diff --git a/docs/cgyro.html b/docs/cgyro.html
index 932cd9f..91b34e8 100644
--- a/docs/cgyro.html
+++ b/docs/cgyro.html
@@ -7,7 +7,7 @@
   <title>CGYRO &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
 
   
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@@ -20,7 +20,7 @@
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         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js"></script>
+        <script src="_static/contentui.js?v=9ee86694"></script>
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@@ -61,8 +61,10 @@
 <li class="toctree-l1"><a class="reference internal" href="neo.html">NEO</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tgyro.html">TGYRO</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">CGYRO</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#brief-description">Brief description</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#simulation-images">Simulation images</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#source-code">Source Code</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#overview">Overview</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#past-and-future">Past and Future</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#data-input">Data input</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#data-output-and-plotting">Data output and plotting</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#normalization">Normalization</a></li>
@@ -108,24 +110,37 @@
              
   <section id="cgyro">
 <h1>CGYRO<a class="headerlink" href="#cgyro" title="Link to this heading"></a></h1>
+<section id="brief-description">
+<h2>Brief description<a class="headerlink" href="#brief-description" title="Link to this heading"></a></h2>
+<p>CGYRO is a global-spectral gyrokinetic code. Core developers are</p>
+<ul class="simple">
+<li><p>Emily Belli, <a class="reference external" href="https://www.ga.com/">General Atomics</a> (collisions, rotation)</p></li>
+<li><p>Jeff Candy, <a class="reference external" href="https://www.ga.com/">General Atomics</a> (global-spectral method)</p></li>
+<li><p>Igor Sfiligoi, <a class="reference external" href="https://www.sdsc.edu/">SDSC</a> (performance)</p></li>
+</ul>
+</section>
+<section id="simulation-images">
+<h2>Simulation images<a class="headerlink" href="#simulation-images" title="Link to this heading"></a></h2>
+<p>Simulation data courtesy Nathan Howard (MIT)</p>
 <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>
 <section id="source-code">
 <h2>Source Code<a class="headerlink" href="#source-code" title="Link 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="Link to this heading"></a></h2>
+<section id="past-and-future">
+<h2>Past and Future<a class="headerlink" href="#past-and-future" title="Link 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
-was 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>.
+was GYRO <span id="id2">[<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>.
 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#id78" 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#id81" 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#id82" 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#id83" 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>
+core plasma turbulence <span id="id3">[<a class="reference internal" href="zreferences.html#id78" 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#id81" 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#id82" 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#id83" 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#id98" title="G. M. Staebler, J. E. Kinsey, and R. E. Waltz. A theory-based transport model with comprehensive physics. Phys. Plasmas, 14(5):055909, 2007. doi:10.1063/1.2436852.">SKW07</a>]</span>.  GYRO was the first global electromagnetic solver,
+such as TGLF <span id="id4">[<a class="reference internal" href="zreferences.html#id98" title="G. M. Staebler, J. E. Kinsey, and R. E. Waltz. A theory-based transport model with comprehensive physics. Phys. Plasmas, 14(5):055909, 2007. doi:10.1063/1.2436852.">SKW07</a>]</span>.  GYRO was the first global electromagnetic solver,
 and pioneered the development of numerical algorithms for the GK equations
 with kinetic electrons.  It is formulated in real space and like all global solvers
 requires <em>ad hoc</em> absorbing-layer boundary conditions when simulating cases
@@ -136,15 +151,15 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 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 CGYRO 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#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>, <a class="reference internal" href="zreferences.html#id43" title="J. Candy, I. Sfiligoi, E. Belli, K. Hallatschek, C. Holland, N. Howard, and E.D`Azevedo. Multiscale-optimized plasma turbulence simulation on petascale architechtures. Computers &amp; Fluids, 188:125, 2019. doi:10.1016/j.compfluid.2019.04.016.">CSB+19</a>]</span>
+from scratch, of the CGYRO code <span id="id5">[<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#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>, <a class="reference internal" href="zreferences.html#id43" title="J. Candy, I. Sfiligoi, E. Belli, K. Hallatschek, C. Holland, N. Howard, and E.D`Azevedo. Multiscale-optimized plasma turbulence simulation on petascale architechtures. Computers &amp; Fluids, 188:125, 2019. doi:10.1016/j.compfluid.2019.04.016.">CSB+19</a>]</span>
 to complement GYRO.  CGYRO is an Eulerian GK solver specifically designed and
 optimized for <strong>collisional, electromagnetic, multiscale simulation</strong>.
