
              
   <section id="diii-d-l-mode-shortfall">
-<span id="shortfall"></span><h1>DIII-D L-mode shortfall<a class="headerlink" href="#diii-d-l-mode-shortfall" title="Permalink to this headline"></a></h1>
+<span id="shortfall"></span><h1>DIII-D L-mode shortfall<a class="headerlink" href="#diii-d-l-mode-shortfall" title="Permalink to this heading"></a></h1>
 <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>This page is designed to serve as a central common resource and collaboration tool for research into the so-called <em>shortfall</em> observed in some gyrokinetic and gyrofluid predictions of DIII-D near-edge (<span class="math notranslate nohighlight">\(\rho_{tor}=0.75\)</span>) transport and fluctuations levels, and the ITPA T&amp;C group work on this topic.  Below are links to key references documenting the issue, equilibrium profiles (in the GACODE input.profiles ASCII format) for DIII-D shot 128913 &#64; 1500 ms which has been the primary discharge for investigating this issue, and results to date from various codes. We encourage and welcome any and all groups interested in investigating this issue with their model or theory to use the profile data below, and compare their results against those documented here.  Questions and comments should be directed to <a class="reference external" href="mailto:chholland&#37;&#52;&#48;ucsd&#46;edu">Chris Holland</a>.</p>
 </section>
 <section id="key-publications-and-presentations">
-<h2>Key publications and presentations<a class="headerlink" href="#key-publications-and-presentations" title="Permalink to this headline"></a></h2>
+<h2>Key publications and presentations<a class="headerlink" href="#key-publications-and-presentations" title="Permalink to this heading"></a></h2>
 <ol class="arabic simple">
 <li><p>Initial publication of discharge characteristics and <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a> comparisons.</p>
 <ul class="simple">
@@ -169,7 +171,7 @@ <h2>Key publications and presentations<a class="headerlink" href="#key-publicati
 </ol>
 </section>
 <section id="experimental-profiles">
-<h2>EXPERIMENTAL profiles<a class="headerlink" href="#experimental-profiles" title="Permalink to this headline"></a></h2>
+<h2>EXPERIMENTAL profiles<a class="headerlink" href="#experimental-profiles" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p>Equilibrium profiles (including Miller parameterization of magnetic geometry) in <a class="reference internal" href="input_gacode.html"><span class="doc">input.gacode</span></a> format are available here:</p>
 <ul>
@@ -189,7 +191,7 @@ <h2>EXPERIMENTAL profiles<a class="headerlink" href="#experimental-profiles" tit
 </ul>
 </section>
 <section id="gyro-results">
-<h2>GYRO results<a class="headerlink" href="#gyro-results" title="Permalink to this headline"></a></h2>
+<h2>GYRO results<a class="headerlink" href="#gyro-results" title="Permalink to this heading"></a></h2>
 <ul>
 <li><p>A series of linear electrostatic initial-value growth rate convergence calculations have been performed, the results of which are shown here</p>
 <figure class="align-default">
@@ -230,7 +232,7 @@ <h2>GYRO results<a class="headerlink" href="#gyro-results" title="Permalink to t
 </ul>
 </section>
 <section id="gkw-results-added-25-jan-2013">
-<h2>GKW results (added 25-jan-2013)<a class="headerlink" href="#gkw-results-added-25-jan-2013" title="Permalink to this headline"></a></h2>
+<h2>GKW results (added 25-jan-2013)<a class="headerlink" href="#gkw-results-added-25-jan-2013" title="Permalink to this heading"></a></h2>
 <a class="reference internal image-reference" href="_images/GKW_physics_freq.png"><img alt="b250" src="_images/GKW_physics_freq.png" style="width: 48%;" /></a>
 <a class="reference internal image-reference" href="_images/GKW_physics_gamma.png"><img alt="b250" src="_images/GKW_physics_gamma.png" style="width: 48%;" /></a>
 <ul class="simple">
@@ -243,7 +245,7 @@ <h2>GKW results (added 25-jan-2013)<a class="headerlink" href="#gkw-results-adde
 </ul>
 </section>
 <section id="cross-code-benchmarking-results">
-<h2>Cross-code benchmarking results<a class="headerlink" href="#cross-code-benchmarking-results" title="Permalink to this headline"></a></h2>
+<h2>Cross-code benchmarking results<a class="headerlink" href="#cross-code-benchmarking-results" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p>The first completed benchmarking study compares results from the gyrokinetic <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a>, <a class="reference external" href="https://bitbucket.org/gyrokinetics/gs2/wiki/Home"><cite>GS2</cite></a>, <a class="reference external" href="https://www.colorado.edu/center/cips/research/plasma-theory-and-simulation/gem-electromagnetic-gyrokinetic-turbulence-simulation"><cite>GEM</cite></a>, and <a class="reference external" href="http://genecode.org"><cite>GENE</cite></a> codes, as well as the gyrofluid <a class="reference internal" href="tglf.html"><span class="doc">TGLF</span></a> model.  <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a>, <a class="reference external" href="https://bitbucket.org/gyrokinetics/gs2/wiki/Home"><cite>GS2</cite></a>, <a class="reference external" href="https://bitbucket.org/gkw/gkw/wiki/Home"><cite>GKW</cite></a> and <a class="reference external" href="http://genecode.org"><cite>GENE</cite></a> are continuum Eulearian (although with different velocity-space discretizations) codes, while <a class="reference external" href="https://www.colorado.edu/center/cips/research/plasma-theory-and-simulation/gem-electromagnetic-gyrokinetic-turbulence-simulation"><cite>GEM</cite></a> is a particle-in-cell code.  Unless otherwise noted, the results shown below are for electromagnetic, collisional simulations with a single gyrokinetic ion species.</p></li>
 <li><p><strong>Update 25-jan-2013:</strong> Results from the continuum gyrokinetic <a class="reference external" href="https://bitbucket.org/gkw/gkw/wiki/Home"><cite>GKW</cite></a> code have been added.</p></li>
@@ -278,7 +280,7 @@ <h2>Cross-code benchmarking results<a class="headerlink" href="#cross-code-bench
 </ul>
 </section>
 <section id="acknowledgments">
-<h2>Acknowledgments<a class="headerlink" href="#acknowledgments" title="Permalink to this headline"></a></h2>
+<h2>Acknowledgments<a class="headerlink" href="#acknowledgments" title="Permalink to this heading"></a></h2>
 <p>Thanks to Ron Bravenec for providing the <a class="reference external" href="https://bitbucket.org/gyrokinetics/gs2/wiki/Home"><cite>GS2</cite></a> and <a class="reference external" href="https://www.colorado.edu/center/cips/research/plasma-theory-and-simulation/gem-electromagnetic-gyrokinetic-turbulence-simulation"><cite>GEM</cite></a> data, Yann Camenen for the <a class="reference external" href="https://bitbucket.org/gkw/gkw/wiki/Home"><cite>GKW</cite></a> results, and Tobias Görler for the <a class="reference external" href="http://genecode.org"><cite>GENE</cite></a> results.</p>
 </section>
 </section>
diff --git a/docs/tglf.html b/docs/tglf.html
index a1bb8df..f956e19 100644
--- a/docs/tglf.html
+++ b/docs/tglf.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>
@@ -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>TGLF</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">TGLF</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/tglf.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -100,9 +102,9 @@
            <div itemprop="articleBody">
              
   <section id="tglf">
-<h1>TGLF<a class="headerlink" href="#tglf" title="Permalink to this headline"></a></h1>
+<h1>TGLF<a class="headerlink" href="#tglf" title="Permalink to this heading"></a></h1>
 <section id="quick-links">
-<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this headline"></a></h2>
+<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this heading"></a></h2>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="tglf/tglf_table.html">Table of inputs and outputs</a></li>
@@ -112,7 +114,7 @@ <h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to thi
 </div>
 </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>The TGLF model is a next generation gyro-Landau-fluid model that improves the accuracy of the trapped particle response and the finite Larmor radius effects compared to its predecessor, GLF23. The model solves for the linear eigenmodes of trapped ion and electron modes (TIM, TEM), ion and electron temperature gradient (ITG, ETG) modes and electromagnetic kinetic ballooning (KB) modes. The TGLF model generalizes the methods of GLF23 to a more accurate system of moment equations and an eigenmode solution method that is valid for shaped geometry and finite aspect ratio. The Miller equilibrium model is used in TGLF for shaped finite aspect ratio geometry. In the first phase of developing TGLF, the linear eigenmodes were benchmarked against a database of 1800 linear stability calculations using the GKS gyrokinetic code. The next phase focused on finding a saturation rule that used the quasilinear (QL) weights from TGLF and accurately fit the fluxes from nonlinear simulations. Using a database of 83 nonlinear GYRO simulations with Miller shaped geometry and kinetic electrons, a model for the saturated fluctuation intensity has been found. With a simple quasilinear (QL) saturation rule, remarkable agreement with the energy and particle fluxes from the GYRO database is obtained for both shaped or circular geometry and also for low aspect ratio. Using this new QL saturation rule along with a new ExB shear quench rule for shaped geometry, the density and temperature profiles have recently been predicted in over 500 transport code runs and the results compared against experimental data from 96 tokamak discharges from DIII-D, JET, and TFTR. Compared to GLF23, the TGLF model demonstrates better agreement between the predicted and experimental temperature profiles. Surprisingly, TGLF predicts that the high-k modes are found to play an important role in the central core region of low (L-mode) and high confinement (H-mode) plasmas lacking transport barriers. Using Miller finite aspect ratio shaped geometry in place of <span class="math notranslate nohighlight">\(s\text{-}\alpha\)</span> infinite aspect ratio circular geometry results in larger transport (especially <span class="math notranslate nohighlight">\(\chi_e\)</span>) and improved agreement with TFTR, which is circular. By contrast, we see little change in the agreement for DIII-D and JET, where the stabilizing effect of elongation compensates for the increase in <span class="math notranslate nohighlight">\(\chi\)</span> due to finite aspect ratio.</p>
 <table class="colwidths-given docutils align-default" id="id4">
 <caption><span class="caption-text"><strong>References: TGLF validation against experimental data</strong></span><a class="headerlink" href="#id4" title="Permalink to this table"></a></caption>
diff --git a/docs/tglf/tglf_list.html b/docs/tglf/tglf_list.html
index 0c0e46d..6d8b0f3 100644
--- a/docs/tglf/tglf_list.html
+++ b/docs/tglf/tglf_list.html
@@ -16,7 +16,9 @@
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@@ -176,9 +178,9 @@
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-      <li>Alphabetical list for input.tglf</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tglf.html">TGLF</a></li>
+      <li class="breadcrumb-item active">Alphabetical list for input.tglf</li>
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@@ -189,9 +191,9 @@
            <div itemprop="articleBody">
              
