From 0ae529c48e2e7fa2de33ad938e97b1f498c7b0ec Mon Sep 17 00:00:00 2001
From: Jeff Candy <candy@jaamweb.com>
Date: Tue, 30 Jul 2024 12:25:56 -0700
Subject: [PATCH] Added lots of geometry content to GACODE page

---
 docs/.buildinfo             |   2 +-
 docs/cgyro.html             |   4 +-
 docs/download.html          |   2 +-
 docs/geometry.html          |  67 +++++-
 docs/gyro.html              |   4 +-
 docs/gyro/gyro_history.html |  50 ++---
 docs/gyro/gyro_vv.html      |   8 +-
 docs/index.html             |   3 +-
 docs/objects.inv            | Bin 11000 -> 11035 bytes
 docs/rotation.html          |  15 +-
 docs/searchindex.js         |   2 +-
 docs/shortfall.html         |  10 +-
 docs/tglf.html              |  14 +-
 docs/tglf/tglf_list.html    |  10 +-
 docs/tgyro/equations.html   |   2 +-
 docs/zreferences.html       | 142 +++++++------
 html/src/geometry.rst       |  86 +++++++-
 html/src/references.bib     | 403 ++++++++++++++++++++----------------
 html/src/rotation.rst       |   7 +-
 19 files changed, 506 insertions(+), 325 deletions(-)

diff --git a/docs/.buildinfo b/docs/.buildinfo
index 5ea2a12..2598f27 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: 556eb8091613b199f169c4c376f2cb96
+config: 711f83b3aa3bbab10fa381c061ae4e28
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/cgyro.html b/docs/cgyro.html
index d039073..7a99af4 100644
--- a/docs/cgyro.html
+++ b/docs/cgyro.html
@@ -138,9 +138,9 @@ <h2>Past and Future<a class="headerlink" href="#past-and-future" title="Link to
 primarily on the core region. A popular kinetic code used for this purpose
 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="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>
+core plasma turbulence <span id="id3">[<a class="reference internal" href="zreferences.html#id79" 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#id83" 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#id84" 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#id85" 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="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,
+such as TGLF <span id="id4">[<a class="reference internal" href="zreferences.html#id100" 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
diff --git a/docs/download.html b/docs/download.html
index aefc0c4..027246e 100644
--- a/docs/download.html
+++ b/docs/download.html
@@ -159,7 +159,7 @@ <h1>Download and user agreement<a class="headerlink" href="#download-and-user-ag
 </tr>
 <tr class="row-odd"><td><p>TGLF</p></td>
 <td><p>transport model</p></td>
-<td><p><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>, <a class="reference internal" href="zreferences.html#id100" title="G.M. Staebler and J.E. Kinsey. Electron collisions in the trapped gyro-landau fluid transport model. Phys. Plasmas, 17:122309, 2010.">SK10</a>]</span></p></td>
+<td><p><span id="id4">[<a class="reference internal" href="zreferences.html#id100" 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>, <a class="reference internal" href="zreferences.html#id103" title="G.M. Staebler and J.E. Kinsey. Electron collisions in the trapped gyro-landau fluid transport model. Phys. Plasmas, 17:122309, 2010.">SK10</a>]</span></p></td>
 </tr>
 <tr class="row-even"><td><p>TGYRO</p></td>
 <td><p>profile evolution</p></td>
diff --git a/docs/geometry.html b/docs/geometry.html
index 1403f18..2b0c7ee 100644
--- a/docs/geometry.html
+++ b/docs/geometry.html
@@ -68,12 +68,13 @@
 <p class="caption" role="heading"><span class="caption-text">Physics</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">FLUX-SURFACE GEOMETRY</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#coordinates">Coordinates</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#clebsch-coordinates">Clebsch coordinates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#bounding-box-method">Bounding-box method</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#effective-field">Effective field</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#equilibria">Equilibria</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#table-of-geometry-parameters">Table of geometry parameters</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#magnetic-field-orientation">Magnetic field orientation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#toroidal-and-poloidal-flux">Toroidal and poloidal flux</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="rotation.html">PLASMA ROTATION THEORY</a></li>
@@ -107,23 +108,44 @@
              
   <section id="flux-surface-geometry">
 <h1>FLUX-SURFACE GEOMETRY<a class="headerlink" href="#flux-surface-geometry" title="Link to this heading"></a></h1>
-<section id="coordinates">
-<h2>Coordinates<a class="headerlink" href="#coordinates" title="Link to this heading"></a></h2>
+<section id="clebsch-coordinates">
+<h2>Clebsch coordinates<a class="headerlink" href="#clebsch-coordinates" title="Link 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>
+<span class="math notranslate nohighlight">\((r,\theta,\alpha)\)</span> and the Clebsch field representation <span id="id1">[<a class="reference internal" href="zreferences.html#id93" title="M.D. Kruskal and R.M. Kulsrud. Equilibrium of a magnetically confined plasma in a toroid. Phys. Fluids, 1:265, 1958.">KK58</a>]</span></p>
 <div class="math notranslate nohighlight">
-\[\mathbf{B} =\nabla \alpha \times \nabla \psi (r) \; ,\]</div>
+\[\mathbf{B} = \nabla\alpha\times\nabla\psi \quad \text{such that} \quad\mathbf{B}\cdot\nabla\alpha = \mathbf{B}\cdot\nabla\psi = 0\]</div>
 <p>where <span class="math notranslate nohighlight">\(\psi\)</span> is the poloidal flux divided by <span class="math notranslate nohighlight">\(2\pi\)</span> and</p>
 <div class="math notranslate nohighlight">
-\[\alpha =\varphi +\nu (r,\theta )\]</div>
+\[\alpha =\varphi +\nu (r,\theta)\]</div>
 <p>is the Clebsch angle. Here, <span class="math notranslate nohighlight">\(\varphi\)</span> is the <strong>toroidal angle</strong>, oriented as shown
 in the figure below, and <span class="math notranslate nohighlight">\(\theta\)</span> is the <strong>poloidal angle</strong> which increases as one
-moves counterclockwise along the flux-surface (shown in blue).</p>
-<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>
+moves counterclockwise along the flux-surface (shown in blue). In these coordinates, the Jacobian is</p>
+<div class="math notranslate nohighlight">
+\[{\mathcal J}_\psi \doteq \frac{1}{\nabla\psi\times\nabla\theta\cdot\nabla\alpha} = \frac{1}{\nabla\psi\times\nabla\theta\cdot\nabla\varphi} \; .\]</div>
+<p>Since the coordinates <span class="math notranslate nohighlight">\((\psi,\theta,\alpha)\)</span> and <span class="math notranslate nohighlight">\((\psi,\theta,\varphi)\)</span> form right-handed systems, the Jacobian <span class="math notranslate nohighlight">\({\mathcal J}_\psi\)</span> is positive-definite.  In the latter coordinates, the magnetic field becomes</p>
+<div class="math notranslate nohighlight">
+\[\mathbf{B} = \nabla\varphi\times\nabla\psi + \frac{\partial \nu}{\partial \theta} \nabla\theta\times\nabla\psi\]</div>
+<p>Using the definition of the safety factor, <span class="math notranslate nohighlight">\(q(\psi)\)</span>, we may deduce</p>
+<div class="math notranslate nohighlight">
+\[q(\psi) \doteq \frac{1}{2\pi} \int_0^{2\pi} \frac{\mathbf{B}\cdot\nabla\varphi}{\mathbf{B}\cdot\nabla\theta} \, d\theta = \frac{1}{2\pi} \int_0^{2\pi} \left( -\frac{\partial \nu}{\partial \theta} \right) \, d\theta = \frac{\nu(\psi,0)-\nu(\psi,2\pi)}{2\pi} \; .\]</div>
+<div class="math notranslate nohighlight">
+\[\]</div>
+<p>For concreteness, we choose the following boundary conditions for <span class="math notranslate nohighlight">\(\nu\)</span>:</p>
+<div class="math notranslate nohighlight">
+\[\begin{split}\nu(\psi,2\pi) = &amp;~-2\pi \, q(\psi) \; , \\
+ \nu(\psi,0)   = &amp;~0 \; .\end{split}\]</div>
+<p>By writing <span class="math notranslate nohighlight">\(\mathbf{B}\)</span> in the standard form</p>
+<div class="math notranslate nohighlight">
+\[\mathbf{B} = \nabla\varphi\times\nabla\psi + I(\psi) \nabla\varphi \; ,\]</div>
+<p>we can derive the following integral for <span class="math notranslate nohighlight">\(\nu\)</span>:</p>
+<div class="math notranslate nohighlight">
+\[\nu(\psi,\theta) = -I(\psi)\int_0^\theta {\mathcal J}_\psi \left|\nabla\varphi\right|^2 d\theta\; .\]</div>
+<p>In the case of concentric (unshifted) circular flux surfaces, one will obtain the approximate result
+<span class="math notranslate nohighlight">\(\nu(\psi,\theta) \sim -q(\psi)\theta\)</span>.  Finally, we remark that 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="Link 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>
+<p>In the MXH parameterization <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>, 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>
 <li><p><strong>major radius</strong> <span class="math notranslate nohighlight">\(R_0\)</span></p></li>
@@ -161,7 +183,7 @@ <h2>Equilibria<a class="headerlink" href="#equilibria" title="Link to this headi
 <li><p>NEO: <a class="reference internal" href="neo/neo_list.html#neo-equilibrium-model"><span class="std std-ref">EQUILIBRIUM_MODEL</span></a> = 0</p></li>
 </ul>
 <p><strong>(2) Shaped Grad-Shafranov equilibrium</strong></p>
-<p>The flux surfaces, which are local G-S equilibria, have the new MXH3 parameterization <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>The flux surfaces, which are local G-S equilibria, have the new MXH3 parameterization <span id="id3">[<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>
 <div class="math notranslate nohighlight">
 \[\begin{split}R(r,\theta) &amp;= R_0(r) + r \cos \theta_R \\
 Z(r,\theta) &amp;= Z_0(r) + \kappa(r) r \sin \theta\end{split}\]</div>
@@ -332,7 +354,7 @@ <h2>Table of geometry parameters<a class="headerlink" href="#table-of-geometry-p
 </tr>
 </tbody>
 </table>
-<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>
+<p>For further information about geometry and normalization conventions, consult the GYRO Technical Guide   <span id="id4">[<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="Link to this heading"></a></h2>
@@ -365,6 +387,29 @@ <h2>Magnetic field orientation<a class="headerlink" href="#magnetic-field-orient
 <div><p>In other words, the safety factor and poloidal flux are negative in the typical case. This will be reflected in a properly-constructed <a class="reference internal" href="input_gacode.html"><span class="doc">input.gacode</span></a> file.</p>
 </div></blockquote>
 </section>
+<section id="toroidal-and-poloidal-flux">
+<h2>Toroidal and poloidal flux<a class="headerlink" href="#toroidal-and-poloidal-flux" title="Link to this heading"></a></h2>
+<p>We can start from the general forms of the toroidal and poloidal fluxes <span id="id5">[<a class="reference internal" href="zreferences.html#id47" title="W.D. Dhaeseleer, W.N.G. Hitchon, J.D. Callen, and J.L. Shohet. Flux coordinates and magnetic field structure. Springer-Verlag, Berlin, 1991.">DHCS91</a>]</span></p>
+<div class="math notranslate nohighlight">
+\[\begin{split}\Psi_t \doteq &amp;~\iint\limits_{S_t} \mathbf{B} \cdot d{\bf S} = \frac{1}{2\pi} \iiint\limits_{V_t} \mathbf{B} \cdot \nabla\varphi \, dV \; , \\
+\Psi_p \doteq &amp;~\iint\limits_{S_p} \mathbf{B} \cdot d{\bf S} = \frac{1}{2\pi} \iiint\limits_{V_p} \mathbf{B} \cdot \nabla\theta \, dV \; .\end{split}\]</div>
+<p>Explicitly inserting the field-aligned coordinate system of the previous section, and differentiating these with respect to <span class="math notranslate nohighlight">\(\psi\)</span>, gives</p>
+<div class="math notranslate nohighlight">
+\[\begin{split}\frac{d\Psi_t}{d\psi} = &amp;~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta \,\, \mathbf{B}\cdot\nabla\varphi \, {\mathcal J}_\psi \; , \\
+= &amp;~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta \,\, \frac{\mathbf{B}\cdot\nabla\varphi}{\mathbf{B}\cdot\nabla\theta} \; , \\
+= &amp;~2 \pi \, q(\psi) \; ,\end{split}\]</div>
+<div class="math notranslate nohighlight">
+\[\begin{split}\frac{d\Psi_p}{d\psi} = &amp;~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta
+\,\, \mathbf{B}\cdot\nabla\theta \, {\mathcal J}_\psi \; , \\
+ = &amp;~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta \; , \\
+ = &amp;~2 \pi \; .\end{split}\]</div>
+<p>Thus, <span class="math notranslate nohighlight">\(\psi\)</span> is the poloidal flux divided by <span class="math notranslate nohighlight">\(2\pi\)</span>.  For this reason, it is useful to also define the toroidal flux divided by <span class="math notranslate nohighlight">\(2\pi\)</span>:</p>
+<div class="math notranslate nohighlight">
+\[\chi_t \doteq \frac{1}{2\pi} \Psi_t\; .\]</div>
+<p>According to these conventions,</p>
+<div class="math notranslate nohighlight">
+\[d\Psi_t = q \, d\Psi_p \quad \mbox{and} \quad d\chi_t = q \, d\psi \; .\]</div>
+</section>
 </section>
 
 
diff --git a/docs/gyro.html b/docs/gyro.html
index c8896b3..8a74d6f 100644
--- a/docs/gyro.html
+++ b/docs/gyro.html
@@ -125,8 +125,8 @@ <h2>Quick links<a class="headerlink" href="#quick-links" title="Link to this hea
 </section>
 <section id="overview">
 <h2>Overview<a class="headerlink" href="#overview" title="Link 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#id53" 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#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 – 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>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#id54" 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#id79" 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#id83" 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#id84" 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#id85" 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#id100" 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 – 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>
 </section>
 </section>
diff --git a/docs/gyro/gyro_history.html b/docs/gyro/gyro_history.html
index fc4a6d7..4ebfdf9 100644
--- a/docs/gyro/gyro_history.html
+++ b/docs/gyro/gyro_history.html
@@ -124,17 +124,17 @@ <h1>Gyrokinetic Simulation in the 2000s<a class="headerlink" href="#gyrokinetic-
 <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="Link 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#id88" 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#id87" 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#id121" 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#id122" 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#id123" 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>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#id90" 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#id89" 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#id125" 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#id126" 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#id127" 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" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></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>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
-<p>Gyrofluid simulations demonstrated that nonlinear, self-generated (zonal) flows control the nonlinear saturation of transport <span id="id7">[<a class="reference internal" href="../zreferences.html#id11" title="M.A. Beer and G.W. Hammett. Toroidal gyrofluid equations for simulations of tokamak turbulence. Phys. Plasmas, 3:4046, 1996.">BH96b</a>, <a class="reference internal" href="../zreferences.html#id49" title="W. Dorland and G.W. Hammett. Gyrofluid turbulence models with kinetic effects. Phys. Fluids B, 5:812, 1993.">DH93</a>, <a class="reference internal" href="../zreferences.html#id59" title="G.W. Hammett, M.A. Beer, J.C. Cummings, W. Dorland, W.W. Lee, H.E. Mynick, S.E. Parker, R.A. Santoro, M. Artun, H.P. Furth, T.S. Hahm, G. Rewoldt, W.M. Tang, R.E. Waltz, G.D. Kerbel, and J.L. Milovich. Advances in simulating tokamak turbulent transport. In Proceedings of the 15th IAEA Fusion Energy Conference, Seville, Spain, 1994, Vol III, p. 273. 1994.">HBC+94</a>, <a class="reference internal" href="../zreferences.html#id121" 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#id122" 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>, and that equilibrium <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shear can quench transport if the shearing rates are comparable to maximum linear growth rates <span id="id8">[<a class="reference internal" href="../zreferences.html#id121" 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#id122" 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>.</p>
+<p>Gyrofluid simulations demonstrated that nonlinear, self-generated (zonal) flows control the nonlinear saturation of transport <span id="id7">[<a class="reference internal" href="../zreferences.html#id11" title="M.A. Beer and G.W. Hammett. Toroidal gyrofluid equations for simulations of tokamak turbulence. Phys. Plasmas, 3:4046, 1996.">BH96b</a>, <a class="reference internal" href="../zreferences.html#id50" title="W. Dorland and G.W. Hammett. Gyrofluid turbulence models with kinetic effects. Phys. Fluids B, 5:812, 1993.">DH93</a>, <a class="reference internal" href="../zreferences.html#id60" title="G.W. Hammett, M.A. Beer, J.C. Cummings, W. Dorland, W.W. Lee, H.E. Mynick, S.E. Parker, R.A. Santoro, M. Artun, H.P. Furth, T.S. Hahm, G. Rewoldt, W.M. Tang, R.E. Waltz, G.D. Kerbel, and J.L. Milovich. Advances in simulating tokamak turbulent transport. In Proceedings of the 15th IAEA Fusion Energy Conference, Seville, Spain, 1994, Vol III, p. 273. 1994.">HBC+94</a>, <a class="reference internal" href="../zreferences.html#id125" 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#id126" 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>, and that equilibrium <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shear can quench transport if the shearing rates are comparable to maximum linear growth rates <span id="id8">[<a class="reference internal" href="../zreferences.html#id125" 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#id126" 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>.</p>
 </div>
-<p>Nonlinear gyrofluid codes were the first to treat trapped electron <span id="id9">[<a class="reference internal" href="../zreferences.html#id10" title="M.A. Beer and G.W. Hammett. Bounce averaged trapped electron fluid equations for plasma turbulence. Phys. Plasmas, 3:4018, 1996.">BH96a</a>]</span> and electromagnetic <span id="id10">[<a class="reference internal" href="../zreferences.html#id96" title="P.B. Snyder and G.W. Hammett. Electromagnetic effects on plasma microturbulence and transport. Phys. Plasmas, 8:744, 2001.">SH01</a>]</span> turbulence.  The first major contribution from nonlinear <em>gyrokinetic</em> codes was the verification of the importance of Rosenbluth-Hinton (RH) residual flows <span id="id11">[<a class="reference internal" href="../zreferences.html#id95" title="M.N. Rosenbluth and F.L. Hinton. Poloidal flow driven by ion-temperature-gradient turbulence in tokamaks. Phys. Rev. Lett., 80:724, 1998.">RH98</a>]</span> as demonstrated by the flux-tube particle-in-cell (PIC) code PG3EQ <span id="id12">[<a class="reference internal" href="../zreferences.html#id47" title="A.M. Dimits, T.J. Williams, J.A. Byers, and B.I. Cohen. Scalings of ion-temperature-gradient-driven anomalous transport in tokamaks. Phys. Rev. Lett., 77:71, 1996.">DWBC96</a>]</span>. RH flows were shown to give rise to an upshift in the nonlinear threshold for ITG-ae <a class="footnote-reference brackets" href="#id80" id="id13" role="doc-noteref"><span class="fn-bracket">[</span>2<span class="fn-bracket">]</span></a> turbulence. The nonlinear upshift was later named the <em>Dimits shift</em> after its discoverer.  The difficulty in properly treating this residual in gyrofluid models was one motivating factor for a switch from gyrofluid to gyrokinetic simulation.  To this end, by building upon the GSTOTAL implicit scheme, Dorland and co-workers created the <strong>nonlinear Eulerian gyrokinetic code</strong> GS2 <span id="id14">[<a class="reference internal" href="../zreferences.html#id50" title="W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers. Electron temperature gradient turbulence. Phys. Rev. Lett., 85:5579, 2000.">DJKR00</a>]</span>.</p>
+<p>Nonlinear gyrofluid codes were the first to treat trapped electron <span id="id9">[<a class="reference internal" href="../zreferences.html#id10" title="M.A. Beer and G.W. Hammett. Bounce averaged trapped electron fluid equations for plasma turbulence. Phys. Plasmas, 3:4018, 1996.">BH96a</a>]</span> and electromagnetic <span id="id10">[<a class="reference internal" href="../zreferences.html#id99" title="P.B. Snyder and G.W. Hammett. Electromagnetic effects on plasma microturbulence and transport. Phys. Plasmas, 8:744, 2001.">SH01</a>]</span> turbulence.  The first major contribution from nonlinear <em>gyrokinetic</em> codes was the verification of the importance of Rosenbluth-Hinton (RH) residual flows <span id="id11">[<a class="reference internal" href="../zreferences.html#id98" title="M.N. Rosenbluth and F.L. Hinton. Poloidal flow driven by ion-temperature-gradient turbulence in tokamaks. Phys. Rev. Lett., 80:724, 1998.">RH98</a>]</span> as demonstrated by the flux-tube particle-in-cell (PIC) code PG3EQ <span id="id12">[<a class="reference internal" href="../zreferences.html#id48" title="A.M. Dimits, T.J. Williams, J.A. Byers, and B.I. Cohen. Scalings of ion-temperature-gradient-driven anomalous transport in tokamaks. Phys. Rev. Lett., 77:71, 1996.">DWBC96</a>]</span>. RH flows were shown to give rise to an upshift in the nonlinear threshold for ITG-ae <a class="footnote-reference brackets" href="#id80" id="id13" role="doc-noteref"><span class="fn-bracket">[</span>2<span class="fn-bracket">]</span></a> turbulence. The nonlinear upshift was later named the <em>Dimits shift</em> after its discoverer.  The difficulty in properly treating this residual in gyrofluid models was one motivating factor for a switch from gyrofluid to gyrokinetic simulation.  To this end, by building upon the GSTOTAL implicit scheme, Dorland and co-workers created the <strong>nonlinear Eulerian gyrokinetic code</strong> GS2 <span id="id14">[<a class="reference internal" href="../zreferences.html#id51" title="W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers. Electron temperature gradient turbulence. Phys. Rev. Lett., 85:5579, 2000.">DJKR00</a>]</span>.</p>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
-<p>GS2 <span id="id15">[<a class="reference internal" href="../zreferences.html#id50" title="W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers. Electron temperature gradient turbulence. Phys. Rev. Lett., 85:5579, 2000.">DJKR00</a>]</span> was the first nonlinear gyrokinetic code to include the crucial nonadiabatic electron dynamics required for trapped electron mode and electromagnetic physics.</p>
+<p>GS2 <span id="id15">[<a class="reference internal" href="../zreferences.html#id51" title="W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers. Electron temperature gradient turbulence. Phys. Rev. Lett., 85:5579, 2000.">DJKR00</a>]</span> was the first nonlinear gyrokinetic code to include the crucial nonadiabatic electron dynamics required for trapped electron mode and electromagnetic physics.</p>
 </div>
 </section>
 <section id="design-history">
@@ -154,7 +154,7 @@ <h2>Design History<a class="headerlink" href="#design-history" title="Link to th
 <h2>Yearly Publication Synopsis<a class="headerlink" href="#yearly-publication-synopsis" title="Link to this heading"></a></h2>
 <section id="id20">
 <h3>2002<a class="headerlink" href="#id20" title="Link 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#id126" 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>
+<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#id130" 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="Link to this heading"></a></h3>
@@ -162,14 +162,14 @@ <h3>2003<a class="headerlink" href="#id22" title="Link to this heading"></a><
 </section>
 <section id="id25">
 <h3>2004<a class="headerlink" href="#id25" title="Link to this heading"></a></h3>