 A key algorithmic aspect of CGYRO is the <strong>radially spectral formulation</strong>
 used to reduce the complicated integral gyroaveraging kernel into a
 multiplication in wavenumber space, but retaining the ability to treat profile
-variation important for edge plasmas <span id="id5">[<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#id44" title="J. Candy, E.A. Belli, and G. Staebler. Spectral treatment of gyrokinetic profile curvature. Plasma Phys. Control. Fusion, 62:042001, 2020. doi:10.1088/1361-6587/ab759c.">CBS20</a>]</span>.  A new coordinate system that is more
+variation important for edge plasmas <span id="id6">[<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#id44" title="J. Candy, E.A. Belli, and G. Staebler. Spectral treatment of gyrokinetic profile curvature. Plasma Phys. Control. Fusion, 62:042001, 2020. doi:10.1088/1361-6587/ab759c.">CBS20</a>]</span>.  A new coordinate system that is more
 suitable for the highly collisional and shaped edge regime was adopted from
-the NEO code <span id="id6">[<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>, <a class="reference internal" href="zreferences.html#id17" title="E.A. Belli and J. Candy. Full linearized Fokker-Planck collisions in neoclassical transport simulations. Plasma Phys. Control. Fusion, 54:015015, 2012.">BC12</a>]</span>, which is the community standard for
+the NEO code <span id="id7">[<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>, <a class="reference internal" href="zreferences.html#id17" title="E.A. Belli and J. Candy. Full linearized Fokker-Planck collisions in neoclassical transport simulations. Plasma Phys. Control. Fusion, 54:015015, 2012.">BC12</a>]</span>, which is the community standard for
 calculation of collisional transport in toroidal geometry.</p>
 </section>
 <section id="data-input">
@@ -161,8 +176,8 @@ <h2>Data output and plotting<a class="headerlink" href="#data-output-and-plottin
 </section>
 <section id="normalization">
 <h2>Normalization<a class="headerlink" href="#normalization" title="Link to this heading"></a></h2>
-<table class="docutils align-default" id="id7">
-<caption><span class="caption-text"><strong>CGYRO Normalization</strong></span><a class="headerlink" href="#id7" title="Link to this table"></a></caption>
+<table class="docutils align-default" id="id8">
+<caption><span class="caption-text"><strong>CGYRO Normalization</strong></span><a class="headerlink" href="#id8" title="Link to this table"></a></caption>
 <colgroup>
 <col style="width: 33.3%" />
 <col style="width: 25.0%" />
diff --git a/docs/genindex.html b/docs/genindex.html
index 1b36d98..a5b7ea9 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -6,7 +6,7 @@
   <title>Index &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
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+      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
 
   
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@@ -19,7 +19,7 @@
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         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js"></script>
+        <script src="_static/contentui.js?v=9ee86694"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