   <section id="alphabetical-list-for-input-tglf">
-<h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-list-for-input-tglf" title="Permalink to this headline"></a></h1>
+<h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-list-for-input-tglf" title="Permalink to this heading"></a></h1>
 <section id="adiabatic-elec">
-<span id="tglf-adiabatic-elec"></span><h2>ADIABATIC_ELEC<a class="headerlink" href="#adiabatic-elec" title="Permalink to this headline"></a></h2>
+<span id="tglf-adiabatic-elec"></span><h2>ADIABATIC_ELEC<a class="headerlink" href="#adiabatic-elec" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Use adiabatic electrons. Adiabatic electrons are assumed to be perfectly Maxwellian and remain so by responding immediately to any change in electrostatic potential along the magnetic field. Generally this assumption works for ITG cases, but not for trapped electron modes, so can be used to distinguish their relative importance.</p>
 <p><strong>Comments</strong></p>
@@ -201,7 +203,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="alpha-e">
-<span id="tglf-alpha-e"></span><h2>ALPHA_E<a class="headerlink" href="#alpha-e" title="Permalink to this headline"></a></h2>
+<span id="tglf-alpha-e"></span><h2>ALPHA_E<a class="headerlink" href="#alpha-e" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies ExB velocity shear for spectral shift model.</p>
 <p><strong>Comments</strong></p>
@@ -211,7 +213,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="alpha-zf">
-<span id="tglf-alpha-zf"></span><h2>ALPHA_ZF<a class="headerlink" href="#alpha-zf" title="Permalink to this headline"></a></h2>
+<span id="tglf-alpha-zf"></span><h2>ALPHA_ZF<a class="headerlink" href="#alpha-zf" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Zonal flow mixing coefficient (for SAT1 and SAT2). Note: Can be used as hidden switch that avoids picking the lowest ky as the peak in gamma/ky when ALPHA_ZF=-1.0. This switch is useful when an MHD mode at the lowest ky causes a large amount of flux.</p>
 <p><strong>Comments</strong></p>
@@ -221,7 +223,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="alpha-mach">
-<span id="tglf-alpha-mach"></span><h2>ALPHA_MACH<a class="headerlink" href="#alpha-mach" title="Permalink to this headline"></a></h2>
+<span id="tglf-alpha-mach"></span><h2>ALPHA_MACH<a class="headerlink" href="#alpha-mach" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies parallel velocity for all species.</p>
 <p><strong>Comments</strong></p>
@@ -231,7 +233,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="alpha-p">
-<span id="tglf-alpha-p"></span><h2>ALPHA_P<a class="headerlink" href="#alpha-p" title="Permalink to this headline"></a></h2>
+<span id="tglf-alpha-p"></span><h2>ALPHA_P<a class="headerlink" href="#alpha-p" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies parallel velocity shear for all species.</p>
 <p><strong>Comments</strong></p>
@@ -241,7 +243,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="alpha-quench">
-<span id="tglf-alpha-quench"></span><h2>ALPHA_QUENCH<a class="headerlink" href="#alpha-quench" title="Permalink to this headline"></a></h2>
+<span id="tglf-alpha-quench"></span><h2>ALPHA_QUENCH<a class="headerlink" href="#alpha-quench" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -255,7 +257,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="alpha-sa">
-<span id="tglf-alpha-sa"></span><h2>ALPHA_SA<a class="headerlink" href="#alpha-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-alpha-sa"></span><h2>ALPHA_SA<a class="headerlink" href="#alpha-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized pressure gradient.</p>
 <p><strong>Comments</strong></p>
@@ -265,7 +267,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="as-1">
-<span id="tglf-as-1"></span><h2>AS_1<a class="headerlink" href="#as-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-as-1"></span><h2>AS_1<a class="headerlink" href="#as-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species array of densities <span class="math notranslate nohighlight">\({\frac {n_{s}}{n_{e}}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -275,7 +277,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="betae">
-<span id="tglf-betae"></span><h2>BETAE<a class="headerlink" href="#betae" title="Permalink to this headline"></a></h2>
+<span id="tglf-betae"></span><h2>BETAE<a class="headerlink" href="#betae" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\(\beta _{e}\,\!\)</span>  defined with respect to <span class="math notranslate nohighlight">\(B_{\rm {unit}}\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -285,7 +287,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="b-model-sa">
-<span id="tglf-b-model-sa"></span><h2>B_MODEL_SA<a class="headerlink" href="#b-model-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-b-model-sa"></span><h2>B_MODEL_SA<a class="headerlink" href="#b-model-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>0/1 to exclude/include the B(theta) factor in k_per.</p>
 <p><strong>Comments</strong></p>
@@ -295,7 +297,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="debye">
-<span id="tglf-debye"></span><h2>DEBYE<a class="headerlink" href="#debye" title="Permalink to this headline"></a></h2>
+<span id="tglf-debye"></span><h2>DEBYE<a class="headerlink" href="#debye" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Debye length/gyroradius.</p>
 <p><strong>Comments</strong></p>
@@ -305,7 +307,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="debye-factor">
-<span id="tglf-debye-factor"></span><h2>DEBYE_FACTOR<a class="headerlink" href="#debye-factor" title="Permalink to this headline"></a></h2>
+<span id="tglf-debye-factor"></span><h2>DEBYE_FACTOR<a class="headerlink" href="#debye-factor" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the debye length.</p>
 <p><strong>Comments</strong></p>
@@ -315,7 +317,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="delta-loc">
-<span id="tglf-delta-loc"></span><h2>DELTA_LOC<a class="headerlink" href="#delta-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-delta-loc"></span><h2>DELTA_LOC<a class="headerlink" href="#delta-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Comments</strong></p>
 <ul class="simple">
@@ -324,7 +326,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="drmajdx-loc">
-<span id="tglf-drmajdx-loc"></span><h2>DRMAJDX_LOC<a class="headerlink" href="#drmajdx-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-drmajdx-loc"></span><h2>DRMAJDX_LOC<a class="headerlink" href="#drmajdx-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\({\frac {\partial R_{maj}}{\partial x}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -334,7 +336,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="drmindx-loc">
-<span id="tglf-drmindx-loc"></span><h2>DRMINDX_LOC<a class="headerlink" href="#drmindx-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-drmindx-loc"></span><h2>DRMINDX_LOC<a class="headerlink" href="#drmindx-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Allows for x different than r <span class="math notranslate nohighlight">\({\frac {\partial r}{\partial x}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -344,7 +346,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="dzmajdx-loc">
-<span id="tglf-dzmajdx-loc"></span><h2>DZMAJDX_LOC<a class="headerlink" href="#dzmajdx-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-dzmajdx-loc"></span><h2>DZMAJDX_LOC<a class="headerlink" href="#dzmajdx-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\({\frac {\partial Z_{maj}}{\partial x}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -354,7 +356,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="etg-factor">
-<span id="tglf-etg-factor"></span><h2>ETG_FACTOR<a class="headerlink" href="#etg-factor" title="Permalink to this headline"></a></h2>
+<span id="tglf-etg-factor"></span><h2>ETG_FACTOR<a class="headerlink" href="#etg-factor" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Exponent for ETG saturation rule.</p>
 <p><strong>Comments</strong></p>
@@ -364,7 +366,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="filter">
-<span id="tglf-filter"></span><h2>FILTER<a class="headerlink" href="#filter" title="Permalink to this headline"></a></h2>
+<span id="tglf-filter"></span><h2>FILTER<a class="headerlink" href="#filter" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Sets threshold for frequency/drift frequency to filter out non-driftwave instabilities.</p>
 <p><strong>Comments</strong></p>
@@ -374,7 +376,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="find-width">
-<span id="tglf-find-width"></span><h2>FIND_WIDTH<a class="headerlink" href="#find-width" title="Permalink to this headline"></a></h2>
+<span id="tglf-find-width"></span><h2>FIND_WIDTH<a class="headerlink" href="#find-width" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -388,7 +390,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="ft-model-sa">
-<span id="tglf-ft-model-sa"></span><h2>FT_MODEL_SA<a class="headerlink" href="#ft-model-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-ft-model-sa"></span><h2>FT_MODEL_SA<a class="headerlink" href="#ft-model-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>1 uses trapped fraction at the outboard midplane.</p>
 <p><strong>Comments</strong></p>
@@ -398,7 +400,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="gchat">
-<span id="tglf-gchat"></span><h2>GCHAT<a class="headerlink" href="#gchat" title="Permalink to this headline"></a></h2>
+<span id="tglf-gchat"></span><h2>GCHAT<a class="headerlink" href="#gchat" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the curvature drift irreducible terms.</p>
 <p><strong>Comments</strong></p>
@@ -408,7 +410,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="geometry-flag">
-<span id="tglf-geometry-flag"></span><h2>GEOMETRY_FLAG<a class="headerlink" href="#geometry-flag" title="Permalink to this headline"></a></h2>
+<span id="tglf-geometry-flag"></span><h2>GEOMETRY_FLAG<a class="headerlink" href="#geometry-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Geometry type.</p>
 <p><strong>Choices</strong></p>
@@ -425,7 +427,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="ghat">
-<span id="tglf-ghat"></span><h2>GHAT<a class="headerlink" href="#ghat" title="Permalink to this headline"></a></h2>
+<span id="tglf-ghat"></span><h2>GHAT<a class="headerlink" href="#ghat" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the curvature drift closure terms.</p>
 <p><strong>Comments</strong></p>
@@ -435,7 +437,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="gradb-factor">
-<span id="tglf-gradb-factor"></span><h2>GRADB_FACTOR<a class="headerlink" href="#gradb-factor" title="Permalink to this headline"></a></h2>
+<span id="tglf-gradb-factor"></span><h2>GRADB_FACTOR<a class="headerlink" href="#gradb-factor" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the gradB terms.</p>
 <p><strong>Comments</strong></p>
@@ -445,7 +447,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="ibranch">
-<span id="tglf-ibranch"></span><h2>IBRANCH<a class="headerlink" href="#ibranch" title="Permalink to this headline"></a></h2>
+<span id="tglf-ibranch"></span><h2>IBRANCH<a class="headerlink" href="#ibranch" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -459,7 +461,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="iflux">
-<span id="tglf-iflux"></span><h2>IFLUX<a class="headerlink" href="#iflux" title="Permalink to this headline"></a></h2>
+<span id="tglf-iflux"></span><h2>IFLUX<a class="headerlink" href="#iflux" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Compute quasilinear weights and mode amplitudes.</p>
 <p><strong>Comments</strong></p>
@@ -469,7 +471,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="kappa-loc">
-<span id="tglf-kappa-loc"></span><h2>KAPPA_LOC<a class="headerlink" href="#kappa-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-kappa-loc"></span><h2>KAPPA_LOC<a class="headerlink" href="#kappa-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Elongation of flux surface, <span class="math notranslate nohighlight">\(\kappa \,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -479,7 +481,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="kx0-loc">
-<span id="tglf-kx0-loc"></span><h2>KX0_LOC<a class="headerlink" href="#kx0-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-kx0-loc"></span><h2>KX0_LOC<a class="headerlink" href="#kx0-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>kx0/ky ballooning mode offset.</p>
 <p><strong>Comments</strong></p>
@@ -489,7 +491,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="ky">
-<span id="tglf-ky"></span><h2>KY<a class="headerlink" href="#ky" title="Permalink to this headline"></a></h2>
+<span id="tglf-ky"></span><h2>KY<a class="headerlink" href="#ky" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\(k_{\theta }\rho _{s,{\rm {unit}}}\,\!\)</span> for single-mode call to TGLF or user-definded ky grid (see KYGRID_MODEL=0 below).</p>
 <p><strong>Comments</strong></p>
@@ -499,7 +501,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="kygrid-model">
-<span id="tglf-kygrid-model"></span><h2>KYGRID_MODEL<a class="headerlink" href="#kygrid-model" title="Permalink to this headline"></a></h2>
+<span id="tglf-kygrid-model"></span><h2>KYGRID_MODEL<a class="headerlink" href="#kygrid-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -514,7 +516,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="linsker-factor">
-<span id="tglf-linsker-factor"></span><h2>LINSKER_FACTOR<a class="headerlink" href="#linsker-factor" title="Permalink to this headline"></a></h2>
+<span id="tglf-linsker-factor"></span><h2>LINSKER_FACTOR<a class="headerlink" href="#linsker-factor" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the Linsker terms.</p>
 <p><strong>Comments</strong></p>
@@ -524,7 +526,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="mass-1">
-<span id="tglf-mass-1"></span><h2>MASS_1<a class="headerlink" href="#mass-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-mass-1"></span><h2>MASS_1<a class="headerlink" href="#mass-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species masses normalized to <span class="math notranslate nohighlight">\(m_{D}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -534,7 +536,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="nbasis-max">
-<span id="tglf-nbasis-max"></span><h2>NBASIS_MAX<a class="headerlink" href="#nbasis-max" title="Permalink to this headline"></a></h2>
+<span id="tglf-nbasis-max"></span><h2>NBASIS_MAX<a class="headerlink" href="#nbasis-max" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum number of parallel basis functions.</p>
 <p><strong>Comments</strong></p>
@@ -544,7 +546,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="nbasis-min">
-<span id="tglf-nbasis-min"></span><h2>NBASIS_MIN<a class="headerlink" href="#nbasis-min" title="Permalink to this headline"></a></h2>
+<span id="tglf-nbasis-min"></span><h2>NBASIS_MIN<a class="headerlink" href="#nbasis-min" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Minimum number of parallel basis functions.</p>
 <p><strong>Comments</strong></p>
@@ -554,7 +556,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="new-eikonal">
-<span id="tglf-new-eikonal"></span><h2>NEW_EIKONAL<a class="headerlink" href="#new-eikonal" title="Permalink to this headline"></a></h2>
+<span id="tglf-new-eikonal"></span><h2>NEW_EIKONAL<a class="headerlink" href="#new-eikonal" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -568,7 +570,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="nky">
-<span id="tglf-nky"></span><h2>NKY<a class="headerlink" href="#nky" title="Permalink to this headline"></a></h2>
+<span id="tglf-nky"></span><h2>NKY<a class="headerlink" href="#nky" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of poloidal modes in the high-k spectrum of TGLF_TM.</p>
 <p><strong>Comments</strong></p>
@@ -578,7 +580,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="nmodes">
-<span id="tglf-nmodes"></span><h2>NMODES<a class="headerlink" href="#nmodes" title="Permalink to this headline"></a></h2>
+<span id="tglf-nmodes"></span><h2>NMODES<a class="headerlink" href="#nmodes" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of modes to store for tglf_ibranch_in = -1.</p>
 <p><strong>Comments</strong></p>
@@ -588,7 +590,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="ns">
-<span id="tglf-ns"></span><h2>NS<a class="headerlink" href="#ns" title="Permalink to this headline"></a></h2>
+<span id="tglf-ns"></span><h2>NS<a class="headerlink" href="#ns" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of species including both electrons and ions.</p>
 <p><strong>Comments</strong></p>
@@ -598,7 +600,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="nwidth">
-<span id="tglf-nwidth"></span><h2>NWIDTH<a class="headerlink" href="#nwidth" title="Permalink to this headline"></a></h2>
+<span id="tglf-nwidth"></span><h2>NWIDTH<a class="headerlink" href="#nwidth" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum number of widths used in search for maximum growth rate.</p>
 <p><strong>Comments</strong></p>
@@ -608,7 +610,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="nxgrid">
-<span id="tglf-nxgrid"></span><h2>NXGRID<a class="headerlink" href="#nxgrid" title="Permalink to this headline"></a></h2>
+<span id="tglf-nxgrid"></span><h2>NXGRID<a class="headerlink" href="#nxgrid" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Number of nodes in Gauss-Hermite quadrature.</p>
 <p><strong>Comments</strong></p>
@@ -618,7 +620,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="park">
-<span id="tglf-park"></span><h2>PARK<a class="headerlink" href="#park" title="Permalink to this headline"></a></h2>
+<span id="tglf-park"></span><h2>PARK<a class="headerlink" href="#park" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the parallel gradient term.</p>
 <p><strong>Comments</strong></p>
@@ -628,7 +630,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="p-prime-loc">
-<span id="tglf-p-prime-loc"></span><h2>P_PRIME_LOC<a class="headerlink" href="#p-prime-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-p-prime-loc"></span><h2>P_PRIME_LOC<a class="headerlink" href="#p-prime-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\({\frac {qa^{2}}{rB_{unit}^{2}}}{\frac {\partial p}{\partial r}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -638,7 +640,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="q-loc">
-<span id="tglf-q-loc"></span><h2>Q_LOC<a class="headerlink" href="#q-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-q-loc"></span><h2>Q_LOC<a class="headerlink" href="#q-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Absolute value of the safety factor, <span class="math notranslate nohighlight">\(ABS(q)\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -648,7 +650,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="q-prime-loc">
-<span id="tglf-q-prime-loc"></span><h2>Q_PRIME_LOC<a class="headerlink" href="#q-prime-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-q-prime-loc"></span><h2>Q_PRIME_LOC<a class="headerlink" href="#q-prime-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\({\frac {q^{2}a^{2}}{r^{2}}}s\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -658,7 +660,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="q-sa">
-<span id="tglf-q-sa"></span><h2>Q_SA<a class="headerlink" href="#q-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-q-sa"></span><h2>Q_SA<a class="headerlink" href="#q-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Absolute value of safety factor.</p>
 <p><strong>Comments</strong></p>
@@ -668,7 +670,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="rlns-1">
-<span id="tglf-rlns-1"></span><h2>RLNS_1<a class="headerlink" href="#rlns-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-rlns-1"></span><h2>RLNS_1<a class="headerlink" href="#rlns-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species array of normalized density gradients <span class="math notranslate nohighlight">\(-{\frac {a}{n_{s}}}{\frac {dn_{s}}{dr}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -678,7 +680,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="rlts-1">