-<p>Turbulent dynamos in the tokamak current-voltage relation <span id="id26">[<a class="reference internal" href="../zreferences.html#id61" 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#id91" 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" role="doc-noteref"><span class="fn-bracket">[</span>3<span class="fn-bracket">]</span></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#id86" 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#id121" 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#id122" 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>
+<p>Turbulent dynamos in the tokamak current-voltage relation <span id="id26">[<a class="reference internal" href="../zreferences.html#id62" 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#id94" 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" role="doc-noteref"><span class="fn-bracket">[</span>3<span class="fn-bracket">]</span></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#id88" 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#id125" 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#id126" 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="Link 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#id53" 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#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>]</span> were also published.</p>
+<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#id54" 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#id83" 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#id127" 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#id129" 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#id128" 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#id127" 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>
+<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#id131" 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#id133" 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#id132" 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#id131" 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>
 <div class="math notranslate nohighlight">
 \[q = \frac{1}{1}, \frac{2}{1}, \frac{3}{1}, \ldots \; ,\]</div>
 <p>and are weaker for successively higher-order surfaces, like</p>
@@ -179,7 +179,7 @@ <h3>2005<a class="headerlink" href="#id33" title="Link to this heading"></a><
 </section>
 <section id="id40">
 <h3>2006<a class="headerlink" href="#id40" title="Link 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#id55" 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#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>]</span> were carried out.  Theory and simulations of gyrokinetic turbulent heating <span id="id43">[<a class="reference internal" href="../zreferences.html#id62" 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#id130" 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#id131" 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#id54" 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>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#id56" 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#id84" 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#id63" 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#id134" 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#id135" 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#id55" 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">
@@ -187,36 +187,36 @@ <h3>2007<a class="headerlink" href="#id49" title="Link to this heading"></a><
 <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>
-<li><p>demonstrate the isotropy of short-wavelength fluctuations <span id="id52">[<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>, <a class="reference internal" href="../zreferences.html#id132" title="R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. Phys. Plasmas, 14:056116, 2007.">WCF07</a>]</span> in the presence of long-wavelength ITG/TEM instabilities,</p></li>
-<li><p>demonstrate the potential for ITG/TEM-scale instabilities to drive ETG transport in ETG-stable regimes <span id="id53">[<a class="reference internal" href="../zreferences.html#id132" title="R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. Phys. Plasmas, 14:056116, 2007.">WCF07</a>]</span>,</p></li>
-<li><p>demonstrate the potential for ETG transport to decouple from ITG transport in regimes where both are unstable <span id="id54">[<a class="reference internal" href="../zreferences.html#id132" title="R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. Phys. Plasmas, 14:056116, 2007.">WCF07</a>]</span>,</p></li>
+<li><p>demonstrate the isotropy of short-wavelength fluctuations <span id="id52">[<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>, <a class="reference internal" href="../zreferences.html#id136" title="R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. Phys. Plasmas, 14:056116, 2007.">WCF07</a>]</span> in the presence of long-wavelength ITG/TEM instabilities,</p></li>
+<li><p>demonstrate the potential for ITG/TEM-scale instabilities to drive ETG transport in ETG-stable regimes <span id="id53">[<a class="reference internal" href="../zreferences.html#id136" title="R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. Phys. Plasmas, 14:056116, 2007.">WCF07</a>]</span>,</p></li>
+<li><p>demonstrate the potential for ETG transport to decouple from ITG transport in regimes where both are unstable <span id="id54">[<a class="reference internal" href="../zreferences.html#id136" title="R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. Phys. Plasmas, 14:056116, 2007.">WCF07</a>]</span>,</p></li>
 <li><p>demonstrate the reduction of ETG-transport by increasing ITG/TEM free energy <span id="id55">[<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>,</p></li>
 <li><p>demonstrate a <em>universal range</em> for ETG transport <span id="id56">[<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>,</p></li>
 <li><p>clarify <a class="reference download internal" download="" href="../_downloads/1ef69c2267187dc8cfbc394d28ff8a6f/etg_prl_comment.pdf"><code class="xref download docutils literal notranslate"><span class="pre">errors</span> <span class="pre">made</span> <span class="pre">in</span> <span class="pre">previous</span> <span class="pre">PIC</span> <span class="pre">simulations</span> <span class="pre">of</span> <span class="pre">ETG</span> <span class="pre">turbulence</span></code></a> .</p></li>
 </ul>
-<p>The first systematic studies of gyrokinetic momentum transport <span id="id57">[<a class="reference internal" href="../zreferences.html#id133" 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#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>.</p>
+<p>The first systematic studies of gyrokinetic momentum transport <span id="id57">[<a class="reference internal" href="../zreferences.html#id137" 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#id85" 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="Link 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#id64" 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#id139" 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>
+<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#id65" 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#id143" 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>
 <li><p>When the effects of the synthetic diagnostics were included, local GYRO simulations also accurately reproduced measured fluctuation spectra and correlation lengths at <span class="math notranslate nohighlight">\(r/a = 0.5\)</span>, but underpredicted the measured fluctuation amplitudes at <span class="math notranslate nohighlight">\(r/a = 0.75\)</span> by an amount consistent with the underprediction of the energy fluxes.  Interestingly, the shapes of the spectra and the correlation functions were still accurately reproduced at <span class="math notranslate nohighlight">\(r/a = 0.75\)</span>.</p></li>
 </ol>
 <p>What the source of the energy flow underprediction is, why the correlation functions and spectral shapes but not amplitudes are accurately predicted at <span class="math notranslate nohighlight">\(r/a = 0.75\)</span>, and whether these results hold for other experimental conditions remain open questions under active investigation at this time.</p>
-<p>More results related to gyrokinetic turbulent heating <span id="id61">[<a class="reference internal" href="../zreferences.html#id134" title="R.E. Waltz and G.M. Staebler. Gyrokinetic theory and simulation of turbulent energy exchange. Phys. Plasmas, 15:014505, 2008.">WS08</a>]</span> were published, and a study of GAMs in the context of the drift-wave-zonal-flow paradigm was carried out <span id="id62">[<a class="reference internal" href="../zreferences.html#id135" title="R.E. Waltz and C. Holland. Numerical experiments on the drift wave-zonal flow paradigm for nonlinear saturation. Phys. Plasmas, 15:122503, 2008.">WH08</a>]</span> showing that it applies equally well to long-wavelength ITG/TEM and short-wavelength ETG turbulence.</p>
+<p>More results related to gyrokinetic turbulent heating <span id="id61">[<a class="reference internal" href="../zreferences.html#id138" title="R.E. Waltz and G.M. Staebler. Gyrokinetic theory and simulation of turbulent energy exchange. Phys. Plasmas, 15:014505, 2008.">WS08</a>]</span> were published, and a study of GAMs in the context of the drift-wave-zonal-flow paradigm was carried out <span id="id62">[<a class="reference internal" href="../zreferences.html#id139" title="R.E. Waltz and C. Holland. Numerical experiments on the drift wave-zonal flow paradigm for nonlinear saturation. Phys. Plasmas, 15:122503, 2008.">WH08</a>]</span> showing that it applies equally well to long-wavelength ITG/TEM and short-wavelength ETG turbulence.</p>
 <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="Link 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#id92" 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>
+<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#id95" 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="Link 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#id140" 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#id115" 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#id141" 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#id56" 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>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#id144" 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#id119" 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#id145" 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#id57" 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#id123" 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#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>, <a class="reference internal" href="../zreferences.html#id97" 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>]</span>.</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#id127" 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#id100" 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>, <a class="reference internal" href="../zreferences.html#id101" 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>]</span>.</p>
 </section>
 <section id="urban-legends">
 <h2>Urban Legends<a class="headerlink" href="#urban-legends" title="Link to this heading"></a></h2>
@@ -224,19 +224,19 @@ <h2>Urban Legends<a class="headerlink" href="#urban-legends" title="Link to this
 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="Link 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#id126" 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>
+<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#id130" 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="Link 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#id127" 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>
+<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#id131" 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="Link 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" role="doc-noteref"><span class="fn-bracket">[</span>4<span class="fn-bracket">]</span></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#id90" title="J.A. Krommes. Thermostatted $\delta f$. Phys. Plasmas, 6:1477, 1999.">Kro99</a>, <a class="reference internal" href="../zreferences.html#id89" 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>
+<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" role="doc-noteref"><span class="fn-bracket">[</span>4<span class="fn-bracket">]</span></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#id92" title="J.A. Krommes. Thermostatted delta-f. Phys. Plasmas, 6:1477, 1999.">Kro99</a>, <a class="reference internal" href="../zreferences.html#id91" 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="Link 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 <span class="math notranslate nohighlight">\(\rho_* &lt; 0.01\)</span>. 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#id62" title="F.L. Hinton and R.E. Waltz. Gyrokinetic turbulent heating. Phys. Plasmas, 13:102301, 2006.">HW06</a>]</span>.</p>
+<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 <span class="math notranslate nohighlight">\(\rho_* &lt; 0.01\)</span>. 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#id63" title="F.L. Hinton and R.E. Waltz. Gyrokinetic turbulent heating. Phys. Plasmas, 13:102301, 2006.">HW06</a>]</span>.</p>
 <aside class="footnote-list brackets">
 <aside class="footnote brackets" id="id79" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id6">1</a><span class="fn-bracket">]</span></span>
@@ -248,11 +248,11 @@ <h3>UL4: The parallel nonlinearity can have a dramatic effect on the transport<a
 </aside>
 <aside class="footnote brackets" id="id81" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id29">3</a><span class="fn-bracket">]</span></span>
-<p>The transition is also dependent on the closeness to marginality <span id="id82">[<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#id126" 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>
+<p>The transition is also dependent on the closeness to marginality <span id="id82">[<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#id130" 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>
 </aside>
 <aside class="footnote brackets" id="id83" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id74">4</a><span class="fn-bracket">]</span></span>
-<p>Since the publication of the Nevins-Hammett theory of PIC noise <span id="id84">[<a class="reference internal" href="../zreferences.html#id93" title="W.M. Nevins, G.W. Hammett, A.M. Dimits, W. Dorland, and D.E. Shumaker. Discrete particle noise in particle-in-cell simulations of plasma microturbulence. Phys. Plasmas, 12:122305, 2005.">NHD+05</a>]</span>, the typical number of particles per cell in PIC simulations seems to have grown, whereas the GYRO resolution has remain unchanged over approximately 6 years and probably over a thousand simulations.</p>
+<p>Since the publication of the Nevins-Hammett theory of PIC noise <span id="id84">[<a class="reference internal" href="../zreferences.html#id96" title="W.M. Nevins, G.W. Hammett, A.M. Dimits, W. Dorland, and D.E. Shumaker. Discrete particle noise in particle-in-cell simulations of plasma microturbulence. Phys. Plasmas, 12:122305, 2005.">NHD+05</a>]</span>, the typical number of particles per cell in PIC simulations seems to have grown, whereas the GYRO resolution has remain unchanged over approximately 6 years and probably over a thousand simulations.</p>
 </aside>
 </aside>
 </section>
diff --git a/docs/gyro/gyro_vv.html b/docs/gyro/gyro_vv.html
index 45d2dbd..2c699b2 100644
--- a/docs/gyro/gyro_vv.html
+++ b/docs/gyro/gyro_vv.html
@@ -138,15 +138,15 @@ <h3>Local limit of Global Simulations (2004)<a class="headerlink" href="#local-l
 </section>
 <section id="gyrokinetic-simulation-of-impurities-2004">
 <h3>Gyrokinetic Simulation of Impurities (2004)<a class="headerlink" href="#gyrokinetic-simulation-of-impurities-2004" title="Link 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#id53" 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>
+<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#id54" 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>
 </figure>
-<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>
+<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#id49" 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="Link 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#id94" 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>
+<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#id97" 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>
 </figure>
@@ -156,7 +156,7 @@ <h3>Electron Temperature Gradient Turbulence (2006)<a class="headerlink" href="#
 </section>
 <section id="energetic-particle-transport-coefficients-2009">
 <h3>Energetic particle transport coefficients (2009)<a class="headerlink" href="#energetic-particle-transport-coefficients-2009" title="Link to this heading"></a></h3>
-<p>Following up on initial work by Estrada-Mila <span id="id6">[<a class="reference internal" href="../zreferences.html#id54" 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>
+<p>Following up on initial work by Estrada-Mila <span id="id6">[<a class="reference internal" href="../zreferences.html#id55" 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>
 </figure>
diff --git a/docs/index.html b/docs/index.html
index 06b867c..773956a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -454,12 +454,13 @@ <h2>Equilibrium and Profiles<a class="headerlink" href="#equilibrium-and-profile
 <p class="caption" role="heading"><span class="caption-text">Physics</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="geometry.html">FLUX-SURFACE GEOMETRY</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="geometry.html#coordinates">Coordinates</a></li>
+<li class="toctree-l2"><a class="reference internal" href="geometry.html#clebsch-coordinates">Clebsch coordinates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#bounding-box-method">Bounding-box method</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#effective-field">Effective field</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#equilibria">Equilibria</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#table-of-geometry-parameters">Table of geometry parameters</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#magnetic-field-orientation">Magnetic field orientation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="geometry.html#toroidal-and-poloidal-flux">Toroidal and poloidal flux</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="rotation.html">PLASMA ROTATION THEORY</a><ul>
diff --git a/docs/objects.inv b/docs/objects.inv
index 51c37cf2c865d32df23fce23faf4b1e6d75d307d..23d0f46ed9c3614e4757a2d85163ccf9a03003b4 100644
GIT binary patch
delta 11008
zcmV+bEC1B^Rhw3jcYk-{I@0dFe}&iDx!AMUtLb!l&zv)JN5Dz*HUSz)f8BT)Fo`E%
z)3!+``SqttC0Vj9gT$V**7TlW*YlJt%Th^IDqUS(Uin42{`WRo##^7g_a9#K>>d6m
zd`yZm%U}QgSnjsJCF`q8pLti8mmh59uSot+Tls&G{68$^KYx56`F~o<|0&A<e{ALd
zMe_gGQvM%8{$G~z|HSe~{wmw;4`oy)SsHEqVwJ?{D)ysv?H`Ib_xEvL?Bi9LJjYhN
z5vvh0LCAoRAtBQVdw##BeXeQ0N9|K3>_w}mH2bxU*AKfmEsJ_-ipMN3H_>)WrMU2W
zb!jhJC(#o0tbf9I8?Wl%@?pDqhyMw;@F?Orq&(yDy}__|-CGR%VK55%Ui1*B>!{B1
zE6bmt82hROx50SO^P=tkF$!Y~jVQ>VQbyB{y)Y2KU9@_%#d2AK-}U+*1;gGJz8Bc3
z0RB9{%dl21q>1A5eK4*HP(-#IAW8VSthcv~EfypR`+wtxu*(?U9yBTx^fy`VCn+?w
zzpt>()=BxLcl^IiT0z3_G6NFENf?pzPN_LskajuLCuLWPlZ7~0hBR&z0WQ3Qf0hM6
zc<(s<QT6yDE#GfP2{=RVgo=(bWU>UCWE&S<<p3$*Ia!=c6owI5&qAXY?e;be5xSDQ
zDGFa&OMhRYc({K|!qlRP?e+{rS&GPT`f(VJy(mqJEZk-5cpLt4vWcKD<HCM#Je*I$
zyU8FJg?|7|wu`peq43K*N{c;o((qpV@-g<;Ns_R&UuI9yE_(8JQMr1I*Z%U=FAgw9
z&?o{!K#}YYTRuQ^J<0R4EQV0VDrL}07${?;jDHDbOekZ^S5{NTG-bW2=!<622gBiz
z4g7^D`kgBJyjJvi#pXpt_}-$W7jUCD58r!BQTH}|=aQ-(d(Uf8^U!}Tu~bl(%Ux0w
zt=glulONJFNgu*hRK$fKLm1Ow*9{&IS~c|PWt5+47AVNL;B~NoK7G-fDR5Z8ml4}E
z=zofa5u_pu=l$L&;FK1_>jei2@$ir)rLFRqacK?@@5jT1#^LrD#H2k3@yQ3t4(S?R
z2U}(@{w^*bvvs4%#~ECfmX<Egg!pxv0%%{tB6+hbBv5hL>&drpKKucN%9D8Guj68s
zC;QUejszAZnJ#(V#Cpqewfc3c-N2h#^nd$bz2za<QVp!L6^il;T*klV_dv&McF6s0
zv@f&00Mswml_`eb_@69G845EY+)ev#pT|(f^zhOuk-9}?yI&sC^6>61NlOiz6&*;p
zLAc5Mn?KL6+aVad$IjAUP*Fj|QwEKoR`0~`-+rG>ye^YRQt47O+?j?%YB6+Qbbl87
z5~E9E;Nx617C|h{WB=;%>gt%~Or-J}<Ko2nRi_}@cQ?Jyt!KxJ^!)IL*KFx+@y1tR
zVb|%nGFplrz(C4x66+#b!f22mBNUa}Cev%Zvx@88d7Gr&+xs)R<oEFsv4oaZ3B4v1
zM(d=4UOHhf$ylNLXN(O*bZUf9^ndmpzhZ88|4qJg%6oh$5E>kMZo%B@zXemf-#tph
z#i<u2iB+}*A?U)xIE}+~ve_KEj0!VlMZkc7DT4lFG#bu_lW`b~gK#jsxw*$*Mzwj2
z3k~tPN+rCmau&=NlUdMGxJlyenyj#M6mqz*iIu{eVK5qyjn-251g7Ku9Dh{=R7yTg
zgW0r2fA*6!pTS)EUAFrx?+4(9_j5P7>wG^jbgtBsoujj2;E$-Ooz8;3dRCzsDxr+*
z)sQ&U)S{;ogry?|D~Tjr)M-MKfoQ=dEk!{Z-UW+~lR?Fu7A}k+JqX5gnCJ=oHci*L
z0|UtqM&t2drn8ieEG4llbbpq&UG(5U!o>$a?s~U^AP#rYi#<WiP&^3ldfz0$PcYFE
zFpCd6*RM~5itjJ@d_NowuV=&iyV@5R=XsWgW#&ST5QdOoHk-`C#YB=(pSRD!at$|I
zm+GVLjw2aIQcpLX4abY{W>i(`CXau*l@<}aus5^dvsTuJXt!&vtA8FN;s6%=x4pYN
zTwkrxxDMfhOpM=xvNm`V@!pkkFUY2Kn)AxHua$3FFW+W+csc7`bEN*RZ*NBT-`el`
zVSfmh$-^$*xhmKn7y$+U^gg^E-rfawI{o8Wg@4ow{;^%?Wbb4tk@#?`ETyMtzjqiX
zNc>Z8I+f$Z)2jpe)qnr=UEsFSZn=)24`04IG!#NHLXCQN*MnX-2(G^e23FTbsB?>!
zsB5S-$F`s27&DjVJ`RO;EgfP+sgS8rnxb%F0_nTnTn&UU6oh56b1KaX;|Lf(!o~2e
zDoKX^tFxLqLG|_y_EZ4Pz18S<`y|Yx^eN2pb?h+m0*)b$5r6J(It*vM@uzSy8w4}K
z%}w|G!J$!eYaJ2XK%d=yubB8K<3dCLVRu(F58G@RZC!W-VjSL%CfB`D#gwC)(1}SP
z#!yj%p~i%6&Ll2es3c?@&Zl6o2J?!ne2iUeRlY_JfN{9^7*zHu&}4a*tlgfk!T{N1
zHW?1IXM9Oqn14We9DW;0be3+DG>&q|kD$WQ7cicTN5gT@o9WFzJ%q8tr<xuZh>!2X
zAW#I(ZR$`ps{2N(I_yL4V{#$eGlGoory+NPYGlrh6xd`l1-g1e1wPl-1$3f)0h`{!
zs8cJ-*uhGo-i%|Y8=EhJX~mb}a+s^JEnvdXp3WvW!+%jwGqU$D4$E37JpCpYwSL+I
zfBK&#=nxgqXb)u`Z5`XY4y7jl`Mx)YCV#(}^+tND$LV&IyVk!z(Hp?Id2d#G2l+1g
zj{_S@&+dBvTcMNG1r5@(yP;ey$}@^2acuw+CtAR4vgj?ED;*9!bK%RLxNu!HD8#zK
zJk(bX3V&ClvJhtFJk$-#B7BS83d7~+;Scr67LU<B4p&*>@Ii14<Cyu!-ZTjNllf(n
z@BJBk?-k$sCg0T=d{>I^s>%1^489MF??a8RII9K=y$<K?S}e}0$3m~kdAlx)vud-@
z>vP_&(c-K+E%aKQo9Y$%zB5=kO0q&{*<d|~Q-5RB`I1fPLWSb<kHZ_e_*cL<<vb4{
z5Df-%7~1N#e;K>@d${x>xSLi}9X_;&`)%g%U>w6ZhT8+-bTpBVC=JLW+{ZZ%=_?0b
ziNz>G#<9`}orlw41~Z>YU+6iki`N}@r#n`s0#cRU59Z(R?t;bayI!sCMqFjXHB7iO
zEPps<z%}hRck`{X-WtZ+VgD;h*Z6TffXU@pg&fNWD{682bvPd2$8rnCmsXL_@ito}
z<*V!5RN}<k^h+?B^oNV@wYlk=J>8rCqiXVRVZ7NmKpBev2!op&oxphopYzD|drnth
zy>}bkxwJO2zipr^C`w0f%G-t^iaaPkZhyiBScJOQ#BC9tOVbkkHeMF1M}L*U>r2w8
zY)*~qu`oiM>Eiu1h4)w7n63`Yvt5@iPRq01l`f9TGhCFXoRi1glI@6~lg`Mq-H<L0
z$iL!xbay&tyB)^N<Kl&XD58hhGJsD9G6MEnTu8r<@}z(UoNauH52~US3;$PAK7aa~
z2tMrMR~+v#L<D2<*V%r*h0ZjOH`{ns;ui?N))Dk17#hhd{jkrYQ<0iVJIgjq7%7!@
zhT2(8JKsJaw6mIahT3_UCunD+y<dAc9xY?>aD$@{x4?&+BfYWiUQ-+-la&vn?n9at
z_$M@{!?qOqR`|aC{VE~GGb%``V1G&l6Dp|2xC#a;c%2w);bbxU><)@K?GJe|&wEr6
z*}H^380&Q<Yw`cbGmF4p(8Zg`N;HV`9$v)tUI%kt@P05;wE%(zZBoJgAZ4DxP?d5v
z=-|pjz7&n?_p8hImw&T)){2oe7+H;xAt8SrRfM2XgsGtjp0*DM>i`3n|9=y$vSkvb
z&1hLHUy*H}<6IR_K=EB*1a$@Nw`u=Z+yj;AD&CiPeGgyTCd+rGNJ1@+Q6Nx@M94tG
zE-uuP;+`NX06HT<yv+Q4_AAZ{)3e1t4^%gmQbB-vi2(W!CJ6d9{+o(_%5UrH;bQy(
zZ!1AZ3%r+hGnY$CEybWthkwdedz2bg7ci#8>FQPVVp+b5{bjU`aNE>z%@QfPS41+2
z>>nleR(V$7+#3e0CGPUsMfnqUoAT>9wiQcZnU0m8vEM(=?X6x{+bqSh6tR!v92KzI
zpC!LXYWSD$Pk(zv$dHgBAyr6y!xtxH$mjP(0j^PZzbZhlDnQUEfPW{(3=Gd~H%2Oi
z7`0GjP)QR|1a>w}A`K@b21>ey#J&sX)@3Vzc-1I?h}^}VvjPk{m~<8Y<L_T#7Lr1-
zVT{~FtN4G8Xf4fJiGo!Woy9n%%`>>X%{u_du}!{g-~p52G>W{}LYn;6H@!Ysgq~q-
z*A&c7E4dW5war#G8h<fT3q>hN3ns3fL-1HLY|K4i?0BdchJBsh6Ql=+;omS5*Y*IN
z?xO`pZRPO?f~DGyBYC;+w9F4X>n&W8yaF=dDw2oP7kgQ)wz?98Nyva0KGIJhEF&1M
z*0sG8FrMI^x$Yo)tjJo3y`<4MR^X@wg7v`rL5IF^(1;Zm=6~6iCLmRBeY6u7W)@+X
z!U&6L)Zp?cu+O5EGy(wWcN|8|X;l{#dJPaId=U0v;zZGaR;p`Jg8~OuV`K|vC@dMK
zy;)DAfmyFT4Nj3I4NQ+K8rzB}wTf6&6_Nc)w^>x%K_jnG^#4FgRJ*;Shdhqa;!x=J
zy?TLal)uSeYJb1Cf*n=2e@rgdxkYa}{W!cFK<A6D!}W`0k4nPSr=q)Y@Qr#^^dLHr
zps*wvjwOlh8rOvgFGYZT(ciS9|4>D@j!xC%Qsd1=?7TNb($rVfDp3(b6V#zzoIJ$o
zbF@9g?%l7#>OHVDyL|L9#CZfWn%IB9b!==rIKMe;d4F~Qw6gwr(#(@|Orv9xjww3E
zQ#eQ)&R=NCZ>91@Q@O_@lxX@F<?w&oSR36|8Pr~axeQ9O3IBDvw33fWK5Y}L&c}F$
zhrm(2CnBm`Mqq+y18_hbYW#(lm_VKJkNX*B+ql=Md#a~NGbJ6EIJ_7h>+*DG5J0DU
zNy5+ylYjCpKG}nCVJ3w+K{%fd7e9iTS5<(|C&O#LsMX#(XRa;zlM$9LNpWmoU|sMX
zcU6>kbnHvKKn5Y_X@TKn15@luqt>CHieIX7RgvV}z?OiZ!88>&yc1#ThAOoPR(A?h
zHwCE2<%6}!4zki<4;Hu5T(3>1&Gpu>dTJANRey2cV2mDOAZ2e<@pP~|7<xu!brUZ*
zsRN2p;_~ZZnZspV?ycrb*i%G&O|vk+P_<R@H_pNoi#AEqSOObe-X=1JK*=qd(7bVz
z<~chLPVYG&R_F1Fh_#^!>b8t?n;GWKaI}D)WP`5JU&*?(NS}hTjAU=n1^RV3SbPMA
zoPTdsjk|X+a}f%}x~Zf+9-Lns=sn1u<XHcr16T#XkbXA5pTWly__x7?JGebug)?Sj
zXs;ncT`1ui5dIhW>jY*g&_ZB@Pu8cnG&Jtmj+jI<j=nic?z!waY40|{D+l=Gwy%Cv
zJVEyjzY5WxcdV@_2;&f@AUBGw$Jsv1TYuiBbjbOzDOJ*kn}y2y@DTa%0v{R-MO+@l
z?&^n#k-%-whnISb5We`fO;#`~Zp=2sMG57rcvA4T*9Wcsh<*aib{j*(fhp%|8x;lE
zCVcoyz&eIr>i1QWuOc7wcXb*=f<kKJKX9%q_{b+fe2mjEo(}A`t(h<Q8#H?kyMKn7
z`-Pl$3LV=c<gh!axi83hN6@joKo6_OsI=+WZu=j53lHpeZd)|_lT=w8{t*8J$t+A?