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diff --git a/docs/index.html b/docs/index.html
index b29603c..31ffe12 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -7,7 +7,7 @@
   <title>The General Atomics GACODE Suite &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
 
   
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@@ -20,7 +20,7 @@
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         <script src="_static/doctools.js?v=9a2dae69"></script>
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-        <script src="_static/contentui.js"></script>
+        <script src="_static/contentui.js?v=9ee86694"></script>
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@@ -296,8 +296,10 @@ <h2>Equilibrium and Profiles<a class="headerlink" href="#equilibrium-and-profile
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="cgyro.html">CGYRO</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="cgyro.html#brief-description">Brief description</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cgyro.html#simulation-images">Simulation images</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cgyro.html#source-code">Source Code</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cgyro.html#overview">Overview</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cgyro.html#past-and-future">Past and Future</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cgyro.html#data-input">Data input</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cgyro.html#data-output-and-plotting">Data output and plotting</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cgyro.html#normalization">Normalization</a></li>
diff --git a/docs/objects.inv b/docs/objects.inv
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index 38c6394..6b74afc 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -6,7 +6,7 @@
   <title>Search &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
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+      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
 
   
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diff --git a/docs/searchindex.js b/docs/searchindex.js
index 8b1140e..c4db86a 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"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"]], "ADIABATIC_ELEC": [[30, "adiabatic-elec"]], "AGENDA": [[41, "agenda"]], "ALPHA_E": [[30, "alpha-e"]], "ALPHA_MACH": [[30, "alpha-mach"]], "ALPHA_P": [[30, "alpha-p"]], "ALPHA_QUENCH": [[30, "alpha-quench"]], "ALPHA_SA": [[30, "alpha-sa"]], "ALPHA_ZF": [[30, "alpha-zf"]], "AMP": [[5, "amp"]], "AMP0": [[5, "amp0"]], "AMP_PHI_N": [[14, "amp-phi-n"]], "ANISO_MODEL_*": [[22, "aniso-model"]], "AS_1": [[30, "as-1"]], "Acknowledgments": [[28, "acknowledgments"]], "Advanced shape parameters": [[6, "id2"]], "Alphabetical list for input.cgyro": [[5, "alphabetical-list-for-input-cgyro"]], "Alphabetical list for input.gyro": [[14, "alphabetical-list-for-input-gyro"]], 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[[3, "id7"]], "CGYRO Workshop 2022": [[41, "cgyro-workshop-2022"]], "CGYRO output