-<span id="tglf-rlts-1"></span><h2>RLTS_1<a class="headerlink" href="#rlts-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-rlts-1"></span><h2>RLTS_1<a class="headerlink" href="#rlts-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species array of normalized temperature gradients <span class="math notranslate nohighlight">\(-{\frac {a}{T_{s}}}{\frac {dT_{s}}{dr}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -688,7 +690,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="rmaj-loc">
-<span id="tglf-rmaj-loc"></span><h2>RMAJ_LOC<a class="headerlink" href="#rmaj-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-rmaj-loc"></span><h2>RMAJ_LOC<a class="headerlink" href="#rmaj-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flux surface centroid major radius <span class="math notranslate nohighlight">\(R_{maj}/a\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -698,7 +700,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="rmaj-sa">
-<span id="tglf-rmaj-sa"></span><h2>RMAJ_SA<a class="headerlink" href="#rmaj-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-rmaj-sa"></span><h2>RMAJ_SA<a class="headerlink" href="#rmaj-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized major radius of flux surface <span class="math notranslate nohighlight">\(R_{maj}/a\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -708,7 +710,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="rmin-loc">
-<span id="tglf-rmin-loc"></span><h2>RMIN_LOC<a class="headerlink" href="#rmin-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-rmin-loc"></span><h2>RMIN_LOC<a class="headerlink" href="#rmin-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flux surface centroid minor radius <span class="math notranslate nohighlight">\(r/a\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -718,7 +720,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="rmin-sa">
-<span id="tglf-rmin-sa"></span><h2>RMIN_SA<a class="headerlink" href="#rmin-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-rmin-sa"></span><h2>RMIN_SA<a class="headerlink" href="#rmin-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized minor radius of flux surface <span class="math notranslate nohighlight">\(r/a\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -728,7 +730,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="sat-rule">
-<span id="tglf-sat-rule"></span><h2>SAT_RULE<a class="headerlink" href="#sat-rule" title="Permalink to this headline"></a></h2>
+<span id="tglf-sat-rule"></span><h2>SAT_RULE<a class="headerlink" href="#sat-rule" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <ul class="simple">
 <li><p>SAT_RULE = 0 finds zonal flow shear at each ky (e.g. Kinsey, Staebler, Waltz, PoP, 2008)</p></li>
@@ -742,7 +744,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="shat-sa">
-<span id="tglf-shat-sa"></span><h2>SHAT_SA<a class="headerlink" href="#shat-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-shat-sa"></span><h2>SHAT_SA<a class="headerlink" href="#shat-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Magnetic shear <span class="math notranslate nohighlight">\({\frac {r}{q}}{\frac {\partial q}{\partial r}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -752,7 +754,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="sign-bt">
-<span id="tglf-sign-bt"></span><h2>SIGN_BT<a class="headerlink" href="#sign-bt" title="Permalink to this headline"></a></h2>
+<span id="tglf-sign-bt"></span><h2>SIGN_BT<a class="headerlink" href="#sign-bt" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Sign of <span class="math notranslate nohighlight">\(B_{T}\)</span>  with repsect to CCW toroidal direction from top.</p>
 <p><strong>Comments</strong></p>
@@ -762,7 +764,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="sign-it">
-<span id="tglf-sign-it"></span><h2>SIGN_IT<a class="headerlink" href="#sign-it" title="Permalink to this headline"></a></h2>
+<span id="tglf-sign-it"></span><h2>SIGN_IT<a class="headerlink" href="#sign-it" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Sign of <span class="math notranslate nohighlight">\(I_{T}\)</span>  with repsect to CCW toroidal direction from top.</p>
 <p><strong>Comments</strong></p>
@@ -772,7 +774,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="s-delta-loc">
-<span id="tglf-s-delta-loc"></span><h2>S_DELTA_LOC<a class="headerlink" href="#s-delta-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-s-delta-loc"></span><h2>S_DELTA_LOC<a class="headerlink" href="#s-delta-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Shear in triangularity, <span class="math notranslate nohighlight">\(r{\frac {\partial \delta }{\partial r}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -782,7 +784,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="s-kappa-loc">
-<span id="tglf-s-kappa-loc"></span><h2>S_KAPPA_LOC<a class="headerlink" href="#s-kappa-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-s-kappa-loc"></span><h2>S_KAPPA_LOC<a class="headerlink" href="#s-kappa-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Shear in elongation, <span class="math notranslate nohighlight">\({\frac {r}{\kappa }}{\frac {\partial \kappa }{\partial r}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -792,7 +794,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="s-zeta-loc">
-<span id="tglf-s-zeta-loc"></span><h2>S_ZETA_LOC<a class="headerlink" href="#s-zeta-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-s-zeta-loc"></span><h2>S_ZETA_LOC<a class="headerlink" href="#s-zeta-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Shear in squareness, <span class="math notranslate nohighlight">\(r{\frac {\partial \zeta }{\partial r}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -802,7 +804,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="taus-1">
-<span id="tglf-taus-1"></span><h2>TAUS_1<a class="headerlink" href="#taus-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-taus-1"></span><h2>TAUS_1<a class="headerlink" href="#taus-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species array of temperatures <span class="math notranslate nohighlight">\({\frac {T_{s}}{T_{e}}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -812,7 +814,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="theta0-sa">
-<span id="tglf-theta0-sa"></span><h2>THETA0_SA<a class="headerlink" href="#theta0-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-theta0-sa"></span><h2>THETA0_SA<a class="headerlink" href="#theta0-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><span class="math notranslate nohighlight">\(\theta _{0}={\frac {k_{x}}{sk_{y}}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -822,7 +824,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="theta-trapped">
-<span id="tglf-theta-trapped"></span><h2>THETA_TRAPPED<a class="headerlink" href="#theta-trapped" title="Permalink to this headline"></a></h2>
+<span id="tglf-theta-trapped"></span><h2>THETA_TRAPPED<a class="headerlink" href="#theta-trapped" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter to adjust trapped fraction model.</p>
 <p><strong>Comments</strong></p>
@@ -832,7 +834,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="units">
-<span id="tglf-units"></span><h2>UNITS<a class="headerlink" href="#units" title="Permalink to this headline"></a></h2>
+<span id="tglf-units"></span><h2>UNITS<a class="headerlink" href="#units" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Units system used for SAT1 (default is GYRO, but with CGYRO you get the more recent Nov. 2019 version of the spectral shift model and overall geometry factors calibrated by CGYRO runs). Note that  UNITS=CGYRO is enforced for SAT2, and GYRO is enforced for SAT0.</p>
 <p><strong>Comments</strong></p>
@@ -842,7 +844,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="use-bisection">
-<span id="tglf-use-bisection"></span><h2>USE_BISECTION<a class="headerlink" href="#use-bisection" title="Permalink to this headline"></a></h2>
+<span id="tglf-use-bisection"></span><h2>USE_BISECTION<a class="headerlink" href="#use-bisection" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Use bisection search method to find width that maximizes growth rate.</p>
 <p><strong>Comments</strong></p>
@@ -852,7 +854,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="use-bpar">
-<span id="tglf-use-bpar"></span><h2>USE_BPAR<a class="headerlink" href="#use-bpar" title="Permalink to this headline"></a></h2>
+<span id="tglf-use-bpar"></span><h2>USE_BPAR<a class="headerlink" href="#use-bpar" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Include compressional magnetic fluctuations, <span class="math notranslate nohighlight">\(\delta B_{\lVert }\)</span>. Note: The BPAR flutter is not well resolved by TGLF (not enough moments) and does not reproduce GYRO linear results for NSTX-U.</p>
 <p><strong>Comments</strong></p>
@@ -862,7 +864,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="use-bper">
-<span id="tglf-use-bper"></span><h2>USE_BPER<a class="headerlink" href="#use-bper" title="Permalink to this headline"></a></h2>
+<span id="tglf-use-bper"></span><h2>USE_BPER<a class="headerlink" href="#use-bper" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Include transverse magnetic fluctuations, <span class="math notranslate nohighlight">\(\delta A_{\lVert }\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -872,7 +874,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="use-inboard-detrapped">
-<span id="tglf-use-inboard-detrapped"></span><h2>USE_INBOARD_DETRAPPED<a class="headerlink" href="#use-inboard-detrapped" title="Permalink to this headline"></a></h2>
+<span id="tglf-use-inboard-detrapped"></span><h2>USE_INBOARD_DETRAPPED<a class="headerlink" href="#use-inboard-detrapped" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Set trapped fraction to zero if eigenmode is inward ballooning.</p>
 <p><strong>Comments</strong></p>
@@ -882,7 +884,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="use-mhd-rule">
-<span id="tglf-use-mhd-rule"></span><h2>USE_MHD_RULE<a class="headerlink" href="#use-mhd-rule" title="Permalink to this headline"></a></h2>
+<span id="tglf-use-mhd-rule"></span><h2>USE_MHD_RULE<a class="headerlink" href="#use-mhd-rule" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Ignore pressure gradient contribution to curvature drift. Recommend setting to .false. for high beta.</p>
 <p><strong>Comments</strong></p>
@@ -892,7 +894,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="use-transport-model">
-<span id="tglf-use-transport-model"></span><h2>USE_TRANSPORT_MODEL<a class="headerlink" href="#use-transport-model" title="Permalink to this headline"></a></h2>
+<span id="tglf-use-transport-model"></span><h2>USE_TRANSPORT_MODEL<a class="headerlink" href="#use-transport-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Comments</strong></p>
 <ul class="simple">
@@ -901,7 +903,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="vexb">
-<span id="tglf-vexb"></span><h2>VEXB<a class="headerlink" href="#vexb" title="Permalink to this headline"></a></h2>
+<span id="tglf-vexb"></span><h2>VEXB<a class="headerlink" href="#vexb" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized of ExB velocity Doppler shift common to all species (not in use, see VPAR).</p>
 <p><strong>Comments</strong></p>
@@ -911,7 +913,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="vexb-shear">
-<span id="tglf-vexb-shear"></span><h2>VEXB_SHEAR<a class="headerlink" href="#vexb-shear" title="Permalink to this headline"></a></h2>
+<span id="tglf-vexb-shear"></span><h2>VEXB_SHEAR<a class="headerlink" href="#vexb-shear" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized toroidal ExB velocity Doppler shift gradient common to all species. For large ExB velocity ordering <span class="math notranslate nohighlight">\(V_{tor}=V_{ExB}\)</span>.
 VEXB_SHEAR = <span class="math notranslate nohighlight">\(-SIGN(I_{tor}){\frac {r}{ABS(q)}}{\frac {\partial }{\partial r}}({\frac {V_{ExB}}{R}}){\frac {a}{c_{s}}}\)</span>.</p>
@@ -922,7 +924,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="vpar-1">
-<span id="tglf-vpar-1"></span><h2>VPAR_1<a class="headerlink" href="#vpar-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-vpar-1"></span><h2>VPAR_1<a class="headerlink" href="#vpar-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species array of parallel velocities, <span class="math notranslate nohighlight">\(SIGN(I_{tor}){\frac {R_{maj}V_{tor}}{Rc_{s}}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -932,7 +934,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="vpar-model">
-<span id="tglf-vpar-model"></span><h2>VPAR_MODEL<a class="headerlink" href="#vpar-model" title="Permalink to this headline"></a></h2>
+<span id="tglf-vpar-model"></span><h2>VPAR_MODEL<a class="headerlink" href="#vpar-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p><strong>Choices</strong></p>
 <ul class="simple">
@@ -945,7 +947,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="vpar-shear-1">
-<span id="tglf-vpar-shear-1"></span><h2>VPAR_SHEAR_1<a class="headerlink" href="#vpar-shear-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-vpar-shear-1"></span><h2>VPAR_SHEAR_1<a class="headerlink" href="#vpar-shear-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Normalized parallel velocity gradient, <span class="math notranslate nohighlight">\(-SIGN(I_{tor})R_{maj}{\frac {\partial }{\partial r}}({\frac {V_{tor}}{R}}){\frac {a}{c_{s}}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -955,7 +957,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="vpar-shear-model">
-<span id="tglf-vpar-shear-model"></span><h2>VPAR_SHEAR_MODEL<a class="headerlink" href="#vpar-shear-model" title="Permalink to this headline"></a></h2>
+<span id="tglf-vpar-shear-model"></span><h2>VPAR_SHEAR_MODEL<a class="headerlink" href="#vpar-shear-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Depricated parameter.</p>
 <p><strong>Comments</strong></p>
@@ -965,7 +967,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="wd-zero">
-<span id="tglf-wd-zero"></span><h2>WD_ZERO<a class="headerlink" href="#wd-zero" title="Permalink to this headline"></a></h2>
+<span id="tglf-wd-zero"></span><h2>WD_ZERO<a class="headerlink" href="#wd-zero" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Cutoff for curvature drift eigenvalues to prevent zero.</p>
 <p><strong>Comments</strong></p>
@@ -975,7 +977,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="width">
-<span id="tglf-width"></span><h2>WIDTH<a class="headerlink" href="#width" title="Permalink to this headline"></a></h2>
+<span id="tglf-width"></span><h2>WIDTH<a class="headerlink" href="#width" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum width of the Gaussian measure for the parallel Hermite polynomial basis.</p>
 <p><strong>Comments</strong></p>
@@ -985,7 +987,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="width-min">
-<span id="tglf-width-min"></span><h2>WIDTH_MIN<a class="headerlink" href="#width-min" title="Permalink to this headline"></a></h2>
+<span id="tglf-width-min"></span><h2>WIDTH_MIN<a class="headerlink" href="#width-min" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Minimum width used in search for maximum growth rate.</p>
 <p><strong>Comments</strong></p>
@@ -995,7 +997,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="write-wavefunction-flag">
-<span id="tglf-write-wavefunction-flag"></span><h2>WRITE_WAVEFUNCTION_FLAG<a class="headerlink" href="#write-wavefunction-flag" title="Permalink to this headline"></a></h2>
+<span id="tglf-write-wavefunction-flag"></span><h2>WRITE_WAVEFUNCTION_FLAG<a class="headerlink" href="#write-wavefunction-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Self-explanatory.</p>
 <p><strong>Comments</strong></p>
@@ -1005,7 +1007,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="xnue">
-<span id="tglf-xnue"></span><h2>XNUE<a class="headerlink" href="#xnue" title="Permalink to this headline"></a></h2>
+<span id="tglf-xnue"></span><h2>XNUE<a class="headerlink" href="#xnue" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Electron-ion collision frequency <span class="math notranslate nohighlight">\({\frac {v_{ei}}{c_{s}/a}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -1015,7 +1017,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="xnu-factor">
-<span id="tglf-xnu-factor"></span><h2>XNU_FACTOR<a class="headerlink" href="#xnu-factor" title="Permalink to this headline"></a></h2>
+<span id="tglf-xnu-factor"></span><h2>XNU_FACTOR<a class="headerlink" href="#xnu-factor" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Multiplies the trapped/passing boundary electron-ion collision terms.</p>
 <p><strong>Comments</strong></p>
@@ -1025,7 +1027,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="xnu-model">
-<span id="tglf-xnu-model"></span><h2>XNU_MODEL<a class="headerlink" href="#xnu-model" title="Permalink to this headline"></a></h2>
+<span id="tglf-xnu-model"></span><h2>XNU_MODEL<a class="headerlink" href="#xnu-model" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Collision model.</p>
 <p><strong>Choices</strong></p>
@@ -1040,7 +1042,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="xwell-sa">
-<span id="tglf-xwell-sa"></span><h2>XWELL_SA<a class="headerlink" href="#xwell-sa" title="Permalink to this headline"></a></h2>
+<span id="tglf-xwell-sa"></span><h2>XWELL_SA<a class="headerlink" href="#xwell-sa" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Magnetic well.</p>
 <p><strong>Comments</strong></p>
@@ -1050,7 +1052,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="zeff">
-<span id="tglf-zeff"></span><h2>ZEFF<a class="headerlink" href="#zeff" title="Permalink to this headline"></a></h2>
+<span id="tglf-zeff"></span><h2>ZEFF<a class="headerlink" href="#zeff" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Effective ion charge.</p>
 <p><strong>Comments</strong></p>
@@ -1060,7 +1062,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="zeta-loc">
-<span id="tglf-zeta-loc"></span><h2>ZETA_LOC<a class="headerlink" href="#zeta-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-zeta-loc"></span><h2>ZETA_LOC<a class="headerlink" href="#zeta-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Squareness, <span class="math notranslate nohighlight">\(\zeta \,\!\)</span> , of flux surface.</p>
 <p><strong>Comments</strong></p>
@@ -1070,7 +1072,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="zmaj-loc">
-<span id="tglf-zmaj-loc"></span><h2>ZMAJ_LOC<a class="headerlink" href="#zmaj-loc" title="Permalink to this headline"></a></h2>
+<span id="tglf-zmaj-loc"></span><h2>ZMAJ_LOC<a class="headerlink" href="#zmaj-loc" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flux surface centroid elevation <span class="math notranslate nohighlight">\(Z_{maj}/a\,\!\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -1080,7 +1082,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <hr class="docutils" />
 </section>
 <section id="zs-1">
-<span id="tglf-zs-1"></span><h2>ZS_1<a class="headerlink" href="#zs-1" title="Permalink to this headline"></a></h2>
+<span id="tglf-zs-1"></span><h2>ZS_1<a class="headerlink" href="#zs-1" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Species charge numbers.</p>
 <p><strong>Comments</strong></p>
diff --git a/docs/tglf/tglf_output_list.html b/docs/tglf/tglf_output_list.html
index 01ca484..d3d878c 100644
--- a/docs/tglf/tglf_output_list.html
+++ b/docs/tglf/tglf_output_list.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>
@@ -101,9 +103,9 @@
         <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><a href="../tglf.html">TGLF</a> &raquo;</li>
-      <li>Alphabetical list for out.tglf files</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tglf.html">TGLF</a></li>
+      <li class="breadcrumb-item active">Alphabetical list for out.tglf files</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tglf/tglf_output_list.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -114,9 +116,9 @@
            <div itemprop="articleBody">
              