zPnixN#Xt)BmvH=@V_us9pk@$?A?o{Z?A1CsG10AcaUGqRxpUNPCwOWhQpp+yCsTb%
zaj}0%Xrw{uoQ+qfw_H8gzDNEVpMQQ;YxloL>oxR4SN~xDiBfbnHNVe>Q3Tk^1;?RG
zgZj6hz8+)t&e#)nYBw0p>6X^EA(xic;q9z9xR&-|GmVDIqQQ-IbGojoS}PG7pNNd4
z=7PMhlHLwZ0aN2-O~YBVEWpTGHTl{TNQ!x?fJ^~7{})BslXrwNFezcSD1X$!L_pL2
z`yOV&Rt`-Oa;2#FWJ4<tFp(#d7spPi*BTm{@25R(xQzzQg<UhhzUu4W!j-3l{H`j&
zlS~Z-yqASn&$4AEwM#d`lY=NwE7wTl*3nEO4X)>BGm&_u&Mzu-NI53+f3)(BJ!rLC
zm}}Q+ZC>NiLQ7;iFygU&lYfTtK;uew`$L|TxB&~-SpKy7L<~g&`$kbQp0Bi{V4!r^
zRO-3zg6-b_Dn9{y%Ne})=Ok`ygx%*b(hC|A=3jXw{83|=h>Kpb%p<Ebk{AB)de+0V
zkqM4=Rsb9YJ!O%IwyYT=3wV>axRM2*R<F!<$*Pcs>-><Eu}41Gu7A04-HA>q2Q}GY
z1MG<pjV$VhS%Gs*x}&oRS?0-fh1e&z^A#E<NM+;A%7lpg(`x1@^mY1Lhckk^HRYw=
zdvxm6Rtt2+0^HUq`y{0<)T*g^ag9py^$PWHec?=xUj@~t^@hFPrd3AT-EG){V-ltf
zH(c0mfuD==<$Vt2i+}r1@vFZ-EVrWLEyPk^T;S4=VeZ*5F96PTxLEkp;h#=w@Sa{S
zEuY}!lFI+>l1l$-^X-264uUv8H!U(6)o^LC!uaX??QAFmR9$zzckg*WZ@0VMK6ibB
zE!w+2y>8B@w@F$&#ksX%E99kVI~tDXpMse*ZsGligjI&8GJp3c01=t0#3N1mAtkC3
z&jXa}7h5KfM1sLLfor?3j$yeEi}2i$g&bHnalBqet0&{EtcwlnNZ@D`L|&|^AQ)Wt
z`k!bt<QkrF4JyPbLzt!8S2r~r%soyF!J4iwlhKzT#K}iE8IQgzg^%%hj|3)7`;k5d
zhDU;bPt`tI7k?E9tai#)I^f@@Q0|zml;rW&{^gP|lFfpVc(u?ECF?`9HO8zQqav6L
zTp`l=aB$xn$><e9&v(AMJipxcT0Oel`&vD90pD$uCz&l{C68?LelYIMh7-<Ip4kja
zQ!`kYnn9VIsUb0G7`8QVyJeT~@J+cjUJJptvzR##<9|FnB$)HmBE`A6JgTd^C3W+b
zI?p!8$OWYqaZ4&<PA5`@=#m#b%M&@k9$S*HB7w;hp`-3P2|Y|haysTjPgcSa7I}$L
z4sLPOd(S1gNjt5{E-6;}7>K`V0K9|0;_Wtq@*WB<SN*E1sv!8L>Y!|GSfAX#GI>L2
z%GL*XPk*#hc~*uMo7^fS1D2+X*Ij}%zx$o!QJ#1Age}KYwV0E%v>Q)5HH$-1mS#E@
zmqaY>6fEZCE2bhhQ?7I*TQNb~DOQZhRZP%&N)@+cD&{mQ?F1?&y)tb|x{QjXFqv8H
z@0(<~ku|>V&4+VtWJ!i3wPyfX$uJyysZ{`5N`J9yV+vc7M-qtcK}J4f9HVDCu0VDK
z^1g%1y%j@=v62(Q-*9)jUf4#d>JM@97=)Ua-9)9W-%ZsDLz~2qBe?ls#^(r~Qu<@n
zbf@)4S?e_LNM%X|&q-|ZfpY>aBQ4%_+(3vFr#2BH!YZU2$@KJ|1hff?CZr0C=19v>
zS$~dggv%<t<%cFI+F`STs&ptyEqqqP+lA075>pthPG=QLtJAf^X%(GIMH$0tIh9?s
zDyI>mGHw+mtfJcxOo9~URsn4z-712PXg5yi8tcVLE#kcpW#<A$#=09=Vl7<360Ey}
zQNn6v55ao=M!aja%7;KbZzJBdGrke28-L(<*V^`qO{wvS!O|3pO&REj!PX>-&6($j
z#LhH|+ZpEwZeiZUdS*C|vi_i3W(KBhdvAq2z^(B;OnvYk51+wYQ#Md8j0vVF*e0A!
z7IhLBIr8M$iHZ@VA`HQTAATWPG8F#KKT$jDhgF}nUqjdVUiM*%J1`w6U-pbcntvQM
z;*A62rlQ)^INA|pM`^gYj;)bFckRH1(i*bHBz;E?bQPq@Q6ujBR6BVkqQOvOg%7f|
z@#!e30MzjY$}r`AcxPrNa7MPe9`pSAxQ+_bVli`v(0<S1#}C0bvUTWbJ3lQIaiE#6
zL)F9cS&9H=;;Jcmj$Qg6l-7_<rhjmg9rDCv@*HDi5@lfG8ss{-G{H@aedfMcE`$?O
zEc?lIaA}^4CBTNJ@@!3|Nz<Z3(^;0CRMxieq(-x)S1ASC;_?i22x}?=>*Ug)!kOHZ
z)f1(E+K^yMPQ02wX4Z3Ekfo{a?Bhhuba4k-h>;SZm4SrfJg|aAJU?bQ`F|43!k(Z?
zQYWe;RaC=q2UU3GNXD*oy6}n!kEG!2U_6?96Xgs0X?Zh$Cc&+Z`exotg1^PK%JqDi
z0^8af*oj3+z~T-;j_t^_*?~9a*sSrqcjBq#)~xYdIq}qTYSwr@IPuhSX)2z=v4%`J
zG#hO19oZVWGaGDIj%<ybnSTwo4~}e&T$wssJFDe!wsww8jm?d#ksFhEV!Pgz1m_<E
z(XSd(YIXrtGEENbN~PHW??|FaR1RY-2#c<6KGerhu}I@UL;y)ft2!ECX+1M8X=c1o
zGh^H{Yqy%ACj_mK_A7uWPV0Z1LtFhLBI~t3BEpqFB2w#q<zpVlYkx4fmoDpegaYGz
zSuNo$KF)$*5C-3_Lwz+*<F|fy8arV$ZtV>cvny+jQL(+*RU{?4<N(WYPi2ziC>X~a
ztP>QM)(MV%$~wslo?C0XJCwNj?)TOH@VCxwO<bHQaR$=<IGD}*J~V~V-Th(_%>3W`
z)BC>}s2`lDAB@zuM1TD&jFTsxr0cZLEdIr$@HqGy2E$L2F)qm21<;K@efLs)*M*fd
zHiWt7evHEL0~ByUC)y@&=9P|0xi00Ub_IsQ7A1^&m>+8Y7!_wE8bAW32=v%btF=G1
z?q_>Kgnl-J)2R@q^B|l~f-s!{;dc6i`P>Jm6CX@xJ*1ZVV1MD2)7IDY#k42X2>6Ck
zpq}-LtZ6mYaV7TDDr~lo)8#fQj-1>(0g>xbZ|?CUf%$>I2I<<_z`wyCOo(d71iLKv
z)|Yyj=eV@nTGmwz8%yX$!&t1@*4Aqk^7I0&zBsFJmdmlNrC7yax9-|pb5(e&71qY;
zY7=d@m}*`~)ql7w7fjoWr3Ma*g;DdOsENyB@v~#$)5LaiebczMshCbLV(JT+HJs&=
zrD?g6^O%zd3UJkv+%Km03n_kNEH<3oEdpQaAQ3cDAFs`ufl7V*W3}67k8yOn*ly#%
zo^fHmd0>i>b9VvXK(OzKe>s`ALIE+qCFNJd>g|rG0e{4k%}4_ilTRRAP)@|nf#(P6
z+W(Joe9wiDn@Zdb|LyG`Uke^5#Itg)G2KvmPe*<0k%X`YWNN1J_VC5SSYht;v@Omg
zr+T|7;bzkB)Z{VsVU3d38D&Q{g#qubS1s@1xet@scdvbJ1hsR#Ue!Gw4gsSf4vVF)
zr4cGRZGUzt&1%w9$)P13Dv;SF>)!>^h$|l75vPY@sV#C<f|d}jcy32snGd--&t2i-
zsyNS0;o_n=+dXlPYvK&Igsn@$$sKXb6`{A1&fS((Iv^Bcp5<|57yKA9E%^CFRP>ax
ztk!~~f1cj)_SySs*WLf*9sOtC#s72}Cw^+<#D8aPocL*#D&;5UNcoJ(QGRZ@ec?Wj
z{JCY6B}W23kLpa`StqvHoYe-+ef8wS4E(9+9DlhCBbm=ip0L~(1>NRLwA*iO4-wFi
zOd>zG*}Od7#5v~0YZUHH-H^>>R$T$qJ}VO1D!hUV#j%W%N|*`ZSrhKL9%a{kh@GvY
zuYc|2%eSf3UJ8_hTeHy^_fq8B(h^k?YQa&KhwNR@*?QdfX!WIWw<Ah&pCf)_4t~on
zpCzZT`BFJSA;5D4+MNb?L5BcxXQt(2CaHML;aEJTwNJInpX%gGJ?2N{M0WKBB!wsi
z)|YPW34^3&oOM}Ydfbt1@O)+9)gtI;CVwW+%`1G|BP@C=o(jIO?9Rj`Mwppkz+CP{
z#b@5MUm41hLWoHY+O+ExcFlC|S^Bb@ery4=Yuy6O8@M3gZQRlk-gJTsn5}NLpIs0L
z-8SBYx(A&wwt7)ks718YYT<vc``(MF<k82@MgjnNEV8!9j9mF)Ymu8C!CZ3QTYrSJ
zd$5$zjE-{X2VlxbA5T}3ieqKsButU$*(;!YVhgG`sHJ}Tga}H`4*4oJo~luyr7rQ4
zPGYGabwRmgCE46suUEuT-rTiG*QiIE)BPzPYQ!gidgrHRgdKA~`ydN*fQ5Z<g*mXo
zKB&SRP+=cTVGg8l38Lr@pl}JE=zk8Ja0!~|4w!HWmgo+Ya0!y=4v?@9jxYyCz}3>q
z5I{jR1OU50L%=GU;zC4GSVd4=h{%chaRKr(tEC_5JQTq0sDX=aeDaWnON%Ub{8$DM
zoDXlu;q`)mi7hY@z##&yV??^*L#$&%OmQK41}sWn*0toQ=eQ!tc@ygu*?;yR%tIIq
z;)mB$X;&qHRe*Vu0!VkUk7v&D6}CKni14t*2mg>JWpP@;4*MhmvkJ@zJU>Paic>tl
zOWK<oTCy&7$JQn}MlDS$%)EolqhZKzn}+pCDv8l4Mso%6$QFpUrZA;r!?u8lpd}cn
zU4ny-1qQ*KHC;nJx>))WQ-8Pg=O!jk%Ld(Xj!}bK<(L-o^Ckmu?#^7d0c2z0hIwVQ
zWYPMW_qg3wyXI85@O$fLJO*p+6G+SVg=E#f(!!FiUjYO@E%Rg9i5p;&ZWLmj6h*S{
z^!ylz#)n;;bJxK@VL2DyrEmK%H(Z$GP6a#EaJM3vhiK`|=gIbEvVS|`$}%ucbO>gZ
zDdCMZX$@_%n@}}uU%VtvlE+$4>Q>dW3Q9~y_e>{GHMu5l5IvGhLl)j04tXb2ju4B<
zx82DzCu!DE%g2+0)R-11Ixpir9>eL;=6FmQBUAHs&3WqiQaFyMh>>}BHQeF|snW<@
zf;1n|ci0<x8Lj-4UVlPUHbjA5bTfOUIYH;DonyA6;`B6onyYhFOSNZW?^12fZu`zs
z?=iJP>%nT76XoF6qIZwWoOThc_2^Z*$W=XR)gfZl9IfgQscMc=)lR5!ALI1nZS-Ld
zgmoJoe~Xlux1$?%yQZT0Dy4{eKTWR2n>(8S0!2OJBbZs6&wtoKo(XDUdNjUJGj%;n
zZubX@vek)@A)X~<(Rkr!;}}UFW9Y7Xi(x+uMnPZj;?sn&Eg?#?*yj;_VW3mA^I4r>
z;Q%7y8Ll+0y%W)1uuOFdJlMdoKmtN!pYMZly-+rDUyTjKi3z5_8q3?pi3P-o<;RU+
zvFo}x1NL4$-hX%D-KE2c4jjK!r#f7#Lmh|<Q!(1oa9N(Lk-(NGWO6XcQa(%tw$4MT
zIE;s83P$V2Y(dvP5mOMInGaUbHd4Yi>4XxOqvnXX<GeXZXMgCNq%)p8M|5w_rRz9S
zj?4a)bKN+*>2Nm#snF(dsuQsrk9OjcXCC&$X&Wd0)PJcYz1<l=f{zP}(|`ot{zxFf
zVLBIxxJuWKrR%&HE^B!R2qz+0It_%tZYN_9$&uqRh}5A#ygaHnPNzW-L+6nYT-rK;
zIVY3SGM70~*d;V40xnCL%?W&d)@vecr@n4ek}3yBAE!3ut|lVe+|fkSNFYrVueRt{
z%q1-_E`JH71-dJ%w2*eo!pu33r()&^+svDsubzIBOSokB;~eG`e>E<fJbyK=da^&_
za@hbyWF5Pph|andpyXJ#1KVv;gd}0HL5lF!*aG({3Cv&ItRx6Kb}V(#3*{~Yix3`b
z1B&gI8^V*Y*nGn!oWj02NmuMQ(OE@h6Ay~==znZ}_oqV<^ms%8c72Mj$V5SBJv^%z
zMM9n%s7PcdqZK*WHeii&)}z)0zI4Is@oR*)j!GkjR%n`Hv99N4gqfhQjT;jj&EPS`
z;!u!!=oXhLoF_(Ip+17nbv*Bi-Vt>6;W&cL6q7?-=LXpjaWm4UNvD+9Mc-7c^$;9l
z`G0T3;gEu3!8pg%h=SNg1CX*tNB~jTdeDiY;YL>!i4%q9P$!D>oT5Zn_l(x51pV3W
zLekLk8MX*Lv6OhQ@BbPL+Z_LwR((0CY3bKQD-`0!+)Mi=MDo~(_(tB#su}ScA=LYR
zAFo}=n8a|xa4~}(CJ-isF<_vBjAZY}!+(V^z7Aj!Et5h-ky(;}d8IJ-^B}w)&VxRN
znrfu`D0ksQaZUv$iOv$cvBZ)k&{&dmnML^;1_`&SM@oTZ3XA;1@%5xP8^FL(e-)r?
z_qcZHJW&Tgr~^gnyN?5{6GcX~Ez@OwhQw-jCLxg@3Ot@qC$oh<TYHXQmX^F+^nXk6
z?OGvCNobDZMKT&>2`QF}xS$bOcMK>D_rE}UksSlayVMcqAOPplYXrG?G2KeUA+lWj
z*=nUDM&~jTt5#BC*2?>94OT{;S(5%*GcNsg0QSXfA}AcDLL{qAg!l!AsW6x4Ght4m
zCc?k+q>RH~(Q~{xq`Zr9Ss>$RrhlVpsqE`)xCp|py)VJd{g`)E+M?M@dT?8(0DxSh
z_%^<;txq7A%j-odl1C=(g~E;4o+C!M=rdk^#ao9JPA-mv)wi#~NUd$Y#T#4q4;TFr
z+}uc{leJsfx^+wU&25(RCTBT6YO|a-drRXD?TjB}Wi(E-Ra?gV1wXL1Y=67`YumbO
zQao<YkG2mPG|tD}sn|X`50I`fh2oSgGOuwKN~_e3V^aJ;Ng~x6Pwmu7`%Vk=snKZr
z=jHBswc)reUTs6BO~{S7_qKdJB;F;?U9Ug`ud3MNHCP%?oi!flbmB<J)?trbgqlme
z^T0=vT*s-yiC)xz03(m{;(regw#rzX<@HC4_K*K6Z@o1hKemTR72-tugc+3Bs_$GO
z6|!D@7#C(@n-m>%CeZHZ{*jtfr~fH>yE6b4t2zl#=de8wQ0Hl$3aI$bIU7(h+no@o
zX*>6vKux9NX@N@lIcEkcy>=%DDs5+-AE?yXo+79eTAwATlr&Ei)PKpG&lS{ZPoFMW
zQ{{BVU`@}FlLnOrm-7Y{yZO{X#ajNQ=45vQp{6bQOWLeXBP9H;6~TXuol8^4ingra
z;OBfewj6%qhu%?-gGs%$@aC!pgu<SiBbkOI4ZPK>0bwrm)XkRTd-;U%Rv}ysnNTxi
zEN#T2b`35$<vYhF!hbQ;FsNb{AA{K)ZxnyDX#e=H^3v?D%I)D+Zkqg6IX^T-H2o7j
z<y<uH$Jl=mC!9y(gmbx<8BaLx+|dj`CV)%;#qMTCz>{aEqv|SzU6l9O_8Zh#ZN8E6
z3j>MAlLiTElslVwz-MF2&v8u>&&XMg!OHdRKdAYn63=DP)PJ;I%9l#pS&qy*#A%U~
zOVbJ|%{m;HTaT@@I_JW*%Y*Bh1NU_PTbJCo-Fa`TV-)%E=Gm5hw4-qv+X)1U&P^96
z$}+d;B&>857z>Wy{>ti=OB9BMGmer6KF%>d9KZIyrxNg~DF&9nyb(p4!)qD$B#=K<
z1zen9_72NKT7Mqi?UJ<Y%2K&a(u3$!NSbl!dqUp9-`-(eyzaW<#LP9LAk+ok59Z(R
zv_P@L_Wi#xADK_b4I_G)J?>iP4zGB4$2!?;c>1?I+X=*~9VF6`^9xjAug~Z}VyUTh
zGBGD)LK8zx0zsPYM^NBJt-#mr1%~Io`nSJ1Y_~A@=6`rJu6EFIl*jOWU{0JUf5pLh
zmE}1M)!SFxNC}hkSgWy)ERdabaK%t7<63K{FoRZBX~pgSl~yLSYPF}d-jCoxZvLAO
z0(JA@-+p}9#(5H@q9Pxo=NQJlXw4gV>_5kVqHwrq1!GUgZm!O1_`swB@xoC7QwmsJ
zfxcbret!hT3(hPaJlvnu;L$U@-9j;|+{_^FuYi)1MgBUEcDM(@kD(2%pl$KQea<iZ
zPyX7ZHl}N1pp70pVp1C;ZH$us)n4?U)bRgu!97ba;e~Jxx+GAp@+Vj6lby0BtK`Wl
zcd|?B<SKJ=l{opZ|AjHbMUp-kC)-^-h+>2iJ%8u)D+UnHhvQp0!9L_msP%0O2H@JV
z4@3l$h<lD7(J#-@{d&yvYVUMy`&;c@t!*#snGRML->REiwcDe5mNV7Xk1D$#`;*11
z4vP?90+@vl7vIIn;xL&@Heh0lmT_1o-DB?avt(2lCNW=hqB&jk>>R!q<mh$r@tWPc
zwtt@8x>MK1pKEsIx_NQC9k}kk+tY4aYmaTyS!<mZp4_tzo>`Mq_E(la6^~ghJ&?Rc
z&Wk=@fA}ipt}d^xytBQyt`1xm->ung>)^39Icx3wv=`)`wRg?7y|S;+mcWYJAC}vy
zTX;>gJ<h*v#v#Hp4bLk4cjBIE+;efyvw1lFgpNLW3tKK@bI13_xWhO^k1+=s7YC1E
z<-#DRkc)zL4(khYRNEv~yP&gK?A_UIPxc!|s}-eT5w+v#FgC5AVaES)6E1=|jW1q1
uA6r+hJf4ir;V_x5gJkR-@NM7wTO+@z=r@|#P4(QScAk3Wr2l`3>eMdbTe!9W

delta 10957
zcmV;;Dl*lZR`^wrcYkx^xY6!Ce+8@77n`jY8INa^bCNsRqHVn+OBzX@uNxL6Q8r_V
z)R2_Fe*Ni20|ZEd5}?hg%4{sMpQk|(1RCf@<Kq1M!Y|6zzc<k$-uUdJ|L~S)AMiin
zV^Wk^{`U9Ba=ZC0SzVm_%)2;0|70tFLGpjv%KwAp|6wWr>3<W+|I<?bPf`B=V=MnJ
zlK;P!^8XO>|FV?-Cze0*m)Ul=FQYQa(rDus%Op;hu^*)?e_zD8zl-x?7ca}?Ikw`B
zSdEYgLI#8k37JmV^RH^!XPWkV)IL$dUbK8lvzJZ0df3KkS=38YJZ5>hjy4-A#hKr$
zOMB5Oi58$|8Gpu`cv%OR51aJ|{7<-nM-k5<<r$an^#{Gn-h6Ns2E*XWiyq>171dc@
zviu2(v8zgO6O8&jFWT%LqcFD6h=L3%WjML*g@FKWqvfM5mdg_Su6K1S7<RVsoxn~6
z@Yfz*hP84bO%z}5gHct0BC_QGNy5)$y}hq(u^>s<pMTecUBvMApi!Zqzs_<$NujCz
zeTi+hPRcKR;QwvX3KE8w8IUke!ic1IOwGZ9w9BDBDZ5e}EyU3>q;aDNaNz^|vn&9@
zdxz-{s>c^;`F=Y}z!`c+RCJUflO<Ruo4DvI2S@?W(c)yHFpS8078<>1yR&JC(3RXx
zQ25+h`hOh7!`)*NrWQ?XyJH~AQbdN6+d(+;qBJS8aGR~-P58&rCW69@3;Vs%U^Wi#
z#{FOz{sA=EHrizS!Y}hEEq2gJ!+Y_|$Jk#bNy1isnLS0@=*izk<?=CJ`HMHd*uxk>
zqX-NEMY7#*_yE!MB+t*X7(yAVltC+Dpp20+CV!MMp^PowSWOwzl=Z5j&znW>4+aC)
z_vfPMcdF>KTG3|}n->+~M~jwTz>VH4{OB!2-P`n?3#xkTJugMgL;tzJQbAoVwn<U6
zYLD7ZzE9I6eF&FP5f_3CVN8QvHh4T})zGJxQGTphpdjOdm%$wR^m%Wpz+nMjMr_ld
zD}NeBkcupvUG;_mr?ePe&p1$shx;@sZI#E2OLKU5KN`$64!6f3Cha+hPd-StPgn3d
z*dlxNw{iKHtr|@}&fv1Nv~+PM#4p<vK>HdN$-7-4fr`ssj=zVq!A~eup2TZ^6&K4q
z*_GyYB(NySbjiym)?1Xz<;$^l18-`6b$|8ETkMk!)xauSqA0(>W&BHi4|Kd```q6|
zyE5AeK>cD}nPT{j|H-nHp)eD|-LxNec?@Mt_phxIsasUG`^7#j_aE+(wA8R!(Sd{;
zgd5Mk`?CzY9fHAo>@58m6%|B0WzYy}^-lb&n;+A$*JbiZDqV_(JJXOzEr#xk&VPbm
zVsuFie4MMsB8a7V>|dN;TpY5TiBw)=T%1_H=@dl!;kx&w_3U_&o*(}3nk~I8-uMbE
z>^dD+Mhnpc7)bd|Vx30|7!C46graiWWO}W4R&l*MZ<Dlpdw)uo{42afETN@ULazyh
z(K@N1=T6vjGFIsR31b5h9UCDOy?=ejubA82f0OT&@*W-vga(J6TQIl!Z^6{=cMsBV
zaq5LhVwr6~2)ghvPUCQutk?T4qryyC5ilTNir{KI91doK@hA*NLD(N$U*F>|quM;i
zg@*W4r4n9OISpp>@ib^DTqp5nMON4;3OQWZ#7g1yAQ<+^Mr$d20@HDKihn8sDkYyM
z!F1B1Klw?T&tNY7HrxJ{_XBXl`?(w6b-o`MI+yCnPSII0@JH0tPNu<?dRCzsDxr+*
z)sQ&U)V!w?gry?|D~TkW*J(nNfoQ=dEk!{Z-Uaj9alhhD3l~O^?gyh8O!NePlcuZO
zfq~@v!_lZe)mchMmXcWJI)BUiHhOR%;o|+DcfA`y5Qp37)t(?`C?14&z3-CX7no=X
zn8o|8>({42#rGF{xgQJ%m(#)hUF{2u^E}JLGIJqE2t!CPosOsBd@RYR&)el-xrXbF
zOZ8EA$B~R9si&Jv2cvm-J*+BqoyWi2N{a|y*z0NVMJww=wB5GWReui=aR7_`o8H|W
zuCLZ;T!(N$CdO|;SsT2Gc;`yF6J(P*&1vP^)yg-imv6n<zn=82IZ}VuH`l}a@9lT}
zu-k`=<Y60cT@~#1jDUiFavxp}Ztj9Ro&NEp!awQ-zik&f**RHCBtDoZOX(@v?HtAl
z693$rOyoH6^yYwm^M6185V%dWU92ML!xwK34TVsQP{ZEcWxp5pgUcU*fz`DU>fE9w
z>KbazvF+zL#LT6+k3*qdONSUyDr9PurYKyPK>DsXQv)Fk1!0+Nol5h{I0D9xa6Y)J
zN|K@f>ZGPlP`$l_JrzK6Z#DYuE(!A}eG0RD6+4W)fMbYbgnzr648mz|^f??)`@vLj
zbJIP4aA?%rT1Nyo(5E*)DkeV4xDXLQ*xeP)!zNoq8y6md7=<^(@nvsVG3DqcbYc>S
z5mZ!vpfRDFGl>fqDhU~dvk4fi!K@-HA7d9=m9LQlU=+@8gUVh7nk>(fmD}@G7$6%@
z$AiB1jIW6c6MsmL!tVo#&eBbi#!>G05mY$(0!HJ}a4-sbQ@#18`!II+RMR~J@zH%4
z1d719P3@~jb>C=J`(4O=OfF<QMv&3{B;;;Tjm)``0-J26Kv!?5z~|b!fKIe8VAER|
zb!tT!J6K87n{f<vW3zcMsrWKn4s$iO1xy&)lj-<+Fn<hcM)vO2VOa}>C*S3w)-QYD