files": [[7, "cgyro-output-files"]], "COLLISION_ENE_DIFFUSION": [[5, "collision-ene-diffusion"]], "COLLISION_ENE_RESTORE": [[5, "collision-ene-restore"]], "COLLISION_FIELD_MODEL": [[5, "collision-field-model"]], "COLLISION_FULL_STRIPES": [[5, "collision-full-stripes"]], "COLLISION_KPERP": [[5, "collision-kperp"]], "COLLISION_MODEL": [[5, "collision-model"], [22, "collision-model"]], "COLLISION_MOM_RESTORE": [[5, "collision-mom-restore"]], "COLLISION_PRECISION_MODE": [[5, "collision-precision-mode"]], "Change-at-your-own-risk parameters": [[32, "id6"]], "Codes": [[17, null]], "Collisions": [[6, "id9"]], "Command-line usage": [[8, "command-line-usage"]], "Common time-dependent output": [[7, "id2"]], "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"]], "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 synthetic diagnostic results with DIII-D BES and CER data": [[16, "comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data"]], "Compressional Electromagnetic Perturbations (2010)": [[16, "compressional-electromagnetic-perturbations-2010"]], "Computation of the Jacobian": [[38, "computation-of-the-jacobian"]], "Concept of platform files": [[0, "concept-of-platform-files"]], "Connection of Fluxes to Powers": [[34, "connection-of-fluxes-to-powers"]], "Connection to experimental data": [[26, "connection-to-experimental-data"]], "Consistency with force balance": [[26, "consistency-with-force-balance"]], "Control": [[32, "id1"]], "Control parameters": [[6, "id3"], [15, "id1"]], "Coordinates": [[10, "coordinates"]], "Cross-code benchmarking results": [[28, "cross-code-benchmarking-results"]], "Cyclone 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"Energy Transport": [[34, "energy-transport"]], "Energy fluxes and sources": [[34, "id3"]], "Environment variables": [[0, "environment-variables"]], "Equations solved in TGYRO": [[34, "equations-solved-in-tgyro"]], "Equilibria": [[10, "equilibria"]], "Equilibrium and Profiles": [[17, "equilibrium-and-profiles"]], "Experimental profiles output files": [[24, "experimental-profiles-output-files"]], "Extra subroutine interface parameters": [[23, "extra-subroutine-interface-parameters"]], "FAQ": [[4, "faq"]], "FIELD_PRINT_FLAG": [[5, "field-print-flag"]], "FILTER": [[30, "filter"]], "FIND_WIDTH": [[30, "find-width"]], "FLUX-SURFACE GEOMETRY": [[10, "flux-surface-geometry"]], "FREQ_TOL": [[5, "freq-tol"]], "FT_MODEL_SA": [[30, "ft-model-sa"]], "Fields": [[6, "id4"]], "File structure": [[18, "id3"]], "First step": [[0, "first-step"]], "Formulation": [[38, "formulation"]], "Formulation on a discrete grid": [[38, "formulation-on-a-discrete-grid"]], "Frequently Asked Questions": [[3, "frequently-asked-questions"]], "GA OMEGA": [[27, "ga-omega"]], "GACODE License": [[19, "gacode-license"]], "GAMMA_E": [[5, "gamma-e"]], "GAMMA_E_SCALE": [[5, "gamma-e-scale"]], "GAMMA_P": [[5, "gamma-p"]], "GAMMA_P_SCALE": [[5, "gamma-p-scale"]], "GCHAT": [[30, "gchat"]], "GEOMETRY_FLAG": [[30, "geometry-flag"]], "GEO_NY": [[22, "geo-ny"]], "GEO_YIN": [[22, "geo-yin"]], "GFLUX_PRINT_FLAG": [[5, "gflux-print-flag"]], "GHAT": [[30, "ghat"]], "GKW results (added 25-jan-2013)": [[28, "gkw-results-added-25-jan-2013"]], "GPU_BIGMEM_FLAG": [[5, "gpu-bigmem-flag"]], "GRADB_FACTOR": [[30, "gradb-factor"]], "GYRO": [[11, "gyro"]], "GYRO Validation Abstracts": [[16, "gyro-validation-abstracts"]], "GYRO results": [[28, "gyro-results"]], "GYRO verification and