   <section id="alphabetical-list-for-out-tglf-files">
-<h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetical-list-for-out-tglf-files" title="Permalink to this headline"></a></h1>
+<h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetical-list-for-out-tglf-files" title="Permalink to this heading"></a></h1>
 <section id="density-spectrum">
-<span id="tglf-density-spectrum"></span><h2>density_spectrum<a class="headerlink" href="#density-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-density-spectrum"></span><h2>density_spectrum<a class="headerlink" href="#density-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Gyro-bohm normalized density fluctuation amplitude spectra, <span class="math notranslate nohighlight">\({\frac {a \delta \tilde{n}_{s,k_y}}{\rho_s n_{e0}}}\)</span>.</p>
 <p><strong>Comments</strong></p>
@@ -126,7 +128,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="eigenvalue-spectrum">
-<span id="tglf-eigenvalue-spectrum"></span><h2>eigenvalue_spectrum<a class="headerlink" href="#eigenvalue-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-eigenvalue-spectrum"></span><h2>eigenvalue_spectrum<a class="headerlink" href="#eigenvalue-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Gyro-bohm normalized eigenvalue spectra</p>
 <p><strong>Comments</strong></p>
@@ -136,7 +138,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="field-spectrum">
-<span id="tglf-field-spectrum"></span><h2>field_spectrum<a class="headerlink" href="#field-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-field-spectrum"></span><h2>field_spectrum<a class="headerlink" href="#field-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Gyro-bohm normalized field fluctuation intensity spectra per mode</p>
 <p><strong>Comments</strong></p>
@@ -145,7 +147,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 </ul>
 </section>
 <section id="intensity-spectrum">
-<span id="tglf-intensity-spectrum"></span><h2>intensity_spectrum<a class="headerlink" href="#intensity-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-intensity-spectrum"></span><h2>intensity_spectrum<a class="headerlink" href="#intensity-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Gyro-bohm normalized intensity fluctuation amplitude spectra per mode</p>
 <p><strong>Comments</strong></p>
@@ -156,7 +158,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="nsts-crossphase-spectrum">
-<span id="tglf-nsts-crossphase-spectrum"></span><h2>nsts_crossphase_spectrum<a class="headerlink" href="#nsts-crossphase-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-nsts-crossphase-spectrum"></span><h2>nsts_crossphase_spectrum<a class="headerlink" href="#nsts-crossphase-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Density-temperature cross phase spectra per mode for each species</p>
 <p><strong>Comments</strong></p>
@@ -166,7 +168,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="ql-flux-spectrum">
-<span id="tglf-ql-flux-spectrum"></span><h2>QL_flux_spectrum<a class="headerlink" href="#ql-flux-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-ql-flux-spectrum"></span><h2>QL_flux_spectrum<a class="headerlink" href="#ql-flux-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>QL weights per mode, species, field and type (type = particle, energy, toroidal stress, parallel stress, exchange)</p>
 <p><strong>Comments</strong></p>
@@ -176,7 +178,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="sat-geo-spectrum">
-<span id="tglf-sat-geo-spectrum"></span><h2>sat_geo_spectrum<a class="headerlink" href="#sat-geo-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-sat-geo-spectrum"></span><h2>sat_geo_spectrum<a class="headerlink" href="#sat-geo-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Saturation model geometry factor per mode <span class="math notranslate nohighlight">\({\frac {&lt;\phi|\phi&gt;}{&lt;\phi| B^2/B_{unit}^2 |\phi&gt;}}\)</span></p>
 <p><strong>Comments</strong></p>
@@ -186,13 +188,13 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="scalar-saturation-parameters">
-<span id="tglf-scalar-saturation-parameters"></span><h2>scalar_saturation_parameters<a class="headerlink" href="#scalar-saturation-parameters" title="Permalink to this headline"></a></h2>
+<span id="tglf-scalar-saturation-parameters"></span><h2>scalar_saturation_parameters<a class="headerlink" href="#scalar-saturation-parameters" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>This output file has all of the scalar saturation parameters used for different settings of <a class="reference internal" href="tglf_list.html#tglf-sat-rule"><span class="std std-ref">SAT_RULE</span></a>,  <a class="reference internal" href="tglf_list.html#tglf-units"><span class="std std-ref">UNITS</span></a>,  <a class="reference internal" href="tglf_list.html#tglf-alpha-zf"><span class="std std-ref">ALPHA_ZF</span></a></p>
 <hr class="docutils" />
 </section>
 <section id="spectral-shift">
-<span id="tglf-spectral-shift"></span><h2>spectral_shift<a class="headerlink" href="#spectral-shift" title="Permalink to this headline"></a></h2>
+<span id="tglf-spectral-shift"></span><h2>spectral_shift<a class="headerlink" href="#spectral-shift" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>kx spectral shift model is used when ALPHA_QUENCH=0 and ALPHA_E=1.0. Note: The mode for the spectral shift, <span class="math notranslate nohighlight">\(kx_e={\frac{&lt;\phi| k_x/k_y |\phi&gt;}{&lt;\phi|\phi&gt;}}\)</span>, depends on which saturation model is being used: SAT_RULE and UNITS settings</p>
 <p><strong>Comments</strong></p>
@@ -202,7 +204,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="sum-flux-spectrum">
-<span id="tglf-sum-flux-spectrum"></span><h2>sum_flux_spectrum<a class="headerlink" href="#sum-flux-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-sum-flux-spectrum"></span><h2>sum_flux_spectrum<a class="headerlink" href="#sum-flux-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>flux spectrum summed over nmodes. A simple sum over nky axis will give total flux.</p>
 <p><strong>Comments</strong></p>
@@ -213,7 +215,7 @@ <h1>Alphabetical list for out.tglf files<a class="headerlink" href="#alphabetica
 <hr class="docutils" />
 </section>
 <section id="temperature-spectrum">
-<span id="tglf-temperature-spectrum"></span><h2>temperature_spectrum<a class="headerlink" href="#temperature-spectrum" title="Permalink to this headline"></a></h2>
+<span id="tglf-temperature-spectrum"></span><h2>temperature_spectrum<a class="headerlink" href="#temperature-spectrum" title="Permalink to this heading"></a></h2>
 <p><strong>Description</strong></p>
 <p>Gyro-bohm normalized temperature fluctuation amplitude spectra</p>
 <p><strong>Comments</strong></p>
diff --git a/docs/tglf/tglf_table.html b/docs/tglf/tglf_table.html
index b97a876..0d6849d 100644
--- a/docs/tglf/tglf_table.html
+++ b/docs/tglf/tglf_table.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>
@@ -88,9 +90,9 @@
         <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><a href="../tglf.html">TGLF</a> &raquo;</li>
-      <li>Table of inputs and outputs</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tglf.html">TGLF</a></li>
+      <li class="breadcrumb-item active">Table of inputs and outputs</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tglf/tglf_table.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -101,7 +103,7 @@
            <div itemprop="articleBody">
              