zFaL`K?V|!3?Y_*TjbnS)q15ER-1lbC<nQOx-cWD#INgqN*ZLPIdILB&?@ep(Am2v+
zabQE~>0R%CD|C{&ph0?iH;}7Ec}9^Wt_?uqL<^XX=e>DzrNg0TE_~S&7p|)Yg;+P3
zh5E`t;eTpW7Q(EYg}Px`gzvFiVYvJ({HZ?K;xXFA;W8^6J_wFs95cJ^O@i=hJUegl
zeLR8hqvHG6<hwY5??UliH2FTA!1qb<eX8*lC)Hq~*Ws*Pi^WOxSm-r5Yu9CQQf(G`
zea_l7TAWm;g<h*OQ@ujpcLFO%Nml4A8?2{rYJZG6U$QP;s8D=%JGhpMe+7(F&hr2Q
z(O@uxp{;KFm$8e#hfB|cyGb?G;X`}4+hh(8#xaazxIGX~hGY4N(ts?&U7X{PzI5P~
zSd21c94n2`SvU!%F!LE-2|fE&@wVmebjRvcK&sOF{_MxyT`-^i(5uzmh^uV4h6#6q
z1%IauxTgK)ZoXC4Tf=zU?_QF0g&)TQm|Tuk$gzyDq82CL2BSWHEH_|$X%+b#Z?a`l
zzPZj#B~HvuzXrqc)nNXkHaC5@r+fE*R!#mrjMr-iC`0j|VQ_t|6F9Hna~`>V&*|!`
z_im#*m)1u1_ce3{Md|2Gd0#U`kq71Hb$>Vqi%|EPxGlnSX<CB+3;sq|PvglxMi=km
z$$mu_kKzfw#A9B>L;k~d=+05E;mQ6&7f<0|@e#Uv2ea)KgWGYH!QU6rLu?sorvn)Q
zuUcG4zl-vufCikceG25M!U_xjB`F{Mbp&5v@e;>7jOD=K`Bk>tZJ^i7<Mk$9mVX#F
z2ESGjeDWB>$SZxn%cEl<l}bCy)=XFvm3D^OSxq~S^B3A#O*=#FJRTFYGtz!ldpI7}
zV)1bOgAX^yhnpe2vF_ed9L<uY55wa_nicpbG^hQh6#AC<zWv=YA;uFbNUC5;1rsW$
z#<&UwDtMh3YvE`yuh<<Fb8<D{#eY2QQAG&uA})BnE@dtL|9EB*feX5L6IqG|aoWR+
z0Nl%9#tVKGOjRv_U_rY{aN|aqXE3IuoDDj-a-T0m<NE#L{NwrGY@W4ZWDQ1EV`NCk
zpGOrTXcS>$D1xVLn87;02;=`m%WRQEX)~-9%U5KZ=Qvlz6Ht5?80uU>uYcOK|10i+
z%5)j;O1!><uWg;>TT{rN7H}vKs6`@V#9tQ|YDsbP4ix~sh9F*M{w{lo^TPCO@vlAA
zO{G*2pk5+?{(}jEs~Z1x#XsS<b@gyDeucM{phpDWOS_rNHK3MaP^Uv>t361KstXuX
z;&k~Yda*2D#{MGOM7Y1{uzzNW6x}N#nM7V4BnG`;?IvkdHs54DbodN-DnW0VX9doz
zVU%0o9-eKKKVe@hKe<C2trV8&So!VySBJU1<=b+TrT73v?Bn1_PgU){k{>aBE$1JP
zf3QTzkdPrE)na`+7bj%M=U<5eT%zu)ssO#J070Vwo)~B___E!Csece+s6&x{B~3sP
zw%N3!G@Ov=E9n{%J3O2@m#y&NWupKhE*HDo3efLh(pCJAzk7o@MheA-fpr}%<NrCJ
zwKQub3RY2c7UP&U&*0ED$M=)lnmpCO19rx76#1rwG<l`3dskpadWMx-Q>Z$v(^62@
zCR^HQ#5gPzr4THbmVbH<p<&ISF!yk<!+~HJ)OCEvj~@Dkf5SXm+u?J(V;2~;QOEBK
zmTI$&<mH~xGT(2lH)u)n3dn$~NFGvO>{PYd$Vw0<A$?-FrJq1pMli;$YC9uf5W*dC
z-68Z?k+lGNNuzI@z@ZKV>tXf%4t=Ab5eY7Ax(&@*s^0owCx0$%Gr};15oXq~!R1ld
zo<%EZg!j?!IE<Qeu`Vd|8X!veAnd_xi(>t(RM%nx1rAKj$QH~{STam{)1F2HQ)PP^
zoL5U4m{V6YwiQuo6)~?WB6~?USybB}Bd<|xe_u*ed%2^BJdV*!QRw!)dVy+`zsX-}
zH@AWvRJVIf&VN_AMQ=K}9h~=}^F_zt>eaGGC1L7Q(V5u)PQ5Dn2OUUISdt7zlEiie
z>r4cXBEY`r?^@A+s-j!Rp6XGj@p>)x)f?hu>IPsXDk5ZpI@F7khd6zXHv8DU`&C%I
z2bN}+j~;|Lk6;=U`wzHEjg1E<Mf(lk`;S)EKaZMul7EhAbWGAQMaOu825H0jb4~e;
zR6cJi_jvpf%^9N{{%;d&quVlr+DkA~K}j~@zmAty@-fM$ZBf<v7|-7jII8zVyp+ob
zOb~4V4v0gIzwi<hs5Aa?Kf@FqcQSR)4>f6~qyrO&7sF$nAMXqT=ycCX7+PUczQ;#<
z5H8H5Fn=cqXOqGFXE61u3h?<1dc{}5+B@USwIzQt!t!-2jtvZ~bH1Ohis6n9PsM^t
z&eOua$p)s#lt!&XKNY`L<*MSuxq&SKL4#=`Zg@w6(hXH=5sK~<gl-BykIM&ZlO1HG
z!5++Sq`6+3gPZHEVfEBz^{V2&!x%llFv;Gq;(zI2cQEvf%IYRwa8w5rqr^4a{UV3U
zxJF#fnXspb_(Eu5exYh3;%}UVDHd&#rm+Mzy1aE{3~-VgFrj(l7R*!j6&&ADK&;N=
z6A^1e6Vz=P=QcCU>%njiJ;@p!pD)R(v`CJEvW#S}(ZTs`(4XG|L(Vs%#@+jqxd??>
zU4K{79uK`Q_VgZPPjaY#(E+RiV8A|`-B01;3H+O2%-z=>F5MY(EwmRNp)Qng4G8~>
z{8a+86lftZ!Y8X^TpAkpV@FJ)8Ao3qB==l)l(hGf;FUdma+^0lDxRSGhF^u~&pXyu
z6ohdIQ;=)L*5hnn<SlPqI%ITMmnx;h^?zLDba;q-c!3WMh9WNaV(;`r#7N+#=fg|A
zK?q-b+aybv6*p!Z;-ZA|RXizp)4Kw#{*ZnG&1Mrr!+|O1auXE=*d~1VOTapYUh4N{
zk}o44vvYMCLxMtT<3Dh&EBMHfKzxkTF`n$}rmdNK2@IM&hdn{f-9XO!fDY{da(~$S
z)7<sryx-^0PM?S6V^rF7Y&Tc8y}1W=JGU*G{Yk1U4u61uf@Bt^Z^ujrkYXSO{YyCd
z!7*>m@J=%b#SrylF!E}hoS5j=y10(c%-lI@wi7(H5UFGhgOjPgq`26fBs9{Xbjr4>
z;~T0TY~Le)jZZJt+Wqg*Y6bn!#eYB8f1(sURL$?RVH5$j^4oDJ)1dy%=WmCYy%TnP
z9oy@LbGn7KZOEmib$B!F^)ID;*i4e4a%6C0-JFc8s@6)x#wQ}<q`4sPtE9JsQ^3?X
zS<!G7EebHQmQB9)1d<|}Dj-up&i_?W_T(L*3`|OxEedro5zw^%zJpn?m46ph1XL+1
zKH1R915D)p<i)X5>a~W3=KE=n8*ZaPb79xaudn+0H*n=CA!n^h-y{=10q=R?)pKZ>
zN$rw}@YEj))XF5%xOFg(NQ3M7*-Ru}sq>2p9TJMk>>jPGVh>vF7UtTuTASB+w0IPm
z?2CA8-=v{D(72NAZl5P5Zhx=BHI_fEJ`qEaz`jvbjAtY5C>SUmG?jX;dtAGBx5`fd
z-*N`;{W*yn+gx`!jP!zrg!xxq3EyfAV{y?-7I|cqB=XE3TuytK6f(il&I*8|pr<Sn
z(Uvu1WDalg23NA+)9RJkHdz+ZaGmXwGWN&^+ch_?d)_Ibpe8$LfPX#lp^-)1Fe`A5
zNq2NMA<I0Oj1c?eb~Zx81gUJiS()yTe_G89guYH+>u`o}x2C+*dyh`N+G>HWSb*C)
zWuK(fg<3ULFRoEZzFwgot}mSE@vETvwBE3j+qB9^d$$c6Y)rzmorVkBE%0+uzP!(&
zd~yFNe)D(x#YS|zg@0J;iwj)(G0Z(1<^{l+4i^i5I{fod4c^o1x#bhQo>Te1pHu1I
zY`)#kKR^)Y=cYwQqZ%$PRv173xS0-QRIBU0_U;|+r|o68+r_R=utj^<r`OH-^d?D*
zr#QDZY=yiuZHI%=>~k=c#x1-bk&epnRObE!AR-Tyc%<=FNPlUl#Pa~<>eZGBB$1&1
zUEtd8t3z1s!y-I)WFZIEO&qTl(elYSE9+vzIubY<1(6qPDhT?Qy{peO8gdQKxCRyC
zlp)O0&6}GV4(1*whG0$C*YWUc5aQ$`9FK-Sl)}gOv_}Gyru|5_f#H$h-&3^<)<p#Z
zt9`JQ4*2&ulz;nSD<yfnv46QFjAYYbC|)h}L&<6%ZHzH1ho}f916PQ2Ht65?hBA6Z
z(DQw*F3&G_wN{TVceYkfUBGu6<w<7CSji*X>?#=brh_qODo<<%rKuUrP0gT8PSlW?
zGz{7rxZSc%c+98V_^!om+gZ$<hjAVrN6dL@;pN<19)H%=-H^IjOPyz%LF9}Qhq$E-
zF((VD;(E!8p5=)gU=J<HSK-6tiO^AZorE4H895$vqNgI^2#c)4C<nJV>Z9k9x}=@7
zWSbOAeGJ6kGyvYgU-4!WL3#HDm#co&RaFptQ*}_bGOSPT-k7{0G-azjyeC?zJSl&Q
zP39Dm0e?%=#p^CXn&16S@+i-{dpefGiCD}jSlW%Jop{9|<w`Tzic6Z6c7hdiY86wF
zn+a7qQmL4r?F1^u)F~!tJz<JlsuXjQly-U)lU|t=C0#^CQkcxF_V-P)+{hYT_GW__
zH?kx{lG-zXtYjFBywoayEv4AC5rwVE0|!L+Ab%sDF^<tQ9Y!EK0(sxT<=%>+#8}BO
z;jg(nT`z2-RP~2AddNY|%Wk65*6${2g`rJi$N=1YFynKCP6_+5YPys5qpWq3ccd~U
zdgmlI*}ge}mTwmCI_^3|ieozu5n&b5jbwWAP6FBlMH5m5MsuWPs4T}e!etfS@<Wpp
z?SHUYK~*{wr4~M`;q5|b6^SW~R;RNHrPb-$;k1g*rJ{^swVcW>T9wlXQ5m<25?0Y|
z2qr;_a;t#0k!}@1N3<I!bdB}mq!#gBh_Z75BV*kSEU^}@U<uaU!6;$1vWH+jJ0sq;
zTIEBao|O^r+8N)7)D3XFYi)bQro?x|V1H=}#ismn#9(U@#pb+nL}F(e#qE4@1h+76
zVm<F0M_GT+Ei(g?vVF8d?%~$x9;QBckB84-CMg>z7sm8a6l@bt$MZS~j2wCL>_o)~
zQW1t=!4JL?Eg1@b=bxyZ^~0)9+OMJOe6PDO#ci7ol&?F+Ax(}N@!ElLT~V!T9DnTy
zvV$~ST*ubPpu2Y9LTL?IW0Jlj2f7N<<fsvMeyW|k6479&vBC%0+W2&kQ~>ID17(<U
zKfE(D6F4JVU5|NweOO0@X|b5OLukLJ@Z*Qz8`(Paw4I-pia5~B*P-g+`6NXEGjY|F
zJjX8m4@zsuCR4c1_IYA5c@8l$iGMOMaSd`ET$<pf#XfUiEEmEFDVF`@I=D2?#S&mc
zQ+cwc(xhqLq3I;cPAY3#cv7R;(yNq$ZE=2rI)pV9fpv0jP~l8&%Grt1zidb_;U-?q
zA2aK@F38eUcX~TkGhN()7Gk7CXk{RwI1j8~5zl@Zj=u)euqUXJ)QKud6@S%W)Ik+q
zIFhjooi4l}!UG95I~Wh9)<pTjep=qlj!AH9qrRCHli=^Mt#UmZroguL26kdm60o>K
zkYhXYXm;R@88mA=ADwt=nKNrV7fw92jF~l_Pfk3wOqq(OaI7IyhRg=rM@P0sX3PfL
zg(F)dBW8o`lOtOr6Q<7A&VN~Xn5~@wQ)6@EYGl47p4hH;CBfNkAo^89!ptt9N|nih
zU5PR~;2kM4iOOM&1!2+E%?A1yDi&!RhzKCbXjMleEUjn8CC!ZIYG#akX6;rp^mLyU
z(tZUH#cBPIb7-r7L}b18M?|>tM?`AfuYAnocm)Rc!e!l#P++_-s(&TC`Rz0a`eE?>
zGSpY|G=A%Mr?C@8<JR6FF}t$X7!}*QT}4tFOAfFc_f(!pj)HN_!8$>4X`SHMr>v8_
z;0d`l+kJ_f?|xtI_J8Z#*2Kk`5@#UokAms!%7>;fyt|*zgQ@@f)#Uzf2I>bV>IWnB
z4N<>@aq`47dmZ<g#eXkM3Xg(sVKDeS9^rzVT>#za^A9h@cU@RXV?&sE?uR5CJ{|!V
zbfQi2ZeHoAl<QJnYFA(=Y*E6fhxws)k5O?#q5&jeia?M3v|9U9>wdQ9Kj<evIGy=m
zI_<&foCnhh4{m2Wm``<ZI?us$l0#~_4;EfIZGBB&O?yI(fPe281?pL^$eLDT9amzH
zt-@xzI9+U_;=sAQV-UF<_GTVG@RuLwYmly;{QDdH!Gx%G2(Zg?Z+)qkd5%lFtz})s
zu(pJ*HH^iYZEd|)A&)Q6>Wi}qXSp2PT8dQ+cI&RqHCKhVT48Oht~Swji>c;?RE^7W
z!L+?tYT&R~7=JY{iki4A7C$={K22;#*Efx8n~Lf9BBs88S;JW_S(=tBIgdGcpa54r
z$^CqCKbPVM#$v<C+#>L$4iZ5l_3_%g8K~5^KUTYab{I#ujqNrL>=+m3n+GNsId>QE
z4FtQ6_?M%3D-;luVp4uZtlsX38bCbRj5IJY`3%AZ<$pw6?|FWpuKoWg$M;+axrxMG
z^WWa?@vY!-LOhk{3eyd>_jJ^^9!UsmKqh7?ZwFsIj1}fiPut>5a;mqR5N;~{PE8(D
zAJ!;ool$mV6BzLBde!nCp6W23{_xtTLQp%$>s8(3(GM^h;;>lyS{k9E(`J{_tR_8?
z99q($0)LrZvi_YRjkx0R9dUXnmf9j$C1?rZisyEamH7y()7%v<u8Py#6fQ1`lid@i
zxF$|;OW3+3oZJzIToHOJ>D+Bur2|4C=2;##cE%4G(}JImL`6?1%W5q+`q%LtZ(qD$
zcHR9i-qC;IUHmVXapIRYPJGeEiC<Q!Qhs5Mlz%Un9Oc)B+ZXQh$X^>qS#l)s%dpPm
zopc_X%}H#~+?P*2%)p<D&heMaFp~MA<O$1tQP6F^M%&%S_T&K#$t3bio6XDPb(~{f
zyhh>P)eYH9rqvZd?Xn`Ft-?#VP#nrAsf3vjo;Km0>p^whN7UIm`r1yue3M%3r9e5j
zHGdtBa4$u^DJ@YYq2?TAd4%2>ot(#gk5*qAcRQja_c`J>=HR#N@>y~Un=h3U6aqX$
zpxs%2XLQ6LcV=2XW|E4>9E`+cTKiPH{Had9)I)w$PGnbKKvIZOV14P<o-jyi##xsY
zrpF!G2G3UpUM+%tYGU%-yuyb)!lJk0sej-L%kE5EVuYCr2F&GNRD9-5`<0<ADTJ8h
zpiR48Vb@G&o~19l>Bkl@yVfnhynzb>-o`B*;Y}yFfZ6I+``HD7&~4*QsC&=}W2+Zs
zg<3>Qtrq_Gy6?S+N*;aeY$O1X$0BQs%*d7RHx{|+5zHlLy?Hpj2TK{v=qQJN0Dq>8
z^zn2hsW?<7PQnz4p1lIfC$^x9(_QLER*0bFY@aV<<53(HTIv!%>G+oV`52T-R+7!E
z^?F4d<;`82bd7qn8Qq`YNl1JGsCRy9M%Xd;vk$T`2Uyq#SC|7U?1L)I0TuSa6y`t*
zmmrGn01B7jiSED&m!OI6fC-miiGS`u36~&=?f?n<;0SYI1Y9kx3;`5GLjbUIGz6@o
zDb7R`g;fN_nTVXI9~U4$vs(I*&O-t0jv6@Y#wQPHxUk4_$B$(I!P($u6kg5=nAidn
z0URLEI!2@`KEygU#1t2zXTYNLWnD{-dX6iSoHemtk!|+EJcPj@et0{Uc7Ig@SOu6h
zDS&hv`*=_tUt!DRhX_v%dhqvYQWnP*Y_U%wFss0fz_UZtpg6@tzofmnrX}lQduVNv
zW7N{5!pu6zJQ{}lwrN<Oq>>n&Vl-0_k8FWxV+vC`G;9l)2wH-H+9f#XP+$<uS<@BN
zql=|4F?CCSW@7TRY|tI&7=JamRgP&PKWj1o=k~;P8$dP|ZkSg_3l^=Od5_y|wQEj=
zGrzZb#<R0lK7q7+Ur1K%D=jSPt}1}Qr)7R9J8=U{(v3o_lA=g<ot_^9(P+PobM89m
zD=g>YyYy`z=9&w0+_7MX8tz6U^AIh)`8?UKOtuGHSq8?j4#BK4C4aoJCas}Ob`z?G
z?TeShN%C0hN!_Y?T0x1)=$`51sV3Lt4WdVKX~@F6!yzAJ$`N8Q`L;WGW+crzYWZ+-
zkQ&n*MQ3Ha!?Qa*+8mE5V`OUHt~pOVUkb<Z6frXIu7;Z*AXOT<OOWOx`VM<TFQb*e
z(o1N{hA7bUZf37ECx7T%wsXvORGgk>PjhuHYpM23>|LtO*=;{q>OG`ZXx&>abD|vF
zn)mK;nbR(UwI01{7rClOtvW=knxj=6B2~>%s@e%P?qi&Oyp2B0fv|3)<8P4?^JaLh
zZr4;)U!@dL@2APtcykByU!bUGd;~LV^BFtHGeIp(kH!~jrhl$y$?g6?QMNh}GQ_il
zEE+HTY#bx$V+`G8Z$7vRgJEzbc=2h%*p?8bS?u$OzA(@!+WD-Guy6no@eEfQ*UpJ(
zCs-yr1s-hRSRer*vM=|+s9q?Wxv$0s;=}|~V2$N{?Zg7&#Pai6u-J87oB?~U9`C#G
z?!w_j2aaE;Q-2*U)u9f=g{c^AX}By;)<|H>6EZoNWGNq}0$b;yR2;@bGX<mdVz!`b
zpNJ`lPRs`@Xd5YEn{+~n%TaSg+;QHVq_aPCPSP1qo+G+<=hAf?DaU31%DHZw-E_E{
zfmCR7IMs>RjYm6i$rBIz;k1ntf9h0{-tG(_!N-NgX@5WhZ+|3^;4qyFL|mn7$I^9P
z441V$1cVcjES&~IV7HSoh~&WW7)0t&AYL9-9H-MDh@taH2rg}%z?_pwX_?EMDC`oN
z69Jc{%;p3>J?k|Qwo_lXDM^)sqmNUYa#s_PZSH8IX(W&)iZ@&I8|IQ07?*_70^OBW
zT1dNPVSnbFhf^_ggl*<c&R0*r$t7H}`*99)ioY6{O`g9RS3TJuak*@OBC?KMP()|l
z3Q%$++kx%2C_<93*dRrCYixo0lmzB4ZdMY69Xpn~=!J5Zfkg<9v;oC-%MIa4SZu!G
z5>8>?oTMxEo9L{fvWW*pd2}|v`^%vSdOV^4yMI1KS7f4~vmTyRj3OaV4OAquqtS{S
zY#Xq~IqOkt0$;k|_4qZyTSui4Ln|~*u~^r0Gr~+z*v5?sj%M(fVsR))J#>r96wVW)
zu23IA=Q^HuMehhY`*0k=W{Sxnu2X|-h`1SP)1*^M?4oZf)_MpIvHUmUa7e+SV4Op0
zM1MhSqX9@+BP4(*Y(3~i(Qu<Hio}URbEp%=X--ihtb0c5RD%9wcOhwL`3zfxo>)rU
z+xLHsg>8=iORK(|)U@<#q7@2pWA3?q6C!zRM0_LfdDV>gjS%X6w~JRUWK3c>VK|>c
z4-*Iz!Wb~nK}NFoqrqGlUwg2K7D*wZ$bT$Jz`RnJ`&kfP4raj>hMH=myC`?zLvc<8
zCW+1xyRpQQCD2%sbdg2*3I++csz*wJWeSV@gVE)<H|@i~QGXSnZ2P!!={!*fK&S&n
z>bu*%)`=pc+Lq}uKSN@*JCl&e4+S30CgbT`pRGN|uM10FF8Ve2eyNbABs2%{B7YeT
zvV;^%MO@GbtUCr2hWlTky~vJ%<6Y{Aa}a>@=rw{|yqIn!;t*Lb{%p0<5u<Y%iB&5p
zF>B?0S%H<2XO^TdE5@b2^})WFjs=CoRET7?i4ecwFcs$Vd?w6E)I|6tPs%uaiJs&2
zKIL7E%K{lkGaXG!W#6WQc@Tc<eSZzE??=3=(iY8L)4kg|1pwq4#rM&DZG8f{TwX6y
zkvuYKFBERX_8c+7MW6Bd5^o$<IJr0uR^Pt`L$$W~9<OcPKV0-@aD6S2PS$Q^>((vZ
zceh#2yPW0xtj%)X?JbRWv@?E^mC-oSR&5#c=lsChvhDV-ZR@T{@wh!d+J8J`&^RBr
z$71{FJV3g_6pB-}$h^i`D6LXAj!E$YC5cokJhf9R?FTK;r$(dgpO?Gm)rRA?c(o0g
zHX%3S-rMr^ka(9kcfA4)ysBak*I;Qpb=G*G(~%<~TZcV%5o#{=&I2DwauufzCwfr>
z0*pM)i$6HnDkE{0*B>p~KY#wKy!F<2_}CsIRfr?)6J}6itG;uERLFYqVO*GsZBlg5
znLxXr`$uYyo&Klj?alyHtm-5{ox}D#K%J*~Dxl&!<!nI3Y<EJSrtQ>o0yUM6rv)nI
zr<@t6^xB;qsI;AQexOokdy1e^XnmHTQqnw8P$zRfS5T)te!5^ym4DM2gEc(|P8w7i
zT+SO*?B-Jk6>IsInv>lLgqpVGFKM$njgau$Rs{bcb}mgFE84PxgP-%^*mC%ZA9_bU
z3dZ%;!keoa5DI&4j$|5=H1Jlh285Z=Q#V@<@8uK5TZM2nWJ1l5v9u8n+BLZ3ly4oI
z2**&vpo*E_2Gcv<D1ZKF(f;vY<)ztQmD|Iu+%);Ca(-xvX!<95%9&{1kFozCPB@Rm
z3FmSzGoEnXxuY3?OaPexirvkOfJe_xN7YpbyD0CW?Kh~g+I%DB=LQmwCk+zTD0epV
zfX~L3pTn9Yo{_T}gO%&se^B#LC7#QoscF5GFO{~l9GQ2B(|;l<m!=g`nsqoXw;oz)
zb<Txrmj~B12k!Cww=TJFyYt@4V-yRF&&Ka@Y4sW;3PZISN6AANXBe}MUm#4(tE70!
z?8n~Gyg5XhS8G}DB#`eMsDSe$%-(*nPs{y>ZIYH<nIktzx)&chNi!~ePsls?+uN^-
zw{2JKmbqpWgnzoF`~K|5off>c-+cTx<_PoY2w+4nGMM!@&jMcZkc(BaUh|Y}dA1dZ
zWjk=ABM%p-!k(DXA;D5p>$G4_$b=?_ngoJ0-4CI_^ICx~-3tuQeerL9z29tLK+N&D
zTJ7-RD377dVxF2Pf5QQDndLbQpPM(_+z1oqSgWy)%zuoXb#TE@E8|*gCnJMaR%yj8
z_?1>Bv}(1dwB8TlL9YLs4+3@b>EC|5-^6(mrJ^DqqvsgLqG-h%c<evNfT9q!XbIy%
z#}2E`YWT#Y0`bC80aFTCU4g!Z>wXBu3r;K^Jlvnu;L%&V*+4O?e90j1FM*PiMgA&}
zwzx0Aj|ia+Eun4kWO|cODHVSb@zq}RpVaXGa=|@I&)u1D*tsM%u5ubzDUF>n8molH
zDxa}SI^!yvah1$?zk9(r-XcjKj1%B49z-!hiJo)v4TE}TgVBwg^zQQo)cPg{qiki_
z2O@$=#68Ck>6ho|5<TP%wReQJeW3R4&$j3DM5m{Vzthdt+3n>#$-#eV>)VvwkNs)i
zRfk20uK~=A2lF4|v~QSTC2KHyMa$T)lI}70`B^e543n6zI?;?SdUj6OGjhJV_+8B|
zS6gpu-O=jeV>P>1-8`$^PE~h*>Ty@9wHLMNK($WQPA*diZ>h;q`jX{O#bZ`W*(0x!