validation (pre 2010)": [[16, "gyro-verification-and-validation-pre-2010"]], "Gallery of classic GYRO images (circa 2003)": [[12, "gallery-of-classic-gyro-images-circa-2003"]], "Gaussian width parameters": [[32, "id3"]], "General models": [[23, "id3"]], "Geometry": [[17, "geometry"]], "Global-spectral parameters": [[6, "id11"]], "Gyrokinetic Simulation in the 2000s": [[13, "gyrokinetic-simulation-in-the-2000s"]], "Gyrokinetic Simulation of Impurities (2004)": [[16, "gyrokinetic-simulation-of-impurities-2004"]], "H_PRINT_FLAG": [[5, "h-print-flag"]], "High-level control": [[40, "id1"]], "History and Overview": [[25, "history-and-overview"]], "IBRANCH": [[30, "ibranch"]], "IFLUX": [[30, "iflux"]], "IPCCW": [[5, "ipccw"], [22, "ipccw"]], "Input parameters": [[26, "input-parameters"]], "Iteration control": [[40, "id2"]], "KAPPA": [[5, "kappa"], [22, "kappa"]], "KAPPA_LOC": [[30, "kappa-loc"]], "KX0_LOC": [[30, "kx0-loc"]], "KY": [[5, "ky"], [30, "ky"]], "KYGRID_MODEL": [[30, "kygrid-model"]], "Key publications and presentations": [[28, "key-publications-and-presentations"]], "LAMBDA_DEBYE": [[5, "lambda-debye"]], "LAMBDA_DEBYE_SCALE": [[5, "lambda-debye-scale"]], "LINSKER_FACTOR": [[30, "linsker-factor"]], "LOC_BETAE_SCALE": [[39, "loc-betae-scale"]], "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"]], "LOC_LOCK_PROFILE_FLAG": [[39, "loc-lock-profile-flag"]], "LOC_RELAX": [[39, "loc-relax"]], "LOC_RESIDUAL_METHOD": [[39, "loc-residual-method"]], "LOC_RESTART_FLAG": [[39, "loc-restart-flag"]], "LOC_SCENARIO": [[39, "loc-scenario"]], "LOC_TE_FEEDBACK_FLAG": [[39, "loc-te-feedback-flag"]], "LOC_TI_FEEDBACK_FLAG": [[39, "loc-ti-feedback-flag"]], "Local limit of Global Simulations (2004)": [[16, "local-limit-of-global-simulations-2004"]], "MACH": [[5, "mach"]], "MACH_SCALE": [[5, "mach-scale"]], "MASS_*": [[5, "mass"], [22, "mass"]], "MASS_1": [[30, "mass-1"]], "MAX_TIME": [[5, "max-time"]], "MOMENT_PRINT_FLAG": [[5, "moment-print-flag"]], "MPI_RANK_ORDER": [[5, "mpi-rank-order"]], "Magnetic field 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"rotation-output-files"]], "Rotation physics": [[6, "id10"], [23, "id5"]], "Running Cases": [[3, "running-cases"], [8, "running-cases"]], "Running GACODE": [[17, "running-gacode"]], "S": [[5, "s"]], "SAT_RULE": [[30, "sat-rule"]], "SHAPE_COS0": [[5, "shape-cos0"], [22, "shape-cos0"]], "SHAPE_COS1": [[5, "shape-cos1"], [22, "shape-cos1"]], "SHAPE_COS2": [[5, "shape-cos2"], [22, "shape-cos2"]], "SHAPE_COS3": [[5, "shape-cos3"], [22, "shape-cos3"]], "SHAPE_SIN3": [[5, "shape-sin3"], [22, "shape-sin3"]], "SHAPE_S_COS0": [[5, "shape-s-cos0"], [22, "shape-s-cos0"]], "SHAPE_S_COS1": [[5, "shape-s-cos1"], [22, "shape-s-cos1"]], "SHAPE_S_COS2": [[5, "shape-s-cos2"], [22, "shape-s-cos2"]], "SHAPE_S_COS3": [[5, "shape-s-cos3"], [22, "shape-s-cos3"]], "SHAPE_S_SIN3": [[5, "shape-s-sin3"], [22, "shape-s-sin3"]], "SHAT_SA": [[30, "shat-sa"]], "SHEAR": [[22, "shear"]], "SHIFT": [[5, "shift"], [22, "shift"]], "SIGN_BT": [[30, "sign-bt"]], "SIGN_IT": [[30, "sign-it"]], "SILENT_FLAG": [[5, 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"standard-output-files"]], "Subroutine