   <section id="table-of-inputs-and-outputs">
-<h1>Table of inputs and outputs<a class="headerlink" href="#table-of-inputs-and-outputs" title="Permalink to this headline"></a></h1>
+<h1>Table of inputs and outputs<a class="headerlink" href="#table-of-inputs-and-outputs" title="Permalink to this heading"></a></h1>
 <table class="colwidths-given docutils align-default" id="id1">
 <caption><span class="caption-text"><strong>Control</strong></span><a class="headerlink" href="#id1" title="Permalink to this table"></a></caption>
 <colgroup>
diff --git a/docs/tgyro.html b/docs/tgyro.html
index 0d5c8ef..21a139d 100644
--- a/docs/tgyro.html
+++ b/docs/tgyro.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" />
@@ -94,8 +96,8 @@
         <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>TGYRO</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">TGYRO</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/tgyro.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -106,9 +108,9 @@
            <div itemprop="articleBody">
              
   <section id="tgyro">
-<h1>TGYRO<a class="headerlink" href="#tgyro" title="Permalink to this headline"></a></h1>
+<h1>TGYRO<a class="headerlink" href="#tgyro" title="Permalink to this heading"></a></h1>
 <section id="quick-links">
-<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this headline"></a></h2>
+<h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to this heading"></a></h2>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="tgyro/tgyro_table.html">input.tgyro Tabular List</a></li>
@@ -122,7 +124,7 @@ <h2>Quick links<a class="headerlink" href="#quick-links" title="Permalink to thi
 </div>
 </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>TGYRO is a parallel transport manager with the ability to call multiple
 instances of TGLF and NEO in order to obtain steady-state temperature,
 density and rotation profiles.  The code was designed to operate with a
@@ -132,17 +134,17 @@ <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this head
 manager for ensembles of independent GYRO/CGYRO simulations.</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>
 <p>The primary TGYRO input file is <a class="reference internal" href="tgyro/tgyro_table.html"><span class="doc">input.tgyro</span></a>, with
 profile data defined in <a class="reference internal" href="input_gacode.html#input-gacode"><span class="std std-ref">input.gacode</span></a>.</p>
 </section>
 <section id="data-output-python-interface-and-plotting">
-<h2>Data output, python interface, and plotting<a class="headerlink" href="#data-output-python-interface-and-plotting" title="Permalink to this headline"></a></h2>
+<h2>Data output, python interface, and plotting<a class="headerlink" href="#data-output-python-interface-and-plotting" title="Permalink to this heading"></a></h2>
 <p>Although there is a description of <a class="reference internal" href="tgyro/output.html"><span class="doc">output data</span></a>, it is
 suggested that users use the <a class="reference internal" href="tgyro/plot.html"><span class="doc">python interface</span></a> to output data.</p>
 </section>
 <section id="transport-equations-and-solution">
-<h2>Transport equations and solution<a class="headerlink" href="#transport-equations-and-solution" title="Permalink to this headline"></a></h2>
+<h2>Transport equations and solution<a class="headerlink" href="#transport-equations-and-solution" title="Permalink to this heading"></a></h2>
 <p>We give a brief description of the transport equations, see <a class="reference internal" href="tgyro/equations.html#tgyro-equations"><span class="std std-ref">Equations solved in TGYRO</span></a>.
 Unlike most other transport solvers, the solution algorithm in TGYRO is <strong>not</strong> based
 on time-integration of the transport equations.  Instead, the steady-state
diff --git a/docs/tgyro/equations.html b/docs/tgyro/equations.html
index 790107d..1683774 100644
--- a/docs/tgyro/equations.html
+++ b/docs/tgyro/equations.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>
@@ -101,9 +103,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>Equations solved in TGYRO</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">Equations solved in TGYRO</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/equations.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -114,7 +116,7 @@
            <div itemprop="articleBody">
              