zL*a_A34D`s7v~oj-pPNSRad8~i$B%uN_Fs}njENhzSA@EncBNc+n&-lXiH$l?e>dJ
z)h)cG*$(H#HscWCnTBT-{s(bSH13(W=UE&{LdTK3hb=d*x#N3h+=&~a7ng&K3w8&v
za<Pt6$b~vPC-NCNk8Kj2ozZzI_AchOcljM7$coaiu-Wl+7%w?i&@kiwybkBVjK&wQ
vog=L)e;rSd=5WAE*WoVqPVu%s{JoKLRP-CojH7zKQ9JLsa-9D^cmST<61HC%

diff --git a/docs/rotation.html b/docs/rotation.html
index e4033d4..8d7bfe3 100644
--- a/docs/rotation.html
+++ b/docs/rotation.html
@@ -114,10 +114,10 @@ <h2>Physical considerations<a class="headerlink" href="#physical-considerations"
 </section>
 <section id="sonic-rotation-formalism">
 <h2>Sonic rotation formalism<a class="headerlink" href="#sonic-rotation-formalism" title="Link 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#id110" 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#id60" 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>
+<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#id113" 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#id61" 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>
+<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 divided by <span class="math notranslate nohighlight">\(2\pi\)</span>.</p>
 </section>
 <section id="the-rotation-profile">
 <h2>The rotation profile<a class="headerlink" href="#the-rotation-profile" title="Link to this heading"></a></h2>
@@ -128,7 +128,7 @@ <h2>The rotation profile<a class="headerlink" href="#the-rotation-profile" title
 </section>
 <section id="input-parameters">
 <h2>Input parameters<a class="headerlink" href="#input-parameters" title="Link 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#id60" 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>
+<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#id61" 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>
 <p>Note that all the inputs are derived from the single free function, <span class="math notranslate nohighlight">\(\omega_0\)</span>.</p>
@@ -187,7 +187,7 @@ <h2>Input parameters<a class="headerlink" href="#input-parameters" title="Link t
 <section id="theoretical-basis-for-sonic-rotation">
 <h2>Theoretical basis for sonic rotation<a class="headerlink" href="#theoretical-basis-for-sonic-rotation" title="Link 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#id60" 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>
+force term in the the Fokker-Planck equation (see <span id="id5">[<a class="reference internal" href="zreferences.html#id61" 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">
 \[\frac{\partial f_i}{\partial t} + \mathbf{v} \cdot \nabla f_i + \frac{e}{m_i}(\mathbf{E}+\mathbf{v} \times \mathbf{B})
 \cdot \frac{\partial f_i}{\partial \mathbf{v}} = C_i + S_i\]</div>
@@ -209,13 +209,12 @@ <h2>Theoretical basis for sonic rotation<a class="headerlink" href="#theoretical
 <div class="math notranslate nohighlight">
 \[\mathbf{U}_0 = \omega_0(\psi) R \mathbf{e}_{\varphi} \quad \text{where} \quad
 \omega_{0}(\psi) \doteq -c \frac{d \Phi_{-1}}{d \psi} \; .\]</div>
-<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>
+<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 <strong>not</strong> 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="Link 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>
+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>
 <div class="math notranslate nohighlight">
 \[\Phi_{-1} + \left\langle \Phi_0 \right\rangle \; ,\]</div>
 <p>where an angle bracket denotes a flux-surface average.  By analogy with the temperature, the rotation frequency can related to the experimentally-deduced radial electric field <span class="math notranslate nohighlight">\(E_r\)</span>, where <span class="math notranslate nohighlight">\(E_r = -|\nabla r| d\Phi/dr\)</span>, according to</p>
@@ -231,7 +230,7 @@ <h2>Consistency with force balance<a class="headerlink" href="#consistency-with-
 \[E_r = \frac{R B_p}{n_a z_a e} \frac{d p_a}{d\psi} + \frac{U_\varphi}{c} B_p - \frac{U_\theta}{c} B_t \; .\]</div>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
-<p>We emphasize that this relation is <em>valid at long wavelength (equilibrium scales) only</em>, and is subject to the same ordering requirements as standard neoclassical and gyrokinetic theory.  This means a restriction on the steepness of gradients in the form <span class="math notranslate nohighlight">\(d \ln p/dr \ll 1/\rho_i\)</span>.  See, for example, the discussion in <span id="id6">[<a class="reference internal" href="zreferences.html#id114" title="H. Sugama, T.-H. Watanabe, M. Nunami, and S. Nishimura. Momentum balance and radial electric fields in axisymmetric and nonaxisymmetric toroidal plasmas. Plasma Phys. Control. Fusion, 53:024004, 2011.">SWNN11</a>]</span>.</p>
+<p>We emphasize that this relation is <em>valid at long wavelength (equilibrium scales) only</em>, and is subject to the same ordering requirements as standard neoclassical and gyrokinetic theory.  This means a restriction on the steepness of gradients in the form <span class="math notranslate nohighlight">\(d \ln p/dr \ll 1/\rho_i\)</span>.  See, for example, the discussion in <span id="id6">[<a class="reference internal" href="zreferences.html#id117" title="H. Sugama, T.-H. Watanabe, M. Nunami, and S. Nishimura. Momentum balance and radial electric fields in axisymmetric and nonaxisymmetric toroidal plasmas. Plasma Phys. Control. Fusion, 53:024004, 2011.">SWNN11</a>]</span>.</p>
 </div>
 <p>The force balance relation contains terms of order 0 and 1, as described in the previous sections.  We can write the velocities in terms of the neoclassical flow coefficient <span class="math notranslate nohighlight">\(K_a\)</span> (see <span id="id7">[<a class="reference internal" href="zreferences.html#id15" title="E.A. Belli and J. Candy. An Eulerian method for the solution of the multi-species drift-kinetic equation. Plasma Phys. Control. Fusion, 51:075018, 2009.">BC09</a>]</span>) as</p>
 <div class="math notranslate nohighlight">
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 834623f..924072f 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, null]], "Alphabetical list for input.gyro": [[14, null]], "Alphabetical list for input.neo": [[22, null]], "Alphabetical list for input.tglf": [[30, null]], "Alphabetical list for out.tglf files": [[31, null]], "Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation": [[16, "anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation"]], "Appropriate References": [[9, "id6"], [42, "id144"]], "BETAE": [[30, "betae"]], "BETAE_UNIT": [[5, "betae-unit"]], "BETAE_UNIT_SCALE": [[5, "betae-unit-scale"]], "BETA_STAR": [[22, "beta-star"]], "BETA_STAR_SCALE": [[5, "beta-star-scale"]], "BOX_SIZE": [[5, "box-size"]], "BTCCW": [[5, "btccw"], [22, "btccw"]], "B_MODEL_SA": [[30, "b-model-sa"]], "Batch submission": [[8, "batch-submission"]], "Bounding-box method": [[10, "bounding-box-method"]], "Brief description": [[3, "brief-description"]], "Build on your laptop": [[0, null]], "Building": [[0, "building"]], "CGYRO": [[3, null]], "CGYRO Normalization": [[3, "id8"]], "CGYRO Workshop 2022": [[41, null]], "CGYRO output files": [[7, null]], "COLLISION_ENE_DIFFUSION": [[5, "collision-ene-diffusion"]], "COLLISION_ENE_RESTORE": [[5, "collision-ene-restore"]], "COLLISION_FIELD_MODEL": [[5, "collision-field-model"]], "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 Base Case with Adiabatic Electrons (2001)": [[16, "cyclone-base-case-with-adiabatic-electrons-2001"]], "DEBYE": [[30, "debye"]], "DEBYE_FACTOR": [[30, "debye-factor"]], "DELTA": [[5, "delta"], [22, "delta"]], "DELTA_LOC": [[30, "delta-loc"]], "DELTA_T": [[5, "delta-t"]], "DELTA_T_METHOD": [[5, "delta-t-method"]], "DENS_*": [[5, "dens"], [22, "dens"]], "DIII-D L-mode shortfall": [[28, null]], "DLNNDRE_ADE": [[22, "dlnndre-ade"]], "DLNNDR_*": [[5, "dlnndr"], [22, "dlnndr"]], "DLNTDRE_ADE": [[22, "dlntdre-ade"]], "DLNTDR_*": [[5, "dlntdr"], [22, "dlntdr"]], "DLNTDR_PARA_*": [[22, "dlntdr-para"]], "DLNTDR_PERP_*": [[22, "dlntdr-perp"]], "DPHI0DR": [[22, "dphi0dr"]], "DRMAJDX_LOC": [[30, "drmajdx-loc"]], "DRMINDX_LOC": [[30, "drmindx-loc"]], "DZMAG": [[5, "dzmag"]], "DZMAJDX_LOC": [[30, "dzmajdx-loc"]], "Data input": [[3, "data-input"], [21, "data-input"], [33, "data-input"]], "Data output": [[21, "data-output"]], "Data output and plotting": [[3, "data-output-and-plotting"]], "Data output, python interface, and plotting": [[33, "data-output-python-interface-and-plotting"]], "Density Transport": [[34, "density-transport"]], "Density fluxes and sources": [[34, "id2"]], "Design History": [[13, "design-history"]], "Detailed description of NEO output files": [[24, "detailed-description-of-neo-output-files"]], "Download and user agreement": [[9, null]], "EPAR0": [[22, "epar0"]], "EPAR0_SPITZER": [[22, "epar0-spitzer"]], "EQUILIBRIUM_MODEL": [[5, "equilibrium-model"], [22, "equilibrium-model"]], "ERROR_TOL": [[5, "error-tol"]], "ETG_FACTOR": [[30, "etg-factor"]], "EXPERIMENTAL profiles": [[28, "experimental-profiles"]], "E_MAX": [[5, "e-max"]], "Effective field": [[10, "effective-field"]], "Electron Temperature Gradient Turbulence (2006)": [[16, "electron-temperature-gradient-turbulence-2006"]], "Energetic particle transport coefficients (2009)": [[16, "energetic-particle-transport-coefficients-2009"]], "Energy Transport": [[34, "energy-transport"]], "Energy fluxes and sources": [[34, "id3"]], "Environment variables": [[0, "environment-variables"]], "Equations solved in TGYRO": [[34, null]], "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, null]], "FIELD_PRINT_FLAG": [[5, "field-print-flag"]], "FILTER": [[30, "filter"]], "FIND_WIDTH": [[30, "find-width"]], "FLUX-SURFACE GEOMETRY": [[10, null]], "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, null]], "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, null]], "GYRO Validation Abstracts": [[16, "gyro-validation-abstracts"]], "GYRO results": [[28, "gyro-results"]], "GYRO verification and validation (pre 2010)": [[16, null]], "Gallery of classic GYRO images (circa 2003)": [[12, null]], "Gaussian width parameters": [[32, "id3"]], "General models": [[23, "id3"]], "Geometry": [[17, "geometry"]], "Global-spectral parameters": [[6, "id11"]], "Gyrokinetic Simulation in the 2000s": [[13, null]], "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 orientation": [[10, "magnetic-field-orientation"]], "Miller geometry parameters": [[32, "id4"]], "Miscellaneous": [[20, null]], "Momentum Transport": [[34, "momentum-transport"]], "Momentum fluxes and sources": [[34, "id4"]], "NBASIS_MAX": [[30, "nbasis-max"]], "NBASIS_MIN": [[30, "nbasis-min"]], "NEO": [[21, null]], "NEO Output Files": [[24, null]], "NERSC PERLMUTTER (CPU)": [[27, "nersc-perlmutter-cpu"]], "NERSC PERLMUTTER (GPU)": [[27, "nersc-perlmutter-gpu"]], "NEW_EIKONAL": [[30, "new-eikonal"]], "NE_ADE": [[22, "ne-ade"]], "NKY": [[30, "nky"]], "NMODES": [[30, "nmodes"]], "NONLINEAR_FLAG": [[5, "nonlinear-flag"]], "NS": [[30, "ns"]], "NUP_ALPHA": [[5, "nup-alpha"]], "NUP_RADIAL": [[5, "nup-radial"]], "NUP_THETA": [[5, "nup-theta"]], "NU_1": [[22, "nu-1"]], "NU_EE": [[5, "nu-ee"]], "NU_GLOBAL": [[5, "nu-global"]], "NWIDTH": [[30, "nwidth"]], "NXGRID": [[30, "nxgrid"]], "N_ENERGY": [[5, "n-energy"], [22, "n-energy"]], "N_FIELD": [[5, "n-field"]], "N_GLOBAL": [[5, "n-global"]], "N_RADIAL": [[5, "n-radial"], [22, "n-radial"]], "N_SPECIES": [[5, "n-species"], [22, "n-species"]], "N_THETA": [[5, "n-theta"], [22, "n-theta"]], "N_TOROIDAL": [[5, "n-toroidal"]], "N_XI": [[5, "n-xi"], [22, "n-xi"]], "Nonaxisymmetric effects": [[23, "id6"]], "Normalization": [[3, "normalization"], [21, "normalization"]], "Numerical Dissipation": [[6, "id6"]], "Numerical Resolution": [[6, "id5"]], "Numerical resolution": [[23, "id1"]], "OMEGA_ROT": [[22, "omega-rot"]], "OMEGA_ROT_DERIV": [[22, "omega-rot-deriv"]], "OSX Sonoma": [[2, null]], "OUTPUT": [[35, null]], "OpenBLAS": [[0, "openblas"]], "Optimization related parameters": [[6, "id13"]], "Output Normalization": [[7, "output-normalization"]], "Output file control": [[6, "id12"]], "Overview": [[11, "overview"], [18, "overview"], [28, "overview"], [29, "overview"], [33, "overview"]], "PARK": [[30, "park"]], "PLASMA ROTATION THEORY": [[26, null]], "PLOT": [[36, null]], "PRINT_STEP": [[5, "print-step"]], "PROFILE_DLNNDR_*_SCALE": [[22, "profile-dlnndr-scale"]], "PROFILE_DLNTDR_*_SCALE": [[22, "profile-dlntdr-scale"]], "PROFILE_EQUILIBRIUM_MODEL": [[22, "profile-equilibrium-model"]], "PROFILE_ERAD0_MODEL": [[22, "profile-erad0-model"]], "PROFILE_MODEL": [[5, "profile-model"], [22, "profile-model"]], "PX0": [[5, "px0"]], "P_PRIME_LOC": [[30, "p-prime-loc"]], "Parameters for input.neo": [[23, null]], "Past and Future": [[3, "past-and-future"]], "Physical considerations": [[26, "physical-considerations"]], "Physics": [[17, null]], "Physics Control": [[40, "id4"]], "Plasma Rotation": [[17, "plasma-rotation"]], "Plasma equilibrium/geometry": [[23, "id2"]], "Plasma shape/geometry": [[6, "id1"]], "Prebuilt Environments": [[27, null]], "Prehistory": [[13, "prehistory"]], "Profile Feedback Control": [[40, "id3"]], "Profile models": [[23, "id4"]], "Q": [[5, "q"], [22, "q"]], "QL_flux_spectrum": [[31, "ql-flux-spectrum"]], "QUASINEUTRAL_FLAG": [[5, "quasineutral-flag"]], "Q_LOC": [[30, "q-loc"]], "Q_PRIME_LOC": [[30, "q-prime-loc"]], "Q_SA": [[30, "q-sa"]], "Quick links": [[11, "quick-links"], [21, "quick-links"], [29, "quick-links"], [33, "quick-links"]], "Quick-start example": [[8, "quick-start-example"]], "RESTART_STEP": [[5, "restart-step"]], "RHO_STAR": [[22, "rho-star"]], "RLNS_1": [[30, "rlns-1"]], "RLTS_1": [[30, "rlts-1"]], "RMAJ": [[5, "rmaj"]], "RMAJ_LOC": [[30, "rmaj-loc"]], "RMAJ_OVER_A": [[22, "rmaj-over-a"]], "RMAJ_SA": [[30, "rmaj-sa"]], "RMIN": [[5, "rmin"]], "RMIN_LOC": [[30, "rmin-loc"]], "RMIN_OVER_A": [[22, "rmin-over-a"]], "RMIN_OVER_A_2": [[22, "rmin-over-a-2"]], "RMIN_SA": [[30, "rmin-sa"]], "ROTATION_MODEL": [[5, "rotation-model"], [22, "rotation-model"]], "References": [[42, null]], "References: TGLF saturation models": [[29, "id9"]], "References: TGLF validation against experimental data": [[29, "id10"]], "Repository access": [[9, "repository-access"]], "Restart data": [[7, "id3"]], "Rotation output files": [[24, "rotation-output-files"]], "Rotation physics": [[6, "id10"], [23, "id5"]], "Running Cases": [[3, "running-cases"], [8, null]], "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, "silent-flag"], [22, "silent-flag"]], "SIM_MODEL": [[22, "sim-model"]], "SPITZER_MODEL": [[22, "spitzer-model"]], "S_DELTA": [[5, "s-delta"], [22, "s-delta"]], "S_DELTA_LOC": [[30, "s-delta-loc"]], "S_KAPPA": [[5, "s-kappa"], [22, "s-kappa"]], "S_KAPPA_LOC": [[30, "s-kappa-loc"]], "S_ZETA": [[5, "s-zeta"], [22, "s-zeta"]], "S_ZETA_LOC": [[30, "s-zeta-loc"]], "S_ZMAG": [[22, "s-zmag"]], "Scenarios and connection to energy sources": [[37, null]], "Simulation images": [[3, "simulation-images"]], "Software": [[17, null]], "Solution strategy": [[38, "solution-strategy"]], "Some comments regarding units": [[38, "some-comments-regarding-units"]], "Sonic rotation formalism": [[26, "sonic-rotation-formalism"]], "Source Code": [[3, "source-code"]], "Source code": [[0, "source-code"], [9, "source-code"]], "Species Parameters": [[40, "id5"]], "Species Vectors": [[32, "id2"]], "Species-dependent parameters": [[23, "id7"]], "Species-related parameters": [[6, "id8"]], "Standard output files": [[24, "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, null]], "TGLF output files": [[32, "id8"]], "TGLF output parameters": [[32, "id7"]], "TGYRO": [[33, null]], "TGYRO solver algorithm": [[38, null]], "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"]], "TOROIDALS_PER_PROC": [[5, "toroidals-per-proc"]], "Table of geometry parameters": [[10, "table-of-geometry-parameters"]], "Table of inputs and outputs": [[32, null]], "Tabular list for input.cgyro": [[6, null]], "Tabular list for input.gyro": [[15, null]], "The General Atomics GACODE Suite": [[17, null]], "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 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"]], "UNITS": [[30, "units"]], "UPWIND_SINGLE_FLAG": [[5, "upwind-single-flag"]], "UP_ALPHA": [[5, "up-alpha"]], "UP_RADIAL": [[5, "up-radial"]], "UP_THETA": [[5, "up-theta"]], "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"]], "Ubuntu/Mint": [[1, null]], "Urban Legends": [[13, "urban-legends"]], "VELOCITY_ORDER": [[5, "velocity-order"]], "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"]], "Verification Studies": [[16, "verification-studies"]], "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"]], "Yearly Publication Synopsis": [[13, "yearly-publication-synopsis"]], "ZEFF": [[30, "zeff"]], "ZETA": [[5, "zeta"], [22, "zeta"]], "ZETA_LOC": [[30, "zeta-loc"]], "ZF_TEST_MODE": [[5, "zf-test-mode"]], "ZMAG": [[5, "zmag"]], "ZMAG_OVER_A": [[22, "zmag-over-a"]], "ZMAJ_LOC": [[30, "zmaj-loc"]], "ZS_1": [[30, "zs-1"]], "Z_*": [[5, "z"], [22, "z"]], "Z_EFF": [[5, "z-eff"]], "Z_EFF_METHOD": [[5, "z-eff-method"]], "density_spectrum": [[31, "density-spectrum"]], "eigenvalue_spectrum": [[31, "eigenvalue-spectrum"]], "field_spectrum": [[31, "field-spectrum"]], "input.gacode": [[18, null]], "input.tgyro Alphabetical List": [[39, null]], "input.tgyro Tabular List": [[40, null]], "intensity_spectrum": [[31, "intensity-spectrum"]], "nsts_crossphase_spectrum": [[31, "nsts-crossphase-spectrum"]], "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.species": [[24, "out-neo-species"]], "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, null]], "s-alpha geometry parameters": [[32, "id5"]], "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"]]}, "docnames": ["build", "build/pre_linux", "build/pre_osx", "cgyro", "cgyro/FAQ", "cgyro/cgyro_list", "cgyro/cgyro_table", "cgyro/outputs", "cgyro/running_cases", "download", "geometry", "gyro", "gyro/gyro_gallery", "gyro/gyro_history", "gyro/gyro_list", "gyro/gyro_table", "gyro/gyro_vv", "index", "input_gacode", "license", "misc", "neo", "neo/neo_list", "neo/neo_table", "neo/outputs", "prgen", "rotation", "setup", "shortfall", "tglf", "tglf/tglf_list", "tglf/tglf_output_list", "tglf/tglf_table", "tgyro", "tgyro/equations", "tgyro/output", "tgyro/plot", "tgyro/scenarios", "tgyro/solver", "tgyro/tgyro_list", "tgyro/tgyro_table", "workshop", "zreferences"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinxcontrib.bibtex": 9}, "filenames": ["build.rst", "build/pre_linux.rst", "build/pre_osx.rst", "cgyro.rst", "cgyro/FAQ.rst", "cgyro/cgyro_list.rst", "cgyro/cgyro_table.rst", "cgyro/outputs.rst", "cgyro/running_cases.rst", "download.rst", "geometry.rst", "gyro.rst", "gyro/gyro_gallery.rst", "gyro/gyro_history.rst", "gyro/gyro_list.rst", "gyro/gyro_table.rst", "gyro/gyro_vv.rst", "index.rst", "input_gacode.rst", "license.rst", "misc.rst", "neo.rst", "neo/neo_list.rst", "neo/neo_table.rst", "neo/outputs.rst", "prgen.rst", "rotation.rst", "setup.rst", "shortfall.rst", "tglf.rst", "tglf/tglf_list.rst", "tglf/tglf_output_list.rst", "tglf/tglf_table.rst", "tgyro.rst", "tgyro/equations.rst", "tgyro/output.rst", "tgyro/plot.rst", "tgyro/scenarios.rst", "tgyro/solver.rst", "tgyro/tgyro_list.rst", "tgyro/tgyro_table.rst", "workshop.rst", "zreferences.