output": [[24, "subroutine-output"]], "TAUS_1": [[30, "taus-1"]], "TEMP_*": [[5, "temp"], [22, "temp"]], "TEMP_PARA_*": [[22, "temp-para"]], "TEMP_PERP_*": [[22, "temp-perp"]], "TE_ADE": [[22, "te-ade"]], "TGLF": [[29, "tglf"]], "TGLF output files": [[32, "id8"]], "TGLF output parameters": [[32, "id7"]], "TGYRO": [[33, "tgyro"]], "TGYRO solver algorithm": [[38, "tgyro-solver-algorithm"]], "TGYRO_DEN_METHOD*": [[39, "tgyro-den-method"]], "TGYRO_ITERATION_METHOD": [[39, "tgyro-iteration-method"]], "TGYRO_MODE": [[39, "tgyro-mode"]], "TGYRO_NEO_METHOD": [[39, "tgyro-neo-method"]], "TGYRO_RELAX_ITERATIONS": [[39, "tgyro-relax-iterations"]], "TGYRO_THERM_FLAG*": [[39, "tgyro-therm-flag"]], "TGYRO_WRITE_PROFILES_FLAG": [[39, "tgyro-write-profiles-flag"]], "THETA0_SA": [[30, "theta0-sa"]], "THETA_PLOT": [[5, "theta-plot"]], "THETA_TRAPPED": [[30, "theta-trapped"]], "THREED_EXB_DPHI0DR": [[22, "threed-exb-dphi0dr"]], "THREED_EXB_MODEL": [[22, "threed-exb-model"]], "THREED_MODEL": [[22, "threed-model"]], "Table of geometry parameters": [[10, "table-of-geometry-parameters"]], "Table of inputs and outputs": [[32, "table-of-inputs-and-outputs"]], "Tabular list for input.cgyro": [[6, "tabular-list-for-input-cgyro"]], "Tabular list for input.gyro": [[15, "tabular-list-for-input-gyro"]], "The General Atomics GACODE Suite": [[17, "the-general-atomics-gacode-suite"]], "The rotation profile": [[26, "the-rotation-profile"]], "Theoretical basis for sonic rotation": [[26, "theoretical-basis-for-sonic-rotation"]], "Time Stepping": [[6, "id7"]], "Time-independent output": [[7, "id1"]], "Transport equations and solution": [[33, "transport-equations-and-solution"]], "UDSYMMETRY_FLAG": [[5, "udsymmetry-flag"]], "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 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\ No newline at end of file
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22], "iter": 40, "jacobian": 38, "jan": 28, "kappa": [5, 22], "kappa_loc": 30, "kei": 28, "kx0_loc": 30, "ky": [5, 30], "kygrid_model": 30, "l": 28, "lambda_deby": 5, "lambda_debye_scal": 5, "laptop": 0, "legend": 13, "level": 40, "licens": 19, "limit": [13, 16], "line": 8, "link": [11, 21, 29, 33], "linsker_factor": 30, "list": [5, 6, 14, 15, 22, 30, 31, 39, 40], "loc_betae_scal": 39, "loc_dx": 39, "loc_dx_max": 39, "loc_er_feedback_flag": 39, "loc_evolve_grad_only_flag": 39, "loc_he_feedback_flag": 39, "loc_lock_profile_flag": 39, "loc_relax": 39, "loc_residual_method": 39, "loc_restart_flag": 39, "loc_scenario": 39, "loc_te_feedback_flag": 39, "loc_ti_feedback_flag": 39, "local": [13, 16], "mach": 5, "mach_scal": 5, "magnet": 10, "mass_": [5, 22], "mass_1": 30, "match": 16, "max_tim": 5, "method": 10, "miller": 32, "mint": 1, "miscellan": 20, "mod": 16, "mode": 28, "model": [23, 29], "moment_print_flag": 5, "momentum": 34, "mpi_rank_ord": 5, "n": 30, "n_energi": [5, 22], "n_field": 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"prebuilt": 27, "prehistori": 13, "present": 28, "print_step": 5, "profil": [17, 23, 24, 26, 28, 40], "profile_dlnndr_": 22, "profile_dlntdr_": 22, "profile_equilibrium_model": 22, "profile_erad0_model": 22, "profile_model": [5, 22], "profiles_gen": 25, "public": [13, 28], "px0": 5, "python": 33, "q": [5, 22], "q_loc": 30, "q_prime_loc": 30, "q_sa": 