   <section id="equations-solved-in-tgyro">
-<span id="tgyro-equations"></span><h1>Equations solved in TGYRO<a class="headerlink" href="#equations-solved-in-tgyro" title="Permalink to this headline"></a></h1>
+<span id="tgyro-equations"></span><h1>Equations solved in TGYRO<a class="headerlink" href="#equations-solved-in-tgyro" title="Permalink to this heading"></a></h1>
 <p>Below we write the most general form of the transport equations solved by TGYRO.  The
 calculation chain in NEO-CGYRO-TGYRO is a faithful representation of the comprehensive
 transport theory of Sugama <span id="id1">[<a class="reference internal" href="../zreferences.html#id104" title="H. Sugama and W. Horton. Nonlinear electromagnetic gyrokinetic equation for plasmas with large mean flows. Phys. Plasmas, 5:2560, 1998.">SH98</a>]</span>.  This paper is <em>required reading</em> for a
@@ -122,7 +124,7 @@
 Sugama’s form of the transport equations, with some practical simplifications and
 notational differences.</p>
 <section id="density-transport">
-<h2>Density Transport<a class="headerlink" href="#density-transport" title="Permalink to this headline"></a></h2>
+<h2>Density Transport<a class="headerlink" href="#density-transport" title="Permalink to this heading"></a></h2>
 <div class="math notranslate nohighlight">
 \[\frac{\partial \langle n_a \rangle}{\partial t} +
 \frac{1}{V^\prime}\frac{\partial}{\partial r} \left( V^\prime \Gamma_a \right)
@@ -167,7 +169,7 @@ <h2>Density Transport<a class="headerlink" href="#density-transport" title="Perm
 </table>
 </section>
 <section id="energy-transport">
-<h2>Energy Transport<a class="headerlink" href="#energy-transport" title="Permalink to this headline"></a></h2>
+<h2>Energy Transport<a class="headerlink" href="#energy-transport" title="Permalink to this heading"></a></h2>
 <div class="math notranslate nohighlight">
 \[\frac{\partial \langle W_a \rangle}{\partial t} + \
 \frac{1}{V^\prime}\frac{\partial}{\partial r} \left( V^\prime Q_a \right) +
@@ -225,7 +227,7 @@ <h2>Energy Transport<a class="headerlink" href="#energy-transport" title="Permal
 </table>
 </section>
 <section id="momentum-transport">
-<h2>Momentum Transport<a class="headerlink" href="#momentum-transport" title="Permalink to this headline"></a></h2>
+<h2>Momentum Transport<a class="headerlink" href="#momentum-transport" title="Permalink to this heading"></a></h2>
 <div class="math notranslate nohighlight">
 \[\frac{\partial}{\partial t} \left( \omega_0 \langle R^2 \rangle \sum_a m_a n_a \right)
 + \frac{1}{V^\prime}\frac{\partial}{\partial r} \left( V^\prime \sum_a \Pi_a \right)
@@ -263,7 +265,7 @@ <h2>Momentum Transport<a class="headerlink" href="#momentum-transport" title="Pe
 </table>
 </section>
 <section id="connection-of-fluxes-to-powers">
-<h2>Connection of Fluxes to Powers<a class="headerlink" href="#connection-of-fluxes-to-powers" title="Permalink to this headline"></a></h2>
+<h2>Connection of Fluxes to Powers<a class="headerlink" href="#connection-of-fluxes-to-powers" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p>Volume element</p></li>
 </ul>
diff --git a/docs/tgyro/output.html b/docs/tgyro/output.html
index 87908e7..9dd38f0 100644
--- a/docs/tgyro/output.html
+++ b/docs/tgyro/output.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" />
@@ -94,9 +96,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>OUTPUT</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">OUTPUT</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/output.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -107,7 +109,7 @@
            <div itemprop="articleBody">
              
   <section id="output">
-<h1>OUTPUT<a class="headerlink" href="#output" title="Permalink to this headline"></a></h1>
+<h1>OUTPUT<a class="headerlink" href="#output" title="Permalink to this heading"></a></h1>
 </section>
 
 
diff --git a/docs/tgyro/plot.html b/docs/tgyro/plot.html
index 191acfd..7c30026 100644
--- a/docs/tgyro/plot.html
+++ b/docs/tgyro/plot.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" />
@@ -94,9 +96,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>PLOT</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">PLOT</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/plot.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -107,7 +109,7 @@
            <div itemprop="articleBody">
              
   <section id="plot">
-<h1>PLOT<a class="headerlink" href="#plot" title="Permalink to this headline"></a></h1>
+<h1>PLOT<a class="headerlink" href="#plot" title="Permalink to this heading"></a></h1>
 </section>
 
 
diff --git a/docs/tgyro/scenarios.html b/docs/tgyro/scenarios.html
index 35d679f..65a66c3 100644
--- a/docs/tgyro/scenarios.html
+++ b/docs/tgyro/scenarios.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>
@@ -95,9 +97,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>Scenarios and connection to energy sources</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">Scenarios and connection to energy sources</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/scenarios.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -108,7 +110,7 @@
            <div itemprop="articleBody">
              
   <section id="scenarios-and-connection-to-energy-sources">
-<span id="tgyro-scenarios"></span><h1>Scenarios and connection to energy sources<a class="headerlink" href="#scenarios-and-connection-to-energy-sources" title="Permalink to this headline"></a></h1>
+<span id="tgyro-scenarios"></span><h1>Scenarios and connection to energy sources<a class="headerlink" href="#scenarios-and-connection-to-energy-sources" title="Permalink to this heading"></a></h1>
 <div class="math notranslate nohighlight">
 \[\begin{split}\begin{align}
 q_e^\mathrm{aux} = &amp;~\mathtt{qohme}+\mathtt{qbeame}+\mathtt{qrfe}+\mathtt{qione} \\
diff --git a/docs/tgyro/solver.html b/docs/tgyro/solver.html
index 667ade4..aa8bd98 100644
--- a/docs/tgyro/solver.html
+++ b/docs/tgyro/solver.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>
@@ -102,9 +104,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>TGYRO solver algorithm</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">TGYRO solver algorithm</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/solver.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -115,14 +117,14 @@
            <div itemprop="articleBody">
              