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [3, 4, 6, 7, 8, 9, 10, 11, 13, 16, 18, 19, 22, 24, 29, 30, 31, 34, 38, 42], "0": [0, 4, 5, 6, 7, 8, 10, 13, 15, 16, 18, 21, 22, 23, 24, 26, 28, 30, 31, 32, 38, 39, 40, 41], "00": [4, 8, 13, 42], "00035": 42, "00079": 42, "001": [5, 6, 22, 23], "0010": 42, "0029": 42, "005": 28, "00am": 41, "01": [4, 5, 6, 13], "012001": 42, "012008": 42, "012043": 42, "012502": 42, "014004": 42, "014505": 42, "015013": 42, "015015": 42, "016": 42, "02": [9, 39], "020": 42, "022305": 42, "022509": 42, "024004": 42, "03": [4, 13, 42], "032301": 42, "032310": 42, "036036": 42, "039": 42, "04": [39, 42], "042001": 42, "045001": 42, "045005": 42, "05": [13, 30, 39, 42], "052301": [28, 42], "055003": 42, "055013": 42, "055908": 42, "055909": 42, "056116": [28, 42], "06": [9, 16, 39, 42], "060704": 42, "060901": [28, 42], "062302": 42, "062518": 42, "066015": 42, "07": [9, 42], "072303": 42, "072304": 42, "072307": 42, "072505": 24, "0741": 42, "074501": 42, "074505": 42, "075018": 42, "08": [13, 28, 39, 42], "09": [8, 9, 13, 16, 28, 42], "095010": 42, "096005": 42, "0_": 38, "0a": 24, "0th": [5, 22], "1": [0, 4, 5, 6, 7, 8, 9, 10, 13, 16, 18, 21, 22, 23, 24, 26, 27, 30, 31, 32, 34, 37, 38, 39, 40, 42], "10": [3, 5, 6, 13, 18, 28, 39, 42], "100": [4, 5, 6, 28], "1000": 5, "1016": 42, "102301": 42, "102306": 42, "102508": 42, "1051": 42, "1063": 42, "1088": 42, "11": [9, 16, 22, 24, 41, 42], "110": 42, "1103": 42, "112007": 42, "1121": 42, "112303": 42, "112503": [28, 42], "113017": 42, "116007": 42, "11am": 41, "12": [30, 32, 42], "1209": 42, "122305": 42, "122306": 42, "122307": [28, 42], "122309": 42, "122503": 42, "122505": [28, 42], "122507": 42, "125": 42, "128": [13, 27, 42], "128913": 28, "13": [29, 42], "1361": 42, "14": [28, 42], "1477": 42, "1493": 24, "15": [5, 6, 28, 42], "1500": 28, "15th": 42, "16": [3, 5, 6, 11, 24, 27, 28, 30, 32, 42], "1695358": 42, "17": [22, 23, 24, 42], "1741": 42, "18": [28, 29, 42], "1800": 29, "186": 42, "1879": 42, "188": 42, "1897": 24, "19": [3, 18, 24, 29, 42], "1938": 42, "195004": 42, "1973": 24, "1976": 24, "1977": 24, "1982": 24, "1985": 42, "1988": [24, 42], "1990": 13, "1993": 42, "1994": [13, 42], "1995": 42, "1996": 42, "1997": [24, 42], "1998": 42, "1999": [13, 24, 42], "1_": 38, "1e": [5, 6, 14, 15], "1st": [5, 22], "1th": [5, 22], "2": [0, 4, 5, 6, 7, 8, 9, 10, 13, 16, 18, 21, 22, 23, 24, 26, 27, 30, 31, 32, 34, 37, 38, 39, 40, 42], "20": [24, 29, 30, 42], "2000": [11, 17, 42], "2001": [13, 42], "2002": 42, "2003": [11, 16, 17, 42], "2004": 42, "2005": [25, 42], "2006": 42, "2007": 42, "2008": [28, 42], "2009": [28, 42], "2010": [11, 17, 25, 42], "2011": [28, 42], "2012": [24, 28, 42], "2013": [9, 17, 42], "2014": [28, 42], "2016": [28, 42], "2017": 42, "2018": [9, 19, 42], "2019": [30, 42], "2020": 42, "2021": 42, "2022": [17, 20, 42], "21": [28, 29, 30, 32, 42], "2107": 42, "22": [29, 30, 42], "2229": 42, "23": [28, 42], "239": 24, "24": [3, 5, 6, 30, 41], "2408": 42, "2433": 42, "2436852": 42, "2482": 42, "25": [17, 24, 30, 32, 41, 42], "256": 27, "2560": 42, "26": 42, "27": [21, 22, 24, 28], "273": 42, "28": 42, "2834": 24, "2889008": 42, "2d": 22, "2m": 22, "2nd": [5, 6, 22, 32], "2t_e": 5, "2th": [5, 22], "3": [2, 3, 5, 6, 9, 10, 13, 16, 18, 21, 22, 23, 24, 30, 32, 34, 37, 38, 39, 42], "30": [24, 28, 42], "300": 13, "3082": 42, "310": 2, "32": [5, 22, 27], "3211": 42, "3230": 24, "324": 42, "32664": 42, "33": 42, "3335": 42, "3412": 42, "345": 3, "3452e": [21, 22], "356": 42, "384": 39, "3d": [22, 23], "3rd": [5, 6, 13, 22], "4": [0, 4, 5, 6, 9, 13, 14, 15, 16, 22, 23, 24, 27, 30, 32, 39, 42], "40": 42, "400": 16, "4018": 42, "4046": 42, "405": 24, "418": 24, "43": 42, "4326": 42, "44577e": 4, "448": 42, "45": 42, "45am": 41, "4655": 42, "47th": 42, "48": [24, 42], "49": 42, "4904301": 42, "4954905": 42, "4th": 22, "5": [5, 6, 9, 13, 16, 22, 23, 24, 28, 30, 32, 39, 42], "50": [28, 42], "500": 29, "51": 42, "512": 8, "53": 42, "54": 42, "545": 42, "5515": 42, "5579": 42, "56": 42, "58644e": 4, "59": [27, 42], "5th": [5, 28], "6": [4, 5, 13, 16, 22, 23, 24, 39, 42], "60": 16, "61": 42, "62": 42, "63": 42, "64": [0, 5], "65": [30, 32], "6587": 42, "667": 42, "6th": 13, "7": [4, 5, 16, 24, 30, 32], "71": 42, "724": 42, "724e": 5, "73": 42, "741": 42, "744": 42, "74754e": 4, "75": [13, 16, 28, 39], "77": 42, "78": 42, "8": [0, 4, 5, 6, 22, 24, 27, 42], "80": 42, "812": 42, "81550e": 4, "83": 29, "836": 24, "84003e": 4, "85": 42, "865350": 42, "88": 42, "9": [41, 42], "900": 16, "91": 42, "92020e": 4, "94": [13, 42], "95": 42, "96": 29, "97": [13, 42], "9991": 42, "9am": 41, "9i4": 42, "A": [3, 5, 8, 16, 17, 19, 21, 24, 28, 31, 38, 42], "AND": 19, "AS": [9, 19], "AT": 9, "As": [3, 13, 16, 26], "At": [13, 16], "BE": 19, "BES": 13, "BUT": 19, "By": [9, 13, 25, 26, 29, 39], "FOR": 19, "For": [4, 5, 10, 11, 13, 14, 16, 18, 21, 22, 24, 26, 30, 32, 39], "IN": 19, "If": [0, 5, 9, 19, 22, 26, 38, 39], "In": [0, 5, 10, 13, 16, 21, 22, 24, 26, 29, 33, 38, 39, 42], "It": [0, 3, 5, 7, 8, 11, 16, 22, 26, 38, 39], "NO": 19, "NOT": [4, 19], "No": [5, 23, 39], "OF": 19, "ON": 5, "OR": 19, "Of": 22, "On": [5, 8, 13, 38], "One": 13, "THE": 19, "TO": 19, "The": [3, 4, 5, 8, 9, 10, 16, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 38, 39, 42], "Then": [4, 38], "There": [0, 5, 13, 16, 17, 18], "These": [4, 13, 18, 23, 24, 28], "To": [0, 4, 5, 8, 9, 12, 13, 18, 19, 27, 38, 39], "WITH": 19, "With": [13, 22, 29], "_": [5, 10, 21, 22, 24, 26, 30, 31, 32, 38], "_0": 26, "_1": [22, 26], "_ade": 22, "_deriv": 22, "_dlnndr": 22, "_dlntdr": 22, "_dphi0dr": 22, "_energi": 24, "_exb": 22, "_in": 21, "_model": 23, "_p": 39, "_para": 22, "_perp": 22, "_r": 22, "_radial": 24, "_relax": 39, "_rot": 22, "_rp": 22, "_scale": [17, 23], "_scenario": 37, "_size": 5, "_speci": 24, "_spitzer": 22, "_theta": 24, "_xi": 24, "_z": 22, "_zp": 22, "a_": [5, 7, 14, 24, 30, 32], "ab": [30, 32], "ab759c": 42, "abc63b": 42, "abc861": 42, "abil": [3, 13, 25, 33], "abl": 13, "about": [10, 13, 16, 17, 18, 22, 27], "abov": [5, 8, 9, 10, 19, 22, 26, 28, 38], "absenc": 5, "absent": 13, "absolut": [16, 30, 32], "absorb": [3, 11], "abstract": 17, "ac": 42, "ac243a": 42, "ac592b": 42, "ac7a4d": 42, "acb20": [10, 18, 42], "acceler": 5, "accept": 8, "access": 17, "accord": 26, "accordingli": 8, "account": 9, "accur": [13, 28, 29, 38], "accuraci": [5, 13, 16, 21, 29, 42], "achiev": [13, 16], "acknowledg": 17, "acm": 42, "acquisit": 13, "across": [4, 13, 24, 28, 42], "action": 19, "activ": [5, 13, 22], "actual": [13, 16], "ad": [3, 8, 11, 13, 16, 17, 18, 22, 24], "adapt": [4, 5, 41], "add": 27, "addit": [8, 13, 21, 22, 24, 26, 30, 33], "address": 16, "adequ": 13, "adiabat": [13, 22, 23, 24, 28, 30, 32], "adiabatic_elec": [17, 32], "adjust": [30, 32, 39], "adopt": [3, 38], "advanc": [13, 16, 42], "advantag": 13, "ae": 13, "affect": [13, 22, 39], "after": [0, 5, 13, 16, 38], "against": [13, 16, 28], "agenda": 17, "agre": [9, 16], "agreement": [13, 16, 17, 19, 29], "agt": [29, 42], "al": [24, 28], "alam": 42, "alcat": [16, 42], "alfv\u00e9n": 13, "algorithm": [3, 11, 13, 17, 33], "align": [4, 10, 24, 26, 30, 37, 38], "alik": 13, "all": [3, 4, 5, 8, 9, 11, 13, 16, 18, 19, 22, 24, 26, 28, 30, 31, 32, 39, 40], "allow": [5, 13, 16, 18, 22, 23, 26, 30, 32, 39], "almost": 0, "along": [5, 10, 22, 29, 30], "alpha": [4, 5, 10, 13, 16, 22, 24, 29, 30, 34, 39, 42], "alpha_": [17, 31, 32], "alpha_mach": [17, 32], "alpha_p": [17, 32], "alpha_quench": [17, 31, 32], "alpha_sa": [17, 32], "alpha_zf": [17, 31, 32], "alphabet": [3, 11, 17, 21, 29, 33], "also": [5, 8, 11, 13, 16, 17, 21, 22, 25, 28, 29, 33, 38], "altern": [26, 28], "although": [3, 13, 28, 33], "altix": 13, "alwai": [5, 13, 24, 26, 39], "am": 42, "ambigu": 13, "ambipolar": 24, "among": [13, 16], "amount": [13, 30, 39, 40], "amp": 6, "amp0": 6, "amp_phi_n": [15, 17], "amper": 13, "amplifi": 26, "amplitud": [5, 6, 13, 14, 15, 30, 31, 32], "an": [0, 3, 4, 5, 8, 13, 16, 18, 19, 21, 22, 25, 26, 29, 30, 38, 39, 42], "analog": 13, "analogi": 26, "analys": 26, "analysi": [13, 26, 28, 41, 42], "analyt": [21, 22, 23, 24], "analyz": 13, "angioni": [16, 42], "angl": [5, 6, 10, 22, 24, 26, 28], "angular": [13, 22, 23, 24, 26, 32, 34, 42], "ani": [5, 9, 19, 28, 30, 38, 39], "aniso": [23, 24], "aniso_model_": [17, 23], "aniso_model_1": 22, "aniso_model_2": 22, "aniso_model_3": 22, "anisotrop": [22, 23, 24], "anisotropi": 16, "anomal": 42, "anomali": 16, "anti": [10, 30], "antisymmetr": [5, 6, 22], "apart": 13, "app": [16, 42], "appar": 16, "appear": [13, 26], "append": 21, "appli": [5, 13, 26, 38], "applic": [13, 16, 28, 42], "approach": [3, 11], "appropri": 19, "approxim": [13, 21, 26, 30, 38, 39], "apt": 1, "ar": [3, 4, 5, 8, 9, 10, 11, 16, 17, 18, 19, 21, 22, 23, 24, 26, 28, 29, 30, 33, 38, 39], "arash": 41, "arbitrari": [4, 18, 21, 22, 23, 38], "arbon": 42, "architechtur": 42, "area": [9, 34, 42], "aris": [19, 26, 39], "around": 26, "arrai": [5, 22, 23, 24, 30, 32], "arrow": 26, "articl": [9, 19, 28], "artifici": [4, 13], "artun": 42, "as_1": [17, 32], "ascii": [24, 28], "asdex": [29, 42], "ash": [13, 39, 42], "ashourvan": 41, "ask": 17, "aspect": [3, 11, 22, 29], "assess": 39, "associ": [16, 19, 22, 24, 28, 38], "assum": [22, 24, 30], "assumpt": [30, 38], "asymmetr": [18, 24], "asymmetri": [21, 22, 24, 26, 28], "asymptot": [13, 21], "atom": [3, 8, 12, 13, 27, 42], "attempt": [13, 16], "attend": 13, "attent": [8, 38], "attenu": 16, "attribut": 12, "austin": 42, "author": [9, 19], "auto": [8, 10], "autodetect": 4, "automat": 5, "aux": [34, 37], "auxiliari": [34, 39], "avail": [3, 5, 9, 13, 19, 22, 23, 28], "availbl": 28, "averag": [5, 13, 16, 22, 24, 26, 28, 34, 42], "avoid": 30, "axi": [31, 42], "axisymmetr": [22, 26, 42], "azevedo": 42, "b": [5, 6, 10, 13, 14, 16, 22, 24, 26, 30, 31, 32, 42], "b_": [4, 5, 7, 10, 14, 16, 22, 24, 30, 31, 32], "b_model_sa": [17, 32], "b_p": [5, 18, 22, 26], "b_t": [5, 22, 26], "balanc": [13, 17, 39, 40, 42], "ball": [8, 41], "balloon": [5, 29, 30, 32, 42], "banana": 26, "bar": [13, 16, 28], "barn": [28, 42], "barrier": [13, 25, 26, 29], "base": [5, 9, 13, 19, 22, 25, 28, 33, 39, 42], "baselin": 42, "bashrc": 27, "basi": [17, 22, 28, 30, 32, 38], "basic": 16, "bc08": [3, 9, 21, 26, 42], "bc09": [21, 26, 42], "bc12": [3, 9, 21, 42], "bc17": [3, 11, 42], "bc18": [3, 11, 42], "bcbh11": [28, 42], "beam": [16, 18, 26, 34, 42], "becam": 25, "becaus": [5, 26, 38, 39], "becom": [3, 11, 26], "been": [10, 13, 16, 21, 28, 29, 38], "beer": [13, 42], "befor": 13, "began": 13, "begin": [4, 23, 24, 26, 37, 38], "begun": 13, "behav": 16, "behaviour": 39, "being": [5, 13, 31, 32], "believ": [13, 26], "belli": [3, 42], "below": [9, 10, 13, 16, 24, 26, 27, 28, 30, 34], "benchamark": 21, "benchmark": [13, 16, 17, 29], "beta": [5, 6, 13, 17, 22, 32, 39, 40, 42], "beta_": [4, 5, 10, 22], "beta_star": [10, 17, 23], "beta_star_scal": [6, 10], "betae_unit": [6, 10, 41], "betae_unit_scal": 6, "better": [5, 29], "between": [4, 5, 13, 16, 24, 25, 28, 29, 38], "beyond": 21, "bf": 22, "bh96a": [13, 42], "bh96b": [13, 42], "bin": [0, 5, 7, 27], "binari": [0, 7], "binorm": [5, 6], "bisect": [30, 32], "bit": 5, "black": 16, "block": 38, "blue": [10, 16], "bogacki": 5, "bohm": [13, 16, 31, 32, 42], "bonanomi": 42, "bootstrap": [18, 24], "both": [5, 10, 13, 16, 25, 26, 29, 30, 32, 38, 41], "bottino": 42, "bounc": 42, "bound": [17, 22], "boundari": [3, 11, 13, 22, 30, 32, 38], "box": [5, 17, 41], "box_siz": 6, "bpar": 30, "bracket": 26, "bravenec": [13, 28, 42], "breadth": 5, "break": 13, "bremsstrahlung": 18, "brief": [11, 17, 33], "bring": 16, "broad": 13, "broken": 42, "bt": 22, "btccw": [6, 10, 17, 23], "build": [13, 17, 30], "bull": 42, "bunit": 4, "burden": 8, "burrel": 42, "byer": 42, "c": [4, 7, 13, 18, 22, 24, 26, 28, 42], "c1": 39, "c2": 39, "c3": 39, "c4": 39, "c5": 39, "c6": 39, "c_": [3, 5, 7, 16, 24, 26, 28, 30, 32, 38, 39], "c_0": 10, "c_1": 10, "c_2": 10, "c_3": 10, "c_i": 26, "c_n": 10, "ca": 42, "cal": [26, 38], "calcul": [3, 13, 21, 24, 25, 28, 29, 34, 39, 40, 42], "calibr": [3, 11, 30], "call": [6, 13, 21, 25, 28, 30, 32, 33], "camenen": 28, "can": [0, 4, 5, 8, 10, 16, 17, 18, 21, 22, 26, 28, 30, 38, 39], "can05": [13, 42], "cancel": [13, 26], "candi": [3, 12, 16, 28, 42], "cannot": [13, 26], "capabl": [13, 16, 38], "captur": [21, 30], "carbon": [5, 16], "carefulli": 13, "carri": [13, 16, 18, 26], "carrington": 42, "carter": 42, "casati": 16, "case": [5, 10, 11, 13, 17, 21, 22, 24, 26, 27, 28, 30, 38, 39], "cash": 5, "casson": 42, "cat": 18, "caus": [26, 30], "caution": 30, "cb10": [3, 10, 11, 42], "cb18": [3, 11, 42], "cbb16": [3, 4, 9, 11, 42], "cbs20": [3, 42], "cc": 13, "ccw": [30, 32], "cd": [0, 8], "cdot": [22, 26], "cece": 13, "cell": [13, 28, 42], "center": [5, 13, 22, 24], "central": [28, 29], "centrifug": [21, 26, 42], "centroid": [30, 32], "cer": 28, "certain": 13, "cg": 38, "cgyro": [0, 4, 8, 9, 10, 11, 17, 18, 20, 21, 26, 27, 30, 33, 34, 39, 42], "cgyro_plot": 8, "ch": 24, "chain": 34, "challeng": 25, "chang": [5, 9, 19, 22, 24, 29, 30, 39], "character": [3, 11, 13, 42], "characterist": 28, "charg": [5, 6, 18, 19, 22, 23, 24, 30, 32], "chassi": 13, "check": [13, 22, 41], "chen": 42, "chi": [10, 29], "chi_": 16, "chi_e": [16, 29], "chi_i": 16, "choic": [5, 22, 30, 39], "choos": [5, 7], "chowdhuri": [28, 42], "chri": 28, "chw": [9, 42], "circa": [11, 17, 25], "circl": [10, 16], "circul": 13, "circular": [10, 29], "circumst": 26, "citat": [9, 29, 42], "cj": 24, "claim": [13, 19], "clarifi": [13, 16, 26], "classic": [5, 11, 17], "clean": 0, "clear": [13, 25], "clebsch": 10, "clock": 27, "clockwis": [5, 10, 22], "clone": [0, 9], "close": [8, 13, 16, 38], "closur": [30, 32], "cluster": 13, "cm": [34, 38], "cmat": 5, "co": [10, 13, 24], "coars": [13, 39], "code": [4, 11, 16, 19, 21, 22, 24, 25, 26, 27, 29, 33, 39, 41, 42], "coeffici": [7, 13, 22, 23, 24, 26, 30], "cohen": 42, "col": [24, 34], "collabor": 28, "collect": 17, "collis": [3, 4, 5, 13, 21, 22, 23, 24, 28, 30, 32, 42], "collision": [3, 5, 11, 13, 21, 24, 28, 34, 39, 42], "collision_ene_diffus": 6, "collision_ene_restor": 6, "collision_field_model": 6, "collision_kperp": 6, "collision_model": [6, 17, 23], "collision_mom_restor": 6, "collision_precision_mod": 6, "collisionless": 5, "colloc": 22, "colorado": 16, "column": [18, 31], "com": [0, 9, 19, 41], "combin": [13, 24, 26], "command": [0, 2, 18], "comment": [5, 14, 17, 18, 22, 23, 28, 30, 31, 39], "commment": [5, 22], "commod": 13, "common": [27, 28, 30, 32], "commonli": 13, "commun": [3, 5, 6, 11, 13, 16, 42], "compar": [13, 16, 28, 29, 33, 39, 42], "comparison": [13, 28, 42], "compars": 16, "compens": 29, "compfluid": 42, "compil": [0, 2, 9, 13, 19], "complement": [3, 11, 21], "complementari": 16, "complet": [0, 3, 11, 16, 21, 26, 27, 28], "complex": 26, "complic": 3, "compon": [6, 24, 38], "comprehens": [13, 34, 42], "compression": [30, 32], "comput": [5, 10, 16, 17, 22, 30, 32, 39, 42], "concentr": 16, "concept": 17, "conceptu": 25, "conclus": 13, "condit": [3, 9, 11, 13, 16, 19, 22, 38], "conduct": [16, 18], "conf": 42, "confer": [13, 42], "configur": [8, 10], "confin": [28, 29, 42], "confirm": 13, "confront": 13, "connect": [13, 17, 18, 19, 33, 38, 39], "connor": [5, 22], "consequ": 42, "conserv": [5, 6, 13], "consid": 13, "consider": 17, "consist": [5, 6, 13, 17, 24, 39, 42], "constant": [5, 22, 26], "construct": 10, "consult": 10, "contact": 16, "contain": [7, 13, 16, 18, 21, 24, 26], "context": 13, "continu": [13, 39], "continuum": 28, "contour": 10, "contract": 19, "contrast": [16, 29, 42], "contribut": [13, 30, 32], "control": [4, 5, 13, 16, 39, 42], "convect": [16, 18, 24], "conveni": [18, 38], "convent": 10, "converg": [5, 13, 28, 38, 42], "coordin": [3, 5, 7, 17, 22], "copi": [0, 5, 9, 19], "copyright": [9, 19], "core": [3, 8, 11, 13, 27, 28, 29, 42], "cori": 41, "corioli": [13, 26], "correct": 13, "correl": [13, 16], "correspond": [5, 10, 16, 21, 22, 39], "corrug": [13, 42], "cosin": [22, 24], "cost": 5, "could": [8, 13], "count": [5, 8], "counter": [5, 10, 22], "counterclockwis": 10, "coupl": [13, 21, 22, 30, 38, 42], "courant": 13, "courtesi": [3, 12], "cover": [3, 11, 16, 30], "cowlei": 42, "cpc": [13, 42], "cpu": [5, 17], "crai": [13, 42], "creat": [0, 13, 25], "crictic": 13, "critic": 26, "cross": [17, 21, 31, 32, 42], "crucial": [13, 16], "csb": [3, 42], "cum": 42, "curiou": 38, "current": [5, 6, 13, 18, 22, 23, 24, 28, 42], "curv": [13, 16], "curvatur": [26, 30, 32, 42], "custom": 41, "cut": [3, 11], "cutoff": [30, 32], "cw03a": [3, 11, 13, 42], "cw03b": [3, 9, 11, 13, 16, 42], "cw06": [13, 42], "cwc": [28, 42], "cwd04": [3, 11, 13, 16, 42], "cwfh07a": [13, 42], "cwfh07b": [13, 42], "cwpc06": [13, 42], "cwr04": [13, 42], "cyclon": 13, "cyclotron": 16, "cylindr": 10, "d": [3, 5, 10, 13, 17, 18, 20, 21, 22, 24, 26, 29, 30, 32, 34, 42], "dai": 41, "damag": 19, "damp": 13, "dannert": 42, "dash": 16, "data": [5, 6, 10, 13, 17, 18, 22, 24, 25, 28, 39], "databas": [3, 11, 13, 29], "dataset": 18, "date": [0, 13, 25, 28, 41], "dcd": [29, 30, 42], "deal": [19, 38], "deby": [6, 17, 32], "debye_factor": [17, 32], "decad": [3, 13], "decid": 25, "decoupl": [13, 39, 40], "decreas": [4, 5, 16], "decyk": 42, "dedic": 27, "deduc": 26, "default": [4, 5, 6, 14, 15, 22, 23, 30, 32, 39, 40], "defin": [5, 10, 21, 22, 24, 26, 30, 32, 33, 38], "defind": 30, "definit": [4, 5, 10, 14, 18, 22, 23, 26, 30, 32, 34, 39], "deform": 10, "delai": 13, "delta": [4, 6, 7, 10, 13, 14, 16, 17, 18, 23, 28, 30, 31, 32, 38, 39, 42], "delta_": [22, 38], "delta_loc": [17, 32], "delta_t": [4, 6], "delta_t_method": [4, 6], "demand": 5, "demonstr": [13, 