30, "ql_flux_spectrum": 31, "quasineutral_flag": 5, "question": 3, "quick": [8, 11, 21, 29, 33], "refer": [9, 29, 42], "reflectomet": 16, "regard": 38, "relat": 6, "repositori": 9, "resolut": [6, 13, 23], "restart": 7, "restart_step": 5, "result": [16, 28], "rho_star": 22, "risk": 32, "rlns_1": 30, "rlts_1": 30, "rmaj": 5, "rmaj_loc": 30, "rmaj_over_a": 22, "rmaj_sa": 30, "rmin": 5, "rmin_loc": 30, "rmin_over_a": 22, "rmin_over_a_2": 22, "rmin_sa": 30, "rotat": [6, 17, 23, 24, 26], "rotation_model": [5, 22], "run": [3, 8, 17], "s_delta": [5, 22], "s_delta_loc": 30, "s_kappa": [5, 22], "s_kappa_loc": 30, "s_zeta": [5, 22], "s_zeta_loc": 30, "s_zmag": 22, "sat_geo_spectrum": 31, "sat_rul": 30, "satur": 29, "scalar_saturation_paramet": 31, "scenario": 37, "scienc": 13, "shape": 6, "shape_cos0": [5, 22], "shape_cos1": [5, 22], "shape_cos2": [5, 22], "shape_cos3": [5, 22], "shape_s_cos0": [5, 22], "shape_s_cos1": [5, 22], "shape_s_cos2": [5, 22], "shape_s_cos3": [5, 22], "shape_s_sin3": [5, 22], "shape_sin3": [5, 22], "shat_sa": 30, "shear": 22, "shift": [5, 22], "shortfal": 28, "sign_bt": 30, "sign_it": 30, "silent_flag": [5, 22], "sim_model": 22, "simul": [3, 13, 16], "softwar": 17, "solut": [33, 38], "solv": 34, "solver": 38, "some": 38, "sonic": 26, "sonoma": 2, "sourc": [0, 3, 9, 34, 37], "space": 13, "speci": [6, 23, 24, 32, 40], "spectral": 6, "spectral_shift": 31, "spitzer_model": 22, "standard": 24, "start": 8, "step": [0, 6], "strategi": 38, "structur": 18, "studi": 16, "submiss": 8, "subroutin": [23, 24], "suit": 17, "sum_flux_spectrum": 31, "supercomput": 16, "supra": 16, "surfac": 10, "sweep": 16, "synopsi": 13, 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"use_inboard_detrap": 30, "use_mhd_rul": 30, "use_transport_model": 30, "user": [9, 13], "valid": [16, 29], "variabl": 0, "vector": 32, "vel": 24, "vel_fouri": 24, "veloc": 13, "velocity_ord": 5, "verif": 16, "vexb": 30, "vexb_shear": 30, "vpar_1": 30, "vpar_model": 30, "vpar_shear_1": 30, "vpar_shear_model": 30, "wd_zero": 30, "width": [30, 32], "width_min": 30, "workshop": 41, "write_wavefunction_flag": 30, "xnu_factor": 30, "xnu_model": 30, "xnue": 30, "xwell_sa": 30, "yearli": 13, "your": [0, 32], "z_": [5, 22], "z_eff": 5, "z_eff_method": 5, "zeff": 30, "zeta": [5, 22], "zeta_loc": 30, "zf_test_mod": 5, "zmag": 5, "zmag_over_a": 22, "zmaj_loc": 30, "zs_1": 30}})
\ No newline at end of file
diff --git a/html/src/cgyro.rst b/html/src/cgyro.rst
index 0d6638d..63addec 100644
--- a/html/src/cgyro.rst
+++ b/html/src/cgyro.rst
@@ -1,6 +1,20 @@
 CGYRO
 =====
 
+Brief description
+-----------------
+
+CGYRO is a global-spectral gyrokinetic code. Core developers are
+
+* Emily Belli, `General Atomics <https://www.ga.com/>`_ (collisions, rotation)
+* Jeff Candy, `General Atomics <https://www.ga.com/>`_ (global-spectral method)
+* Igor Sfiligoi, `SDSC <https://www.sdsc.edu/>`_ (performance)
+
+Simulation images
+-----------------
+
+Simulation data courtesy Nathan Howard (MIT)
+
 .. image:: cgyro/figures/b250.png
 	:width: 48 %
 	:alt: b250
@@ -19,8 +33,8 @@ Source Code
 
 `CGYRO source code <http://github.com/gafusion/gacode>`_  is available at GitHub.
    
-Overview
---------
+Past and Future
+---------------
 
 **The past: GYRO**