   <section id="tgyro-solver-algorithm">
-<span id="tgyro-solver"></span><h1>TGYRO solver algorithm<a class="headerlink" href="#tgyro-solver-algorithm" title="Permalink to this headline"></a></h1>
+<span id="tgyro-solver"></span><h1>TGYRO solver algorithm<a class="headerlink" href="#tgyro-solver-algorithm" title="Permalink to this heading"></a></h1>
 <p>TGYRO solves the <em>steady-state transport problem</em>; that is, the transport
 equations with <span class="math notranslate nohighlight">\(\partial_t \rightarrow 0\)</span>.  This algorithm was originally
 envisioned to form the basis for a time-implicit solver, but frankly there has
 been little interest or need for this capability.  Instead, flexibility in
 dealing with multiple ions and solver robustness have been emphasized.</p>
 <section id="formulation">
-<h2>Formulation<a class="headerlink" href="#formulation" title="Permalink to this headline"></a></h2>
+<h2>Formulation<a class="headerlink" href="#formulation" title="Permalink to this heading"></a></h2>
 <p>To describe the algorithm, we will restrict attention to coupled <span class="math notranslate nohighlight">\(T_i\)</span>
 and <span class="math notranslate nohighlight">\(T_e\)</span> evolution, even though density and rotation can also be
 evolved.</p>
@@ -144,7 +146,7 @@ <h2>Formulation<a class="headerlink" href="#formulation" title="Permalink to thi
 detail in the <a class="reference internal" href="equations.html#tgyro-equations"><span class="std std-ref">Equations solved in TGYRO</span></a> .</p>
 </section>
 <section id="some-comments-regarding-units">
-<h2>Some comments regarding units<a class="headerlink" href="#some-comments-regarding-units" title="Permalink to this headline"></a></h2>
+<h2>Some comments regarding units<a class="headerlink" href="#some-comments-regarding-units" title="Permalink to this heading"></a></h2>
 <p>In TGYRO, we have found it convenient to use CGS units rather than employing some variant of the more
 popular dimensionless normalizations.  Thus, we have</p>
 <div class="math notranslate nohighlight">
@@ -156,7 +158,7 @@ <h2>Some comments regarding units<a class="headerlink" href="#some-comments-rega
 \end{align}\end{split}\]</div>
 </section>
 <section id="solution-strategy">
-<h2>Solution strategy<a class="headerlink" href="#solution-strategy" title="Permalink to this headline"></a></h2>
+<h2>Solution strategy<a class="headerlink" href="#solution-strategy" title="Permalink to this heading"></a></h2>
 <p>Rather than solving the equations directly, we prefer to solve the volume-integrated form
 of the equation so that we can deal directly with the fluxes:</p>
 <div class="math notranslate nohighlight">
@@ -192,7 +194,7 @@ <h2>Solution strategy<a class="headerlink" href="#solution-strategy" title="Perm
 \end{equation}\]</div>
 </section>
 <section id="formulation-on-a-discrete-grid">
-<h2>Formulation on a discrete grid<a class="headerlink" href="#formulation-on-a-discrete-grid" title="Permalink to this headline"></a></h2>
+<h2>Formulation on a discrete grid<a class="headerlink" href="#formulation-on-a-discrete-grid" title="Permalink to this heading"></a></h2>
 <p>On a discrete grid <span class="math notranslate nohighlight">\(r_j\)</span>, the temperature profile can be approximately determined using
 the trapezoidal rule</p>
 <div class="math notranslate nohighlight">
@@ -336,7 +338,7 @@ <h2>Formulation on a discrete grid<a class="headerlink" href="#formulation-on-a-
 iteration component.</p>
 </section>
 <section id="computation-of-the-jacobian">
-<h2>Computation of the Jacobian<a class="headerlink" href="#computation-of-the-jacobian" title="Permalink to this headline"></a></h2>
+<h2>Computation of the Jacobian<a class="headerlink" href="#computation-of-the-jacobian" title="Permalink to this heading"></a></h2>
 <p>We approximate the derivatives in the Jacobian matrix using a forward difference approximation</p>
 <div class="math notranslate nohighlight">
 \[\frac{\partial \widehat{Q}_{\sigma,j}}{\partial z_{\sigma^\prime,j^\prime}} \simeq
diff --git a/docs/tgyro/tgyro_list.html b/docs/tgyro/tgyro_list.html
index 2113c5f..59a7748 100644
--- a/docs/tgyro/tgyro_list.html
+++ b/docs/tgyro/tgyro_list.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>
@@ -117,9 +119,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>input.tgyro Alphabetical List</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">input.tgyro Alphabetical List</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/tgyro_list.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -130,9 +132,9 @@
            <div itemprop="articleBody">
              
   <section id="input-tgyro-alphabetical-list">
-<h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphabetical-list" title="Permalink to this headline"></a></h1>
+<h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphabetical-list" title="Permalink to this heading"></a></h1>
 <section id="loc-betae-scale">
-<span id="tgyro-loc-betae-scale"></span><h2>LOC_BETAE_SCALE<a class="headerlink" href="#loc-betae-scale" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-betae-scale"></span><h2>LOC_BETAE_SCALE<a class="headerlink" href="#loc-betae-scale" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Amount to scale electron beta</p>
 <p><strong>Comments</strong></p>
@@ -144,7 +146,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="tgyro-den-method">
-<span id="id1"></span><h2>TGYRO_DEN_METHOD*<a class="headerlink" href="#tgyro-den-method" title="Permalink to this headline"></a></h2>
+<span id="id1"></span><h2>TGYRO_DEN_METHOD*<a class="headerlink" href="#tgyro-den-method" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Rules for evolving species.</p>
 <p><strong>Choices</strong></p>
@@ -187,7 +189,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="loc-dx">
-<span id="tgyro-loc-dx"></span><h2>LOC_DX<a class="headerlink" href="#loc-dx" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-dx"></span><h2>LOC_DX<a class="headerlink" href="#loc-dx" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Step length, <span class="math notranslate nohighlight">\(\Delta z\)</span>, used to compute the finite-difference approximation to the Jacobian.</p>
 <p><strong>Comments</strong></p>
@@ -200,7 +202,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="loc-dx-max">
-<span id="tgyro-loc-dx-max"></span><h2>LOC_DX_MAX<a class="headerlink" href="#loc-dx-max" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-dx-max"></span><h2>LOC_DX_MAX<a class="headerlink" href="#loc-dx-max" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum length, <span class="math notranslate nohighlight">\(\Delta z_\mathrm{max}\)</span>, of any Newton step.</p>
 <p><strong>Comments</strong></p>
@@ -213,7 +215,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="loc-er-feedback-flag">
-<span id="tgyro-loc-er-feedback-flag"></span><h2>LOC_ER_FEEDBACK_FLAG<a class="headerlink" href="#loc-er-feedback-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-er-feedback-flag"></span><h2>LOC_ER_FEEDBACK_FLAG<a class="headerlink" href="#loc-er-feedback-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to signal electric field evolution</p>
 <p><strong>Comments</strong></p>
@@ -226,7 +228,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="loc-evolve-grad-only-flag">
-<span id="tgyro-loc-evolve-grad-only-flag"></span><h2>LOC_EVOLVE_GRAD_ONLY_FLAG<a class="headerlink" href="#loc-evolve-grad-only-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-evolve-grad-only-flag"></span><h2>LOC_EVOLVE_GRAD_ONLY_FLAG<a class="headerlink" href="#loc-evolve-grad-only-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to allow decoupling of profile and corresponding gradient scale length evolution</p>
 <p><strong>Choices</strong></p>
@@ -243,7 +245,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="loc-he-feedback-flag">
-<span id="tgyro-loc-he-feedback-flag"></span><h2>LOC_HE_FEEDBACK_FLAG<a class="headerlink" href="#loc-he-feedback-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-he-feedback-flag"></span><h2>LOC_HE_FEEDBACK_FLAG<a class="headerlink" href="#loc-he-feedback-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to signal helium ash evolution</p>
 <p><strong>Comments</strong></p>
@@ -256,7 +258,7 @@ <h1>input.tgyro Alphabetical List<a class="headerlink" href="#input-tgyro-alphab
 <hr class="docutils" />
 </section>
 <section id="tgyro-iteration-method">
-<h2>TGYRO_ITERATION_METHOD<a class="headerlink" href="#tgyro-iteration-method" title="Permalink to this headline"></a></h2>
+<h2>TGYRO_ITERATION_METHOD<a class="headerlink" href="#tgyro-iteration-method" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Variation of Newton method used for root-finding.</p>
 <p><strong>Choices</strong></p>
@@ -284,7 +286,7 @@ <h2>TGYRO_ITERATION_METHOD<a class="headerlink" href="#tgyro-iteration-method" t
 <hr class="docutils" />
 </section>
 <section id="loc-lock-profile-flag">
-<span id="tgyro-loc-lock-profile-flag"></span><h2>LOC_LOCK_PROFILE_FLAG<a class="headerlink" href="#loc-lock-profile-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-lock-profile-flag"></span><h2>LOC_LOCK_PROFILE_FLAG<a class="headerlink" href="#loc-lock-profile-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to manage calculation of initial profile</p>
 <p><strong>Choices</strong></p>
@@ -303,7 +305,7 @@ <h2>TGYRO_ITERATION_METHOD<a class="headerlink" href="#tgyro-iteration-method" t
 <hr class="docutils" />
 </section>
 <section id="tgyro-mode">
-<h2>TGYRO_MODE<a class="headerlink" href="#tgyro-mode" title="Permalink to this headline"></a></h2>
+<h2>TGYRO_MODE<a class="headerlink" href="#tgyro-mode" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>High-level control of TGYRO operational mode.</p>
 <p><strong>Choices</strong></p>
@@ -370,7 +372,7 @@ <h2>TGYRO_MODE<a class="headerlink" href="#tgyro-mode" title="Permalink to this
 <hr class="docutils" />
 </section>
 <section id="tgyro-neo-method">
-<h2>TGYRO_NEO_METHOD<a class="headerlink" href="#tgyro-neo-method" title="Permalink to this headline"></a></h2>
+<h2>TGYRO_NEO_METHOD<a class="headerlink" href="#tgyro-neo-method" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Control of NEO code.</p>
 <p><strong>Choices</strong></p>
@@ -384,7 +386,7 @@ <h2>TGYRO_NEO_METHOD<a class="headerlink" href="#tgyro-neo-method" title="Permal
 <hr class="docutils" />
 </section>
 <section id="tgyro-relax-iterations">
-<h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" title="Permalink to this headline"></a></h2>
+<h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Maximum number of Newton iterations.</p>
 <p><strong>Comments</strong></p>
@@ -396,7 +398,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="loc-relax">
-<span id="tgyro-loc-relax"></span><h2>LOC_RELAX<a class="headerlink" href="#loc-relax" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-relax"></span><h2>LOC_RELAX<a class="headerlink" href="#loc-relax" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Parameter <span class="math notranslate nohighlight">\(C_\eta\)</span> controlling shrinkage of relaxation parameter.</p>
 <blockquote>
@@ -410,7 +412,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 </ul>
 </section>
 <section id="loc-residual-method">
-<span id="tgyro-loc-residual-method"></span><h2>LOC_RESIDUAL_METHOD<a class="headerlink" href="#loc-residual-method" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-residual-method"></span><h2>LOC_RESIDUAL_METHOD<a class="headerlink" href="#loc-residual-method" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Formula for residual (error) in TGYRO root finding.</p>
 <p><strong>Choices</strong></p>
@@ -429,7 +431,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="loc-restart-flag">
-<span id="tgyro-loc-restart-flag"></span><h2>LOC_RESTART_FLAG<a class="headerlink" href="#loc-restart-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-restart-flag"></span><h2>LOC_RESTART_FLAG<a class="headerlink" href="#loc-restart-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>TGYRO startup control (new or restart).</p>
 <p><strong>Choices</strong></p>
@@ -442,7 +444,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="loc-scenario">
-<span id="tgyro-loc-scenario"></span><h2>LOC_SCENARIO<a class="headerlink" href="#loc-scenario" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-scenario"></span><h2>LOC_SCENARIO<a class="headerlink" href="#loc-scenario" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Power-balance scenario.</p>
 <p><strong>Choices</strong></p>
@@ -460,7 +462,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="tgyro-therm-flag">
-<span id="id2"></span><h2>TGYRO_THERM_FLAG*<a class="headerlink" href="#tgyro-therm-flag" title="Permalink to this headline"></a></h2>
+<span id="id2"></span><h2>TGYRO_THERM_FLAG*<a class="headerlink" href="#tgyro-therm-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Thermal/nonthermal species toggle.  First ion is TGYRO_THERM_FLAG1, etc.</p>
 <p><strong>Choices</strong></p>
@@ -478,7 +480,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="loc-te-feedback-flag">
-<span id="tgyro-loc-te-feedback-flag"></span><h2>LOC_TE_FEEDBACK_FLAG<a class="headerlink" href="#loc-te-feedback-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-te-feedback-flag"></span><h2>LOC_TE_FEEDBACK_FLAG<a class="headerlink" href="#loc-te-feedback-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to signal electron temperature evolution</p>
 <p><strong>Comments</strong></p>
@@ -491,7 +493,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="loc-ti-feedback-flag">
-<span id="tgyro-loc-ti-feedback-flag"></span><h2>LOC_TI_FEEDBACK_FLAG<a class="headerlink" href="#loc-ti-feedback-flag" title="Permalink to this headline"></a></h2>
+<span id="tgyro-loc-ti-feedback-flag"></span><h2>LOC_TI_FEEDBACK_FLAG<a class="headerlink" href="#loc-ti-feedback-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Flag to signal ion temperature evolution</p>
 <p><strong>Comments</strong></p>
@@ -504,7 +506,7 @@ <h2>TGYRO_RELAX_ITERATIONS<a class="headerlink" href="#tgyro-relax-iterations" t
 <hr class="docutils" />
 </section>
 <section id="tgyro-write-profiles-flag">
-<h2>TGYRO_WRITE_PROFILES_FLAG<a class="headerlink" href="#tgyro-write-profiles-flag" title="Permalink to this headline"></a></h2>
+<h2>TGYRO_WRITE_PROFILES_FLAG<a class="headerlink" href="#tgyro-write-profiles-flag" title="Permalink to this heading"></a></h2>
 <p><strong>Definition</strong></p>
 <p>Manage how new <a class="reference internal" href="../input_gacode.html#input-gacode"><span class="std std-ref">input.gacode</span></a> files are written.</p>
 <p><strong>Choices</strong></p>
diff --git a/docs/tgyro/tgyro_table.html b/docs/tgyro/tgyro_table.html
index 1ad6f0c..1c49ac5 100644
--- a/docs/tgyro/tgyro_table.html
+++ b/docs/tgyro/tgyro_table.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>
@@ -95,9 +97,9 @@
         <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><a href="../tgyro.html">TGYRO</a> &raquo;</li>
-      <li>input.tgyro Tabular List</li>
+      <li><a href="../index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="../tgyro.html">TGYRO</a></li>
+      <li class="breadcrumb-item active">input.tgyro Tabular List</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/tgyro/tgyro_table.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -108,7 +110,7 @@
            <div itemprop="articleBody">
              