16, 29], "den": [5, 22], "denot": [13, 26, 38], "dens_": [6, 17, 23], "dens_1": [5, 22], "dens_2": 22, "dens_3": 22, "densiti": [3, 5, 6, 13, 16, 17, 18, 21, 22, 23, 24, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 42], "density_spectrum": [17, 32], "depart": 9, "departur": 13, "depend": [5, 13, 22, 26, 31, 32, 38, 42], "deprec": 32, "depress": 13, "depric": 30, "depth": 5, "deriv": [5, 22, 26, 38], "describ": [13, 17, 26, 38], "descript": [6, 7, 13, 15, 17, 18, 21, 23, 26, 31, 32, 33, 40], "design": [3, 16, 17, 28, 33], "desir": [5, 38], "desktop": 17, "detail": [0, 13, 16, 17, 22, 26, 28, 34, 38, 39], "determin": [5, 22, 23, 38], "dettrick": 42, "deuterium": [3, 5, 21, 22, 24], "dev": 1, "develop": [2, 3, 9, 11, 13, 17, 21, 29, 39], "deviat": [13, 21, 28], "devic": 29, "dh93": [13, 42], "dh95": [16, 42], "diagnos": 13, "diagnost": [8, 13, 22, 28, 41, 42], "diagon": [16, 38], "diamagnet": [16, 22, 24, 26], "dickinson": 42, "did": 13, "differ": [22, 24, 28, 30, 31, 32, 34, 38, 39], "differenti": 13, "difficulti": [13, 16], "diffus": [5, 6, 13, 16], "diii": [5, 10, 13, 17, 20, 22, 29, 42], "dimens": [7, 22], "dimension": [13, 24], "dimensionless": [5, 18, 24, 25, 38, 39], "dimit": [13, 42], "dir": 39, "direct": [5, 13, 16, 22, 28, 30, 32, 42], "directli": [7, 22, 38], "directori": 0, "dirichlet": 13, "disabl": 5, "discharg": [13, 16, 28, 29, 42], "disclaim": [9, 19], "discontinu": [13, 42], "discover": 13, "discoveri": 13, "discret": [5, 13, 17, 28, 42], "discuss": [5, 16, 26], "dishcharg": 28, "dispar": 42, "displaystyl": [4, 5, 18, 24, 26, 38, 39], "dissimilar": 13, "dissip": [5, 13, 42], "distanc": 5, "distinct": [13, 38], "distinguish": 30, "distribut": [5, 6, 9, 13, 16, 17, 24], "divid": [5, 10], "divisor": 5, "djkr00": [13, 42], "dke": [22, 23, 24], "dlnndr": [5, 22], "dlnndr_": [6, 17, 23], "dlnndr_1": 22, "dlnndr_2": 22, "dlnndr_3": 22, "dlnndre": 22, "dlnndre_ad": [17, 23], "dlntdr": [5, 22], "dlntdr_": [6, 17, 23], "dlntdr_1": 22, "dlntdr_2": 22, "dlntdr_3": 22, "dlntdr_para_": [17, 23], "dlntdr_para_1": 22, "dlntdr_para_2": 22, "dlntdr_para_3": 22, "dlntdr_perp_": [17, 23], "dlntdr_perp_1": 22, "dlntdr_perp_2": 22, "dlntdr_perp_3": 22, "dlntdre": 22, "dlntdre_ad": [17, 23], "dn": 34, "dn_": [30, 32], "do": [13, 19, 39], "document": [13, 19, 28], "doe": [4, 9, 13, 16, 22, 30, 39], "doi": 42, "domain": [6, 7, 13, 22], "domin": [3, 11, 13, 30], "done": [16, 22, 28], "dong": [16, 42], "dopper": 6, "doppler": [6, 30, 32], "dorland": [13, 42], "dot": 16, "doteq": [4, 5, 22, 26, 38], "down": [6, 10, 16, 18, 21, 24, 28], "download": [2, 17, 28], "dp": 5, "dphi0dr": [17, 23], "dr": [5, 10, 22, 24, 26, 30, 32, 34], "draft": [9, 19], "drain": 13, "drastic": 5, "draw": 13, "drift": [13, 21, 22, 23, 26, 28, 30, 32, 42], "driftwav": [30, 32], "drive": 13, "driven": [18, 26, 42], "drmajdx_loc": [17, 32], "drmindx_loc": [17, 32], "dt": 39, "dt_": [30, 32], "du": 42, "dud": 42, "dud22": [29, 30, 42], "due": [5, 13, 16, 22, 26, 28, 29, 30, 42], "dunigan": 42, "dure": [5, 13], "dux": 42, "dv": 34, "dwbc96": [13, 42], "dx": 38, "dynam": [13, 21, 37, 39, 42], "dynamo": 13, "dz": 39, "dzmag": [6, 10], "dzmajdx_loc": [17, 32], "e": [4, 5, 6, 7, 8, 13, 14, 16, 18, 21, 22, 23, 24, 26, 28, 30, 32, 38, 42], "e0": 31, "e19": 24, "e_": [22, 24], "e_a": [5, 7], "e_max": 6, "e_r": [18, 22, 23, 26], "each": [0, 22, 24, 30, 31, 32, 39], "earli": [13, 42], "earliest": 13, "easiest": 8, "edg": [3, 11, 28], "edit": 0, "edlund": 42, "ee": 5, "eff": [5, 16, 18], "effect": [4, 5, 16, 17, 18, 22, 24, 26, 28, 29, 30, 32, 39, 42], "effici": [13, 39], "effort": [3, 13], "efit": [25, 28], "egrid": 7, "ei": [5, 30, 32, 37], "eigenmod": [29, 30, 32], "eigenvalu": [5, 30, 31, 32, 42], "eigenvalue_spectrum": [17, 32], "eikon": [30, 32], "either": [13, 27], "electon": 13, "electr": [5, 22, 23, 24, 26, 39, 40, 42], "electrion": 28, "electromagnet": [3, 6, 11, 13, 28, 29, 39, 42], "electron": [3, 5, 6, 11, 13, 18, 22, 23, 24, 26, 28, 29, 30, 32, 38, 39, 40, 42], "electrostat": [13, 24, 26, 28, 30], "element": [22, 34], "elev": [5, 6, 10, 18, 22, 23, 30, 32], "elimin": 39, "elit": [30, 32], "ell": 10, "elong": [5, 6, 10, 18, 22, 23, 29, 30, 32], "elsewher": 8, "em": 28, "email": [9, 19, 41], "emcw05": [11, 13, 16, 42], "emcw06a": [13, 16, 42], "emcw06b": [13, 42], "emf": 13, "emili": 3, "emiss": 16, "emphas": [13, 26, 38], "emploi": 38, "enabl": [5, 6], "encount": 16, "encourag": [7, 28], "end": [4, 13, 24, 26, 37, 38], "energet": [13, 39], "energi": [5, 6, 7, 9, 13, 16, 17, 18, 22, 24, 29, 31, 32, 33, 38, 39, 42], "energy_grid": 28, "enforc": [4, 5, 6, 13, 30, 38, 39], "enhanc": [26, 42], "enorm": 13, "enough": 30, "ensembl": 33, "ensur": [9, 19, 28], "enter": [0, 22], "entir": [0, 18], "entri": 24, "entropi": [13, 42], "env": [0, 27], "environ": [13, 17, 41], "envis": 38, "epar0": [17, 23], "epar0_spitz": [17, 23], "eq": 38, "equal": [13, 22, 23, 26, 30, 32, 39], "equat": [3, 4, 7, 11, 13, 17, 21, 22, 24, 26, 29, 38, 39, 42], "equilibria": [17, 18], "equilibrium": [5, 7, 10, 13, 16, 18, 22, 24, 25, 26, 28, 29], "equilibrium_model": [6, 10, 17, 23], "equival": [5, 10, 13], "era": 11, "erg": [34, 38], "error": [4, 5, 6, 7, 13, 16, 28, 38, 39], "error_tol": [4, 6], "esl": 21, "esoter": 13, "especi": 29, "essenti": 16, "establish": [8, 13, 25], "estim": 5, "estrada": [16, 42], "et": [24, 28], "eta": 39, "eta_": 38, "etc": [13, 39, 41], "etg": [13, 16, 29, 30, 32], "etg_factor": [17, 32], "ethes": 42, "ethier": 42, "eulearian": 28, "eulerian": [3, 21, 42], "eurofus": 42, "european": 16, "evalu": [38, 42], "even": [5, 13, 38], "event": 19, "eventu": 13, "everi": [5, 18, 39], "evid": 16, "evolut": [5, 9, 28, 38, 39, 40, 42], "evolv": [5, 6, 13, 38, 39, 40], "exact": [38, 39], "exactli": [0, 22], "exam": 28, "examin": [13, 28], "exampl": [0, 10, 13, 26, 39], "exb": [23, 29, 30, 32], "exch": 39, "exchang": [18, 31, 32, 34, 37, 39, 42], "exclud": [30, 32], "exec": 0, "execut": 8, "exercis": 16, "exist": 0, "exp": 38, "expans": 22, "expect": [10, 13], "expens": 38, "experi": [13, 16, 26, 39, 42], "experiment": [5, 10, 13, 16, 17, 18, 21, 22, 23, 25], "explanatori": [30, 32], "explicit": [4, 5, 13, 38], "explor": 13, "expon": [30, 32], "export": [0, 27], "express": [19, 26], "extens": 21, "extra": [17, 28], "extrem": 16, "extrema": 10, "f": [13, 28, 34, 39, 42], "f_": [24, 26], "f_c": 16, "f_i": 26, "f_p": 39, "fabl": 42, "fact": 13, "factor": [5, 6, 10, 13, 16, 18, 22, 23, 24, 30, 31, 32, 42], "fahei": [13, 42], "failur": 13, "faith": 34, "fals": [13, 30, 32], "faq": 3, "fast": [18, 39, 42], "faster": 5, "fastest": 5, "fc04": [13, 42], "featur": [13, 23, 38], "februari": [16, 41], "feedback": 13, "few": [8, 13, 39], "fftw": [1, 2], "field": [4, 5, 8, 16, 17, 22, 23, 24, 26, 30, 31, 32, 39, 40, 42], "field_print_flag": [6, 7], "field_spectrum": [17, 32], "fig": 16, "figur": [10, 12, 16, 28], "file": [5, 8, 10, 17, 19, 21, 22, 28, 29, 33, 39, 41], "filenam": [7, 24, 32], "filesystem": 13, "fill": 23, "filter": [17, 32], "final": [25, 26, 39], "find": [0, 8, 16, 29, 30, 32, 39], "find_width": [17, 32], "fine": 13, "finit": [5, 13, 14, 22, 28, 29, 38, 39], "fior": 42, "first": [3, 5, 8, 11, 13, 17, 18, 21, 22, 24, 28, 29, 39, 42], "fit": [19, 29], "fix": [4, 5, 13, 24, 38, 39, 41], "flag": [5, 8, 22, 39], "flexibl": 38, "flow": [5, 6, 13, 16, 22, 24, 26, 30, 42], "flr": 6, "fluct": 41, "fluctuat": [5, 13, 16, 26, 28, 29, 30, 31, 32, 39, 42], "fluid": [24, 29, 42], "flutter": 30, "flux": [5, 6, 7, 13, 16, 17, 18, 21, 22, 24, 26, 28, 29, 30, 31, 32, 38, 39, 41, 42], "focus": [3, 13, 29], "fokker": [21, 22, 26, 42], "folder": 0, "follow": [0, 5, 9, 13, 16, 19, 21, 24, 26, 27, 38], "forc": 17, "forgotten": 11, "form": [10, 13, 21, 22, 26, 34, 38], "formal": [13, 17], "format": [5, 13, 17, 24, 25, 26, 28, 42], "formul": [3, 11, 17, 26], "formula": [26, 39, 40], "fortran": [0, 1, 2], "forward": 38, "found": [0, 9, 13, 16, 28, 29, 38], "foundat": [13, 34], "fourier": [5, 22, 23, 24, 30, 32], "fp": 22, "frac": [4, 5, 7, 10, 13, 18, 22, 24, 26, 30, 31, 32, 34, 38, 39], "fraction": [13, 26, 30, 32], "francisco": 42, "frankli": 38, "free": [9, 13, 19, 26], "freq": [7, 31], "freq_tol": 6, "frequenc": [5, 6, 7, 16, 18, 22, 23, 24, 26, 30, 32], "frequent": 17, "fridai": 41, "friend": 41, "from": [0, 3, 5, 10, 11, 16, 17, 19, 21, 22, 24, 25, 26, 28, 29, 30, 32, 39], "ft_model_sa": [17, 32], "fu": [16, 37, 42], "full": [0, 5, 16, 21, 22, 26, 42], "fulli": 13, "function": [5, 13, 16, 22, 24, 26, 30, 32, 38], "fund": 9, "fundament": 4, "furnish": 19, "furth": 42, "further": 10, "fusion": [3, 9, 11, 13, 18, 19, 27, 41, 42], "futur": [13, 17, 28, 42], "g": [3, 8, 10, 18, 21, 22, 24, 42], "g_": 24, "ga": [13, 17], "gacod": [0, 3, 4, 5, 9, 10, 21, 25, 26, 27, 28, 33, 34, 39, 40, 41], "gacode_platform": [0, 27], "gacode_qsub": [8, 27], "gacode_root": [0, 27], "gacode_setup": [0, 27], "gafus": 0, "galleri": [11, 17], "gam": 13, "gamma": [22, 30, 31], "gamma_": [6, 7, 24, 26, 32, 39, 41], "gamma_1": 32, "gamma_2": 32, "gamma_a": [7, 34], "gamma_e_scal": 6, "gamma_p": [6, 26, 41], "gamma_p_scal": 6, "gamot": 42, "gap": 13, "gat": [9, 19, 41], "gauss": [30, 32], "gaussian": 30, "gb": [7, 24, 32, 38], "gcc": 2, "gcc13": 2, "gchat": [17, 32], "ge": 28, "gem": [16, 28], "gene": [16, 28], "gener": [3, 5, 8, 10, 12, 13, 18, 21, 22, 26, 28, 29, 30, 34, 38, 39, 41, 42], "geo": [7, 22, 28, 41], "geo_ni": [17, 23], "geo_yin": [17, 23], "geometr": [22, 30], "geometri": [3, 16, 22, 24, 25, 28, 29, 30, 31, 42], "geometry_flag": [17, 32], "georg": 42, "geqdsk": 28, "get": [9, 21, 30], "gfile": 25, "gflux_print_flag": 6, "gfortran": [0, 1], "ghat": [17, 32], "git": 0, "github": [0, 3, 9, 17], "give": [4, 10, 13, 26, 27, 31, 33], "given": [4, 5, 13, 22, 26, 38, 39], "gk": [3, 6, 7, 11, 13, 29, 30], "gkw": 17, "glf23": [13, 29], "global": [3, 5, 11, 22, 27, 28, 39, 42], "goal": [13, 38], "good": [13, 16, 39], "gpu": [5, 6, 17], "gpu_bigmem_flag": 6, "grad": [10, 22], "grad_r0": 30, "gradb": [30, 32], "gradb_factor": [17, 32], "gradient": [3, 5, 6, 11, 13, 22, 23, 24, 26, 29, 30, 32, 38, 39, 40, 42], "graduat": 13, "grain": 13, "grant": 19, "greater": 4, "greatli": [3, 11], "green": 16, "greenwald": 42, "grid": [5, 7, 13, 17, 18, 22, 30, 39], "gridpoint": [5, 6, 13, 18, 22, 23, 24, 38], "grierson": 42, "groebner": 42, "group": [13, 16, 17, 19, 28, 42], "grow": 13, "grown": 13, "growth": [13, 16, 28, 30, 32], "growthrat": [30, 32], "gs2": [13, 16, 28], "gss": [29, 42], "gstotal": 13, "gtc": 16, "guid": [5, 10, 42], "gv": 24, "gwt": [28, 42], "gyro": [3, 5, 9, 10, 13, 17, 21, 25, 26, 29, 30, 31, 32, 33, 39, 42], "gyroaverag": [3, 13], "gyrobohm": [7, 30, 32, 38, 39, 42], "gyrofluid": [13, 28, 42], "gyrokinet": [3, 4, 9, 11, 17, 21, 25, 26, 28, 29, 42], "gyroradii": 13, "gyroradiu": [4, 7, 13, 30, 32], "gyrovisc": 24, "gyroviscos": 24, "g\u00f6rler": [28, 42], "h": [13, 24, 28, 29, 42], "h_print_flag": 6, "ha": [3, 11, 13, 16, 21, 27, 28, 29, 30, 31, 32, 38, 39], "had": 13, "hahm": 42, "half": [7, 13], "hallatschek": 42, "hammett": [13, 42], "hamper": 13, "hand": [5, 10, 13, 22], "handl": 25, "hardwar": [5, 13], "harmon": [5, 6, 10], "harri": 42, "hat": [18, 22, 24, 38], "have": [3, 10, 11, 16, 26, 28, 29, 38, 39], "hazeltin": 24, "hazltin": 24, "hbc": [13, 42], "hcw": [13, 42], "he": 42, "he4": 39, "heat": [13, 16, 24, 34, 39, 42], "heavi": 26, "hein": 42, "helium": [13, 39, 42], "help": [0, 16], "henc": 26, "here": [4, 5, 10, 13, 18, 21, 26, 28, 38], "herebi": 19, "hermit": [30, 32], "heurist": [5, 42], "hh": 24, "hhw": [3, 11, 42], "hidden": 30, "hierarchi": 41, "high": [4, 5, 21, 29, 30, 32, 39, 42], "higher": [5, 13, 22, 23, 26, 39], "highli": [3, 13, 42], "hinton": [13, 17, 22, 24, 26, 42], "hirshman": [22, 24, 39], "histor": [10, 13], "histori": [11, 17], "hoc": [3, 11, 22], "hol16": [28, 42], "hold": [13, 26, 39], "holder": 19, "holland": [13, 16, 28, 42], "home": 0, "homogen": 42, "horton": [24, 42], "host": 7, "hostnam": 7, "houlberg": 24, "how": [4, 5, 6, 18, 22, 39], "howard": [3, 42], "howev": [9, 10, 13, 16, 19], "hpc": [13, 17, 41], "hr": 24, "http": [0, 2, 42], "hu": 42, "huck": 42, "human": 7, "hw06": [13, 42], "hw85": [26, 42], "hwc04": [13, 42], "hwm": [28, 42], "hybrid": 42, "hybridtest": 0, "hypothesi": 13, "i": [0, 3, 4, 5, 7, 8, 9, 10, 11, 13, 14, 16, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42], "i0": 26, "i1": 26, "i_": [30, 32], "iaea": 42, "ibm": 13, "ibranch": [17, 32], "idea": 25, "ident": 13, "identifi": 13, "identit": 28, "idiosyncrat": 11, "ie": 24, "ieee": 42, "iflux": [17, 32], "ignor": [13, 18, 22, 26, 30, 32, 38], "igor": [3, 41], "iii": 42, "imag": [11, 16, 17, 42], "imex": 13, "immedi": 30, "impact": 42, "implement": [13, 16, 26, 28, 42], "impli": 19, "implic": [41, 42], "implicit": [4, 13, 38], "import": [0, 3, 13, 26, 29, 30, 38], "impos": [13, 16], "improv": [13, 25, 29, 30], "impur": [13, 26, 39, 42], "inc": 0, "includ": [5, 9, 11, 12, 13, 16, 18, 19, 21, 22, 23, 24, 28, 30, 32, 38, 42], "inclus": [5, 26, 28], "incorpor": 16, "incorrect": 16, "increas": [5, 10, 13, 16, 26, 29, 39], "increasingli": [3, 11], "inde": 13, "independ": [5, 13, 22, 26, 33, 38, 39], "index": [7, 22, 31], "indic": 13, "individu": 28, "induc": [5, 13, 22, 26], "induct": [22, 23], "infer": [5, 10, 13, 22], "infinit": 29, "influenc": [26, 38], "info": [4, 5, 7], "inform": [3, 7, 10, 11, 18, 24, 27], "initi": [5, 6, 9, 13, 14, 15, 16, 25, 28, 39, 40, 42], "inject": 26, "inner": 5, "input": [4, 7, 8, 10, 11, 17, 24, 25, 28, 29, 31, 41], "insid": 5, "insofar": 21, "instabl": [13, 30, 32, 42], "instal": [0, 1, 2, 17], "instanc": [26, 33, 39], "instead": [22, 33, 38], "instruct": 27, "instrument": 16, "int": 34, "int_": 22, "int_0": [34, 38], "int_r": 38, "integ": [5, 22, 23], "integr": [3, 4, 5, 6, 13, 22, 33, 38, 39], "intens": [5, 16, 29, 31, 32, 42], "intensity_spectrum": [17, 32], "interact": 8, "intercod": 16, "interconnect": 13, "interest": [11, 28, 38], "interestingli": 13, "interfac": [3, 7, 17, 21, 22, 32], "intern": [5, 6, 22, 42], "interpol": 24, "interpret": 24, "interprocess": 42, "interv": 6, "intev": 16, "introduc": 38, "invari": 4, "invent": 13, "investig": [13, 28], "invit": 42, "inward": [30, 32], "ion": [5, 6, 7, 13, 16, 18, 22, 24, 26, 28, 29, 30, 32, 38, 39, 40, 42], "ip": [5, 22], "ipccw": [6, 10, 17, 23], "ipm": 13, "irreduc": [30, 32], "isotop": 42, "isotrop": 22, "isotropi": 13, "issu": [0, 9, 13, 19, 28], "itb": 13, "iter": [38, 39, 42], "iterdb": 28, "iterdb2gyro": 25, "iterdb_read": 25, "itg": [13, 16, 29, 30], "itpa": 28, "its": [3, 5, 13, 16, 22, 29, 33], "ix": 24, "j": [12, 16, 24, 28, 38, 42], "j_": 24, "j_r": 34, "jacobian": [17, 34, 39, 40], "jan": 17, "jb": [18, 21], "jbstor": 18, "jcp": 42, "jeff": 3, "jenko": 42, "jet": [13, 29], "jift": 41, "jj": 38, "jnb": 18, "job": [8, 25, 27, 33, 39], "journal": 13, "jr": 42, "jrf": 18, "jt60": 13, "juli": 16, "june": [16, 42], "justifi": 26, "k": [22, 24, 29, 30, 32, 42], "k_": [5, 16, 24, 30, 32], "k_a": 26, "k_per": [30, 32], "k_r": 16, "k_x": [5, 6, 7, 31, 32], "k_y": [4, 5, 6, 7, 31, 32], "kaiser": 42, "kappa": [6, 10, 17, 18, 23, 30, 32], "kappa_loc": [17, 32], "karp": 5, "kay": 42, "kb": 29, "keep": 0, "kei": [3, 4, 13, 16, 17, 38], "kept": 5, "kerbel": 42, "kernel": [3, 7], "kev": [4, 18, 24], "kg": [21, 22, 24], "kh94": [13, 42], "kiefer": 42, "kim": 42, "kind": 19, "kinet": [3, 5, 11, 13, 21, 22, 23, 24, 28, 29, 39, 42], "kinsei": 42, "kishimoto": 42, "kkh": [13, 42], "knolker": 42, "know": 10, "known": [13, 26], "knoxvil": 42, "koh": 24, "kojak": 13, "kone": 42, "kot88": [13, 42], "kotschenreuth": [13, 42], "kramer": 42, "kro99": [13, 42], "kromm": [13, 42], "krt95": [13, 42], "ksw08": [29, 42], "kutta": 13, "kwc05": [3, 11, 13, 42], "kwc06": [3, 11, 13, 42], "kwc07": [3, 11, 13, 42], "kx": [31, 32], "kx0": [30, 32], "kx0_loc": [17, 32], "kx_e": [31, 32], "kx_phi": 41, "kxky_apar": [5, 7], "kxky_bpar": [5, 7], "kxky_e": 7, "kxky_n": 7, "kxky_phi": [5, 7], "kxky_v": 7, "ky": [4, 6, 17, 32], "ky_cflux": 7, "ky_flux": [7, 41], "ky_phi": 41, "kygrid_model": [17, 32], "kymin": 30, "l": [5, 13, 16, 17, 20, 22, 29, 42], "l11": 22, "l12": 22, "l21": 22, "l22": 22, "l25": 42, "l_": 24, "l_0": 5, "l_m": 22, "l_t": 16, "l_x": [5, 39], "label": 18, "lack": 29, "laguerr": [5, 22, 24], "lambda": [5, 22], "lambda_": 24, "lambda_deby": 6, "lambda_debye_scal": 6, "landau": [13, 29, 42], "landmark": 13, "langl": [26, 34], "languag": 13, "laptop": 17, "larg": [3, 4, 5, 8, 11, 13, 16, 22, 26, 30, 32, 39, 42], "larger": [3, 5, 11, 13, 16, 29], "larmor": [13, 16, 22, 23, 24, 29], "last": [0, 26, 30, 32, 39], "later": [13, 16], "latter": [13, 16], "law": 42, "layer": [3, 11, 13], "layout": [13, 27], "lcf": 5, "ldot": [5, 13, 24, 26], "le": [5, 16, 22], "le3": 22, "lead": 26, "leav": [5, 26], "leboeuf": 42, "lebrun": 42, "led": 25, "lee": 42, "left": [4, 5, 10, 22, 23, 24, 26, 34, 37, 38, 39], "legaci": [4, 11], "legend": 17, "legendr": [5, 22, 24], "leht02": [13, 42], "length": [3, 5, 6, 13, 21, 22, 24, 30, 32, 39, 40], "less": [5, 13, 39], "lett": [16, 42], "letter": [9, 19], "level": [0, 16, 28, 39], "li": 42, "liabil": 19, "liabl": 19, "libfftw3": 1, "libmpich": 1, "librari": 1, "licens": 17, "like": [3, 8, 10, 11, 13, 16, 18], "limit": [19, 21, 22, 24, 26, 30, 31, 32, 42], "lin": [16, 42], "line": [0, 2, 13, 16, 18, 23, 27, 41], "linear": [5, 8, 13, 14, 16, 21, 22, 28, 29, 30, 41, 42], "link": [0, 17, 28, 41], "linsker": [30, 32], "linsker_factor": [17, 32], "linux": 0, "list": [3, 8, 9, 11, 17, 19, 21, 28, 29, 33], "littl": [13, 29, 38], "ll": [21, 26], "llnl": 16, "ln": [5, 16, 22, 24, 26], "loc": [37, 39], "loc_betae_scal": [17, 40], "loc_dx": [17, 40], "loc_dx_max": [17, 40], "loc_er_feedback_flag": [17, 40], "loc_evolve_grad_only_flag": [17, 40], "loc_he_feedback_flag": 17, "loc_iteration_method": 39, "loc_lock_profile_flag": [17, 40], "loc_rad": [4, 41], "loc_relax": [17, 40], "loc_residual_method": [17, 40], "loc_restart_flag": [17, 40], "loc_scenario": [17, 40], "loc_te_feedback_flag": [17, 40], "loc_ti_feedback_flag": [17, 40], "local": [5, 10, 17, 21, 22, 23, 24, 28, 38, 39, 42], "locat": [13, 16], "locpargen": 4, "log": 5, "logarithm": [23, 30], "logic": 27, "long": [5, 13, 26], "longrightarrow": 26, "look": [10, 18], "loop": 5, "lorentz": [5, 26], "loss": [5, 13, 26, 42], "lost": 13, "low": [3, 5, 11, 13, 16, 25, 29, 30, 32], "lower": [5, 13, 22], "lowest": [5, 22, 30], "lpe": [13, 42], "luda": 42, "lvert": [16, 30, 32], "m": [5, 18, 24, 26, 28, 42], "m2": 0, "m_": [3, 5, 21, 22, 24, 30, 32], "m_a": 34, "m_d": [4, 5, 7, 22, 24], "m_e": 5, "m_i": 26, "m_theta": 24, "ma": 18, "mac": 0, "mach": [6, 26, 30, 32], "mach_scal": 6, "machin": 0, "macport": 2, "made": [9, 13, 19, 21, 30, 32], "magnet": [4, 5, 6, 13, 16, 17, 22, 23, 24, 28, 30, 32, 42], "magnitud": [16, 22], "mahinthakumar": 42, "mai": [16, 26, 28, 42], "main": [5, 25, 26, 32, 39], "maintain": [13, 17, 27], "maj": [30, 32], "major": [5, 6, 10, 13, 18, 22, 23, 24, 30, 32], "make": [0, 5, 9, 13, 19, 38, 39], "makefil": 0, "malonei": 42, "manag": [8, 13, 33, 39, 40], "mani": [6, 11, 13], "manner": 13, "manual": 13, "mar": 28, "margin": [13, 16], "marinoni": 42, "mark": 13, "mass": [3, 5, 6, 13, 21, 22, 23, 24, 26, 30, 32], "mass_": [6, 17, 23], "mass_1": [5, 17, 22, 32], "mass_2": [5, 22], "mass_3": [5, 22], "match": [4, 13, 28, 39, 42], "math": 22, "mathbf": [5, 10, 13, 14, 16, 22, 26, 30], "mathrm": [3, 5, 10, 13, 16, 24, 34, 37, 39], "mathtt": [4, 24, 37], "matric": 38, "matrix": [26, 38], "max": [5, 23, 39], "max_": 10, "max_tim": 6, "maxim": [5, 30, 32], "maximum": [5, 6, 13, 22, 30, 32, 39, 40], "maxwel": 42, "maxwellian": [5, 16, 21, 22, 24, 30], "mbox": 38, "mcclenaghan": 42, "mckee": 42, "md": [30, 32], "me": [30, 32], "mean": [10, 13, 22, 26, 42], "meaning": 24, "measur": [5, 13, 16, 22, 26, 28, 30, 32, 38, 42], "mechan": 30, "meet": 13, "memori": [5, 6, 7, 13], "merchant": 19, "mesh": [5, 7, 33], "meshpoint": 5, "method": [3, 4, 13, 16, 17, 29, 30, 32, 38, 39, 42], "metric": [28, 42], "mhd": [13, 30], "microst": [28, 42], "microturbul": 42, "mid": 13, "midplan": [4, 5, 22, 24, 30, 32], "mikkelsen": 42, "mila": [16, 42], "miller": [5, 22, 28, 29, 30], "milovich": 42, "min": [13, 23, 27], "min_": 10, "mine": 0, "minim": [33, 38, 39], "minimium": 5, "minimum": [5, 30, 32, 42], "minor": [3, 4, 5, 6, 10, 13, 18, 21, 22, 23, 24, 30, 32], "mint": 0, "miscellan": 17, "misunderstand": 13, "mit": [3, 13], "mix": 30, "mod": [13, 24, 42], "mode": [5, 6, 7, 8, 13, 14, 16, 17, 20, 21, 22, 23, 24, 29, 30, 31, 32, 39, 40, 42], "model": [3, 5, 6, 9, 10, 11, 13, 16, 22, 24, 26, 28, 30, 31, 32, 33, 39, 42], "modest": 13, "modif": [9, 19], "modifi": [3, 4, 5, 8, 11, 19, 24, 38], "modul": [21, 22], "modular": 13, "moment": [5, 6, 10, 22, 26, 29, 30], "moment_print_flag": [6, 7], "momentum": [5, 6, 7, 10, 13, 17, 18, 24, 32, 42], "monitor": 41, "monolith": [21, 24], "monomi": 22, "monoton": 13, "moor": 42, "more": [0, 3, 11, 13, 18, 22, 28, 29, 30, 38, 39], "moreov": [13, 16], "morph": 25, "most": [0, 5, 13, 16, 26, 28, 30, 32, 33, 34], "mostli": 13, "motiv": [3, 11, 13, 16, 25], "move": [3, 10, 11, 13], "mp": 2, "mpi": [0, 2, 5, 6, 7, 8, 27], "mpi_rank_ord": 6, "mpich": [1, 2], "mst1": 42, "much": [13, 22], "multi": [11, 13, 16, 21, 39, 42], "multipl": [3, 5, 13, 24, 28, 33, 38], "multipli": [5, 30, 32], "multiscal": [3, 42], "multistream": 13, "must": [0, 5, 10, 13, 22, 38], "mw": 18, "mxh": [10, 18], "mxh3": 10, "mynick": 42, "n": [0, 4, 5, 6, 8, 10, 14, 15, 16, 17, 18, 24, 27, 31, 32, 34, 39, 42], "n_": [5, 21, 22, 24, 30, 31, 32], "n_0": 16, "n_a": [5, 7, 22, 26, 34], "n_c": 16, "n_e": [3, 5, 7, 16, 18, 24, 38], "n_energi": [6, 17, 23, 41], "n_evolv": 39, "n_field": 6, "n_global": 6, "n_mpi": 39, "n_r": 22, "n_radial": [6, 17, 23, 24], "n_speci": [6, 17, 23], "n_theta": [6, 17, 23, 24, 41], "n_toroid": 6, "n_xi": [6, 17, 23, 41], "na": 10, "nabla": [10, 16, 22, 26, 34], "name": [9, 13, 16, 19, 21, 24], "nathan": 3, "natur": 13, "nbasis_max": [17, 32], "nbasis_min": [17, 32], "nbi": 39, "ncc": [16, 42], "nclass": [21, 22, 24], "ne": [18, 22], "ne_ad": [17, 23], "nearli": 13, "need": [0, 5, 8, 14, 25, 38], "neg": [5, 10, 22, 23], "neglect": [10, 13, 16], "neglig": [5, 13], "neo": [0, 3, 9, 10, 16, 17, 25, 26, 27, 33, 34, 38, 39, 40, 42], "neo_": 21, "neo_aniso_model_in": 22, "neo_dens_in": 22, "neo_dlnndr_in": 22, "neo_dlntdr_in": 22, "neo_dlntdr_para_in": 22, "neo_dlntdr_perp_in": 22, "neo_eflux_thchi_out": 24, "neo_eflux_thhhe_out": 24, "neo_eflux_thhhi_out": 24, "neo_eflux_ths_out": 24, "neo_efluxncv_dke_out": 24, "neo_efluxncv_gv_out": 24, "neo_efluxtot_dke_out": 24, "neo_efluxtot_gv_out": 24, "neo_efluxtot_nclass_out": 24, "neo_init": 21, "neo_interfac": [21, 24], "neo_jpar_dke_out": [21, 24], "neo_jpar_nclass_out": 24, "neo_jpar_ths_out": 24, "neo_jtor_dke_out": 24, "neo_jtor_ths_out": 24, "neo_mass_in": 22, "neo_mflux_dke_out": 24, "neo_mflux_gv_out": 24, "neo_n_species_in": 21, "neo_pflux_dke_out": 24, "neo_pflux_gv_out": 24, "neo_pflux_nclass_out": 24, "neo_pflux_thhh_out": 24, "neo_pflux_thhs_out": 24, "neo_profile_dlnndr_scale_in": 22, "neo_profile_dlntdr_scale_in": 22, "neo_rotation_model": 22, "neo_run": 21, "neo_temp_in": 22, "neo_temp_para_in": 22, "neo_temp_perp_in": 22, "neo_vpol_dke_out": 24, "neo_vpol_nclass_out": 24, "neo_vtor_dke_out": 24, "neo_vtor_nclass_out": 24, "neo_z_in": 22, "neoclass": [9, 13, 21, 22, 24, 25, 26, 34, 38, 39, 42], "nersc": [8, 17, 41], "net": 13, "netcdf": 2, "network": [22, 42], "neural": 22, "neutral": [22, 26], "nevin": [13, 42], "new": [0, 3, 10, 16, 18, 25, 29, 30, 32, 39, 42], "new_eikon": [17, 32], "newton": [38, 39, 40], "nexp": 18, "next": [13, 29], "nhd": [13, 42], "ni": 18, "nion": [18, 41], "nishimura": 42, "nky": [17, 31, 32], "nl": 30, "nl00": 8, "nl01": 8, "nl_flag": 41, "nm": 31, "nmode": [17, 31, 32], "no_cbla": 0, "no_lapack": 0, "no_shar": 0, "node": [5, 27, 30, 32], "nois": [13, 42], "nomin": 16, "nomp": [0, 8, 27], "non": [5, 13, 23, 24, 30, 32], "nonadiabat": 13, "nonaxisymmetr": [22, 42], "none": 24, "noninfring": 19, "nonlinear": [3, 5, 6, 8, 11, 14, 16, 28, 29, 41, 42], "nonlinear_flag": 6, "nonloc": [13, 42], "nonreson": 13, "nontherm": [39, 40], "nonuniform": 18, "nonuniformli": 26, "nonzero": [5, 24], "norm": [21, 22, 24, 26], "normal": [5, 6, 10, 13, 16, 17, 22, 23, 24, 30, 31, 32, 34, 38, 39], "normalzi": 38, "notat": [5, 34], "note": [5, 9, 17, 19, 22, 23, 24, 26, 28, 30, 31, 32, 38], "noth": 13, "notic": [9, 19], "nov": 30, "novel": 13, "now": 13, "nq": 4, "ns_in": 31, "nsts_crossphase_spectrum": [17, 32], "nstx": [13, 29, 30, 42], "nth": 39, "ntheta": 41, "nu": [10, 22], "nu_": 5, "nu_1": [17, 23], "nu_e": [6, 41], "nu_ei": 28, "nu_glob": 6, "nucl": 42, "nuclear": 42, "number": [5, 6, 8, 13, 16, 18, 21, 22, 23, 24, 26, 30, 32, 33, 38, 39, 40], "numer": [0, 3, 5, 8, 10, 11, 13, 17, 22, 24, 28, 41, 42], "nunami": 42, "nup_alpha": 6, "nup_radi": 6, "nup_theta": 6, "nwidth": [17, 32], "nx": 28, "nxgrid": [17, 32], "o": [5, 26], "observ": [13, 16, 26, 28], "obtain": [10, 13, 16, 19, 29, 33], "occur": 13, "octob": 42, "odd": 22, "off": [5, 39, 42], "offer": 11, "offload": [5, 6], "offset": [30, 32], "often": [0, 5, 8, 26, 30], "ohm": 42, "ohmic": [16, 18], "oint": 34, "old": 28, "older": 28, "omega": [17, 22, 34], "omega0": 18, "omega_": 26, "omega_0": [18, 22, 24, 26, 34], "omega_1": 26, "omega_intel": 27, "omega_rot": [17, 23, 26], "omega_rot_deriv": [17, 23, 26], "omp": [7, 27], "onc": [5, 27], "one": [5, 10, 13, 22, 30, 32, 38, 39], "ones": [0, 13], "onetwo": [13, 18, 25, 28], "onli": [5, 6, 11, 13, 16, 22, 23, 24, 26, 27, 28, 30, 38, 39], "open": [13, 16], "openbla": 17, "openmp": 0, "oper": [5, 13, 16, 21, 22, 33, 39, 40, 42], "operation": 38, "opposit": 13, "optim": [3, 5, 13, 42], "option": [21, 22, 41], "orbit_grid": 28, "order": [0, 4, 5, 6, 13, 16, 18, 21, 22, 23, 24, 26, 28, 30, 32, 33], "org": 2, "organ": 13, "orient": [5, 6, 17, 22], "orienti": [5, 22], "origin": [13, 28, 38, 39], "ornl": [8, 13, 42], "osx": 0, "other": [5, 10, 13, 16, 19, 22, 25, 28, 33, 39, 42], "otherwis": [9, 19, 22, 28, 30], "our": 13, "out": [5, 7, 8, 13, 16, 17, 18, 19, 22, 26, 29, 30, 32], "outboard": [5, 22, 24, 30, 32], "outer": 5, "output": [5, 8, 17, 22, 23, 25, 28, 29, 30, 31], "outward": 26, "oval": [6, 10], "over": [3, 13, 16, 18, 21, 28, 29, 31, 32], "overal": [4, 30], "overcom": 13, "overestim": 16, "overlin": 32, "overview": [13, 17], "ow": 13, "own": 0, "p": [5, 22, 26, 30, 32, 34, 38, 42], "p_": 24, "p_a": [22, 26], "p_l": 22, "p_prime_loc": [17, 32], "pa": 42, "pace": 42, "packag": 0, "page": 28, "pai": 8, "painstak": 13, "paper": [16, 34], "paradigm": [13, 42], "paradox": [13, 42], "parallel": [5, 7, 14, 18, 22, 23, 24, 26, 30, 31, 32, 33, 39, 42], "paramat": 16, "paramet": [4, 5, 13, 16, 17, 18, 21, 22, 24, 30, 31, 38, 39, 41], "parameter": [5, 10, 28, 42], "paramt": 22, "park": [17, 32], "parker": 42, "parser": 18, "part": [13, 16], "parti": [9, 19], "partial": [4, 5, 10, 22, 24, 26, 30, 32, 34, 38], "partial_t": 38, "particip": 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": 17, "patel": 42, "pathologi": 13, "pattern": 13, "pci": 13, "peak": [13, 30, 42], "pedest": [3, 11, 38, 41], "peebl": 42, "peeter": 42, "per": [6, 13, 27, 31, 32, 38], "perc": 13, "percent": 13, "pereverzev": 42, "perfect": 16, "perfectli": [13, 30], "perform": [3, 13, 16, 28, 39, 41, 42], "period": [13, 22, 25], "perlmutt": [17, 41], "perlmutter_cpu": 27, "perlmutter_gpu": 27, "permiss": 19, "permit": 19, "perp": [5, 22], "perpendicular": [16, 22, 23, 41], "persist": 13, "person": 19, "perspect": 17, "perturb": [5, 13], "petascal": 42, "petti": 42, "pfirsh": 26, "pg3eq": [13, 16], "ph": 16, "phase": [16, 29, 31, 32, 42], "phd": 42, "phenomena": [3, 11, 13], "phenomenon": 13, "phi": [5, 7, 10, 14, 18, 26, 31, 32], "phi_": [22, 24, 26], "phi_0": [22, 24, 26], "phi_1": [24, 26], "php": 2, "phy": [16, 24, 42], "physic": [4, 7, 9, 13, 16, 28, 30, 39, 41, 42], "physrevlett": 42, "pi": [5, 10, 18, 22], "pi_": [7, 24, 32], "pi_1": 32, "pi_2": 32, "pi_a": [7, 34], "pi_e": 32, "pic": [13, 16], "pick": 30, "pictur": 13, "pinch": [13, 42], "pinsker": 42, "pioneer": [3, 11], "pip": 41, "pitch": [5, 6, 22, 24, 28], "pittsburgh": 42, "pivot": 39, "place": 29, "plai": [3, 11, 13, 16, 26, 29], "planck": [21, 26, 42], "plank": 22, "plasma": [3, 5, 11, 13, 16, 18, 21, 22, 24, 25, 28, 29, 39, 42], "platform": [8, 13, 17, 27, 41], "pleas": [0, 12, 18], "plot": [8, 16, 17, 28, 41], "plu": [6, 8], "pmac": 13, "pmatrix": 38, "point": [5, 13, 16, 18, 28, 38, 39], "poisson": 21, "pol": 10, "polflux": 18, "poloid": [5, 6, 10, 13, 18, 22, 23, 24, 26, 30, 32, 41, 42], "polynomi": [5, 22, 23, 24, 30, 32], "popul": 42, "popular": [3, 13, 38], "porkolab": 42, "port": [2, 13], "portion": [9, 19], "posit": [5, 10, 22], "possibl": [6, 13, 28, 38], "possibli": 11, "potenti": [5, 13, 22, 24, 26, 30], "power": [13, 16, 17, 18, 38, 39, 40], "ppc": 13, "ppcf": 24, "pppl": 41, "practic": [13, 21, 26, 34], "pre": [11, 17, 25], "prebuilt": 17, "precis": [5, 6], "predecessor": 29, "predict": [13, 16, 28, 29, 42], "prefer": [30, 38], "prehistori": 17, "prepend": 21, "presenc": [13, 26], "present": [9, 12, 13, 16, 17, 19, 22, 24, 26, 41], "preset": 30, "pressur": [3, 5, 6, 11, 18, 22, 23, 30, 32], "prevent": [30, 32], "previou": [13, 26], "primari": [13, 21, 28, 33], "primarili": 3, "prime": [22, 34, 38], "principl": 13, "print": [5, 8, 22], "print_step": [4, 6], "prior": [13, 16], "priori": 26, "probabl": [13, 39], "problem": [5, 13, 22, 23, 38], "proce": 27, "proceed": 42, "process": [5, 6, 25, 39], "produc": [13, 24, 26], "product": [13, 42], "profil": [3, 5, 6, 9, 10, 11, 13, 16, 18, 21, 22, 25, 29, 33, 38, 39, 42], "profile_dlnndr_": [17, 23], "profile_dlnndr_1_scal": 22, "profile_dlnndr_2_scal": 22, "profile_dlnndr_3_scal": 22, "profile_dlntdr_": [17, 23], "profile_dlntdr_1_scal": 22, "profile_dlntdr_2_scal": 22, "profile_dlntdr_3_scal": 22, "profile_equilibrium_model": [10, 17, 23], "profile_erad0_model": [17, 23], "profile_model": [6, 17, 23, 24], "profiles_gen": [4, 17, 18, 41], "profiles_gen_plot": 41, "program": [0, 13], "progress": 13, "project": [0, 5, 13, 21, 27, 42], "pronounc": 13, "propag": 16, "proper": [10, 19], "properli": [10, 13], "properti": [5, 42], "provid": [3, 11, 13, 19, 25, 28], "pseudospectr": 5, "psfc": 41, "psi": [4, 10, 18, 22, 26, 34], "psi_": 10, "pst": 41, "ptot": 18, "public": [9, 12, 16, 17, 19], "publish": [9, 13, 16, 19], "pueschel": 42, "pull": [9, 19], "pure": [13, 16, 26], "purpos": [3, 5, 9, 19], "push": 26, "put": 38, "pygacod": 41, "python": [0, 2, 3, 7, 17], "python3": 2, "q": [4, 6, 10, 13, 17, 18, 23, 24, 26, 30, 32, 34, 38, 42], "q_": [7, 13, 24, 32, 37, 38, 39], "q_1": 32, "q_2": 32, "q_a": [7, 34], "q_e": [16, 32, 37, 38], "q_i": [37, 38], "q_loc": [17, 32], "q_prime_loc": [17, 32], "q_sa": [17, 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": [17, 32], "qline": [18, 37], "qmom": 18, "qohm": [18, 37], "qpar_beam": 18, "qpar_wal": 18, "qrfe": [18, 37], "qrfi": [18, 37], "qsync": [18, 37], "quad": [26, 34, 38], "quadratur": [30, 32], "qualit": 28, "qualiti": 25, "quantit": 16, "quantiti": [3, 10, 16, 21, 22, 24, 26, 38], "quasi": [22, 26, 30, 42], "quasilinear": [16, 29, 30, 32, 42], "quasineutr": [4, 5, 6, 39], "quasineutral_flag": 6, "quench": [13, 29, 30, 32, 42], "queri": 0, "question": [13, 17, 28], "queue": 8, "quick": 17, "quit": 13, "r": [0, 4, 5, 10, 12, 13, 16, 18, 21, 22, 24, 26, 30, 32, 34, 38, 42], "r_": [30, 32, 38], "r_0": [5, 10, 18, 22, 24, 26], "r_1": 38, "r_2": 38, "r_3": 38, "r_j": [24, 38], "rad": [18, 34, 37], "radial": [3, 5, 6, 11, 13, 16, 22, 23, 24, 26, 33, 38, 39, 42], "radian": 18, "radiat": [18, 34, 39], "radii": [13, 39], "radiu": [3, 4, 5, 6, 10, 13, 16, 18, 21, 22, 23, 24, 29, 30, 32, 39, 42], "rais": 0, "rang": [13, 16, 21, 22], "rangl": [26, 34], "rank": [5, 6, 7, 30, 32], "rapid": 26, "rapidli": [38, 42], "rate": [5, 6, 13, 16, 22, 26, 28, 30, 32, 34], "rather": [7, 13, 26, 38, 39], "ratio": [5, 13, 21, 22, 24, 29, 39], "ration": 13, "rational": 25, "raw": 5, "rb_": [30, 32], "rbf": 28, "rc": 0, "rc_": [30, 32], "re": 22, "reach": 13, "reaction": 39, "reactor": [37, 39, 42], "read": [5, 7, 22, 25, 28, 34, 39], "readabl": 7, "reader": 11, "real": [3, 11, 13, 41], "realist": [13, 42], "realiti": 10, "realli": 26, "reason": 26, "recent": [11, 13, 16, 28, 29, 30], "recipi": 9, "recombin": 18, "recommend": [0, 4, 5, 7, 30], "rectangular": 24, "red": 16, "redistribut": 26, "reduc": [3, 5, 6, 11, 13, 14, 26, 38], "reduct": 13, "reed": 42, "ref": [22, 38], "refer": [5, 13, 17, 19, 24, 28], "refin": [13, 30], "reflect": 10, "refus": 16, "reg08": 8, "reg14": 18, "regard": 17, "regardless": 22, "regim": [3, 13, 16, 26], "region": [3, 11, 13, 29], "regress": [0, 8], "regular": 8, "rel": [5, 6, 16, 22, 30], "relat": [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": [3, 5, 9, 11, 13, 18, 22, 25, 26, 27, 29, 34, 42], "rescal": 16, "research": [3, 11, 13, 16, 28], "reset": 5, "residu": [13, 38, 39, 40], "resolut": [5, 22, 39, 41, 42], "resolv": [13, 30], "resourc": [13, 16, 28], "respect": [5, 21, 22, 26, 30, 32], "respond": 30, "respons": [29, 42], "restart": [5, 6, 39, 40, 41], "restart_step": 6, "restrict": [9, 13, 19, 26, 38], "result": [5, 8, 9, 11, 13, 17, 19, 26, 29, 30, 38, 42], "retain": [3, 5, 10, 13, 21], "return": [5, 14, 22, 30, 31], "rev": [16, 24, 42], "revers": [13, 42], "review": 13, "revis": 16, "rewoldt": 42, "rf": 18, "rh": [13, 22], "rh98": [13, 42], "rho": [4, 5, 16, 18, 30, 32, 42], "rho_": [4, 5, 7, 13, 16, 21, 22, 24, 28, 31, 38], "rho_i": [21, 26], "rho_ion": 30, "rho_star": [17, 23], "rhode": 42, "right": [4, 5, 10, 19, 22, 23, 24, 26, 34, 37, 38, 39], "rightarrow": [4, 5, 13, 22, 24, 38], "rigor": [13, 26], "rise": 13, "rk": 13, "rk4": 5, "rlns_1": [17, 32], "rlts_1": [17, 32], "rm": [4, 5, 7, 10, 16, 18, 21, 22, 23, 24, 26, 30, 32, 34, 38], "rmaj": [6, 10, 18], "rmaj_loc": [17, 32], "rmaj_over_a": [10, 17, 23], "rmaj_sa": [17, 32], "rmin": [6, 10, 18], "rmin_loc": [17, 32], "rmin_over_a": [10, 17, 23], "rmin_over_a_2": [17, 23], "rmin_sa": [17, 32], "roach": 42, "robust": [13, 16, 38, 39], "roger": 42, "role": [13, 16, 26, 29, 33, 42], "ron": 28, "root": [38, 39], "rosenbluth": [13, 24, 42], "rost": 42, "rotat": [3, 5, 18, 21, 22, 28, 33, 38, 39, 42], "rotation_model": [6, 17, 23, 24], "roth": 42, "rough": 16, "roughli": [10, 13, 16, 30], "routin": [13, 39], "row": 24, "rule": [0, 29, 30, 32, 38, 39, 40, 42], "run": [0, 5, 10, 13, 14, 21, 22, 24, 27, 29, 30, 39], "runawai": 13, "rung": 13, "runtim": 24, "s0021": 42, "s_": [5, 10, 22, 34], "s_1": 10, "s_2": 10, "s_3": 10, "s_delta": [6, 10, 17, 23], "s_delta_loc": [17, 32], "s_e": 38, "s_i": [26, 38], "s_kappa": [6, 10, 17, 23], "s_kappa_loc": [17, 32], "s_n": 10, "s_w": 34, "s_zeta": [6, 10, 17, 23], "s_zeta_loc": [17, 32], "s_zmag": [10, 17, 23], "safe": 39, "safeti": [0, 5, 6, 10, 13, 18, 22, 23, 24, 30, 32, 42], "sai": [0, 26], "same": [5, 11, 13, 16, 26, 28, 39], "sampl": [18, 27, 39], "san": 42, "santoro": 42, "sat0": [29, 30], "sat1": [29, 30, 32], "sat2": [29, 30], "sat3": [29, 30], "sat_geo_spectrum": [17, 32], "sat_rul": [17, 31, 32], "satur": [13, 16, 30, 31, 32, 42], "sauter": 24, "save": 5, "sbc": [29, 30, 42], "sc2004": 42, "scalar": [26, 31, 32], "scalar_saturation_paramet": [17, 32], "scale": [4, 5, 6, 10, 13, 16, 22, 23, 24, 26, 30, 39, 40, 42], "scan": [13, 16], "scatter": 28, "scb": [29, 30, 42], "scenario": [17, 18, 33, 39, 40, 42], "scheme": [5, 13, 22, 38, 39, 40], "schh16": [29, 30, 42], "schl\u00fcter": 26, "schmitz": 42, "schumak": 42, "sci": 42, "scidac": [13, 42], "scienc": 17, "scratch": [3, 11], "screen": 8, "script": 8, "scw": [29, 42], "sdsc": 3, "seamlessli": 13, "search": [30, 32], "second": [4, 24, 26, 28, 39], "section": 26, "see": [4, 5, 9, 18, 22, 26, 29, 30, 32, 33, 39], "seem": 13, "seen": 28, "select": [2, 5, 6, 22], "selector": [5, 6, 23], "self": [5, 6, 13, 24, 30, 32, 39, 42], "selfupd": 2, "send": [9, 41], "sensit": 16, "separ": [13, 16, 25], "seri": [16, 24, 28, 42], "serial": [17, 39], "serv": 28, "set": [0, 2, 4, 5, 8, 13, 21, 22, 26, 28, 30, 31, 32, 39], "setup": [5, 27], "sever": 13, "sevil": 42, "sfiligoi": [3, 41, 42], "sgi": 13, "sh01": [13, 42], "sh98": [26, 34, 42], "shafer": 42, "shafranov": [5, 6, 10, 22, 23, 30], "shall": [9, 19], "shampin": 5, "shan": 42, "shape": [3, 5, 10, 13, 16, 18, 21, 22, 25, 29, 39, 42], "shape_cos0": [6, 10, 17, 18], "shape_cos1": [6, 10, 17, 18], "shape_cos2": [6, 10, 17, 18], "shape_cos3": [6, 10, 17, 18], "shape_s_cos0": [6, 10, 17], "shape_s_cos1": [6, 10, 17], "shape_s_cos2": [6, 10, 17], "shape_s_cos3": [6, 10, 17], "shape_s_sin3": [6, 10, 17], "shape_sin3": [6, 10, 17, 18], "share": [0, 27, 39], "shat_sa": [17, 32], "