   <section id="input-tgyro-tabular-list">
-<h1>input.tgyro Tabular List<a class="headerlink" href="#input-tgyro-tabular-list" title="Permalink to this headline"></a></h1>
+<h1>input.tgyro Tabular List<a class="headerlink" href="#input-tgyro-tabular-list" title="Permalink to this heading"></a></h1>
 <table class="colwidths-given docutils align-default" id="id1">
 <caption><span class="caption-text"><strong>High-level control</strong></span><a class="headerlink" href="#id1" title="Permalink to this table"></a></caption>
 <colgroup>
diff --git a/docs/workshop.html b/docs/workshop.html
index 80eb46a..332e548 100644
--- a/docs/workshop.html
+++ b/docs/workshop.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" />
@@ -84,9 +86,9 @@
         <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><a href="misc.html">Miscellaneous</a> &raquo;</li>
-      <li>CGYRO Workshop 2022</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+          <li class="breadcrumb-item"><a href="misc.html">Miscellaneous</a></li>
+      <li class="breadcrumb-item active">CGYRO Workshop 2022</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/workshop.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -97,7 +99,7 @@
            <div itemprop="articleBody">
              
   <section id="cgyro-workshop-2022">
-<h1>CGYRO Workshop 2022<a class="headerlink" href="#cgyro-workshop-2022" title="Permalink to this headline"></a></h1>
+<h1>CGYRO Workshop 2022<a class="headerlink" href="#cgyro-workshop-2022" title="Permalink to this heading"></a></h1>
 <dl class="field-list simple">
 <dt class="field-odd">Dates</dt>
 <dd class="field-odd"><p>February 24-25</p>
@@ -110,7 +112,7 @@ <h1>CGYRO Workshop 2022<a class="headerlink" href="#cgyro-workshop-2022" title="
 </dd>
 </dl>
 <section id="agenda">
-<h2>AGENDA<a class="headerlink" href="#agenda" title="Permalink to this headline"></a></h2>
+<h2>AGENDA<a class="headerlink" href="#agenda" title="Permalink to this heading"></a></h2>
 <p><strong>profiles_gen</strong></p>
 <blockquote>
 <div><ul class="simple">
diff --git a/docs/zreferences.html b/docs/zreferences.html
index 627e13b..c698bf7 100644
--- a/docs/zreferences.html
+++ b/docs/zreferences.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" />
@@ -78,8 +80,8 @@
         <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>References</li>
+      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">References</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/zreferences.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -90,7 +92,7 @@
            <div itemprop="articleBody">
              
   <section id="references">
-<h1>References<a class="headerlink" href="#references" title="Permalink to this headline"></a></h1>
+<h1>References<a class="headerlink" href="#references" title="Permalink to this heading"></a></h1>
 <p class="rubric">References</p>
 <table class="colwidths-given docutils align-default" id="id138">
 <caption><span class="caption-text"><strong>Appropriate References</strong></span><a class="headerlink" href="#id138" title="Permalink to this table"></a></caption>
@@ -128,7 +130,8 @@ <h1>References<a class="headerlink" href="#references" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p id="id6"><dl class="citation">
+<div class="docutils container" id="id6">
+<dl class="citation">
 <dt class="label" id="id8"><span class="brackets">AGT+22</span></dt>
 <dd><p>C. Angioni, T. Gamot, G. Tardini, E. Fable, T. Luda, N. Bonanomi, C.K. Kiefer, G.M. Staebler, the ASDEX Upgrade Team, and the EUROfusion MST1 Team. Confinement properties of L-mode plasmas in ASDEX Upgrade and full-radius predictions of the TGLF transport model. <em>Nucl. Fusion</em>, 62:066015, 2022. <a class="reference external" href="https://doi.org/10.1088/1741-4326/ac592b">doi:10.1088/1741-4326/ac592b</a>.</p>
 </dd>
@@ -382,7 +385,7 @@ <h1>References<a class="headerlink" href="#references" title="Permalink to this
 <dd><p>P. Worley, J. Candy, L. Carrington, K. Huck, T. Kaiser, G. Mahinthakumar, A. Maloney, S. Moore, D. Reed, P. Roth, H. Shan, S. Shende, A. Snavely, S. Sreepathi, F. Wolf, and Y. Zhang. Performance analysis of gyro: a tool evaluation. In <em>Proceedings of the 2005 SciDAC Conference, San Francisco, CA, June 26-30</em>. 2005.</p>
 </dd>
 </dl>
-</p>
+</div>
 </section>
 
 
diff --git a/html/src/setup.rst b/html/src/setup.rst
index c86c1fc..4331de0 100644
--- a/html/src/setup.rst
+++ b/html/src/setup.rst
@@ -15,9 +15,9 @@ Add the following lines to ``.bashrc``::
   . ${GACODE_ROOT}/platform/env/env.$GACODE_PLATFORM
 
 
-Sample job layout (1 node, 32 MPI, 4 OpenMP)::
+Sample job layout (1 node, 32 MPI, 4 OpenMP, 59 min wall-clock time)::
 
-  $ gacode_qsub -code cgyro -n 32 -nomp 4 -repo atom -w 15
+  $ gacode_qsub -code cgyro -n 32 -nomp 4 -repo atom -w 00:59:00
 
 NERSC PERLMUTTER (GPU)
 ----------------------
@@ -30,9 +30,9 @@ Add the following lines to ``.bashrc``::
   . ${GACODE_ROOT}/platform/env/env.$GACODE_PLATFORM
 
 
-Sample job layout (1 node, 4 GPU, 16 MPI, 8 OpenMP)::
+Sample job layout (1 node, 4 GPU, 16 MPI, 8 OpenMP, 59 min wall-clock time)::
 
-  $ gacode_qsub -code cgyro -n 16 -nomp 8 -repo atom_g -w 15
+  $ gacode_qsub -code cgyro -n 16 -nomp 8 -repo atom_g -w 00:59:00
 
 GA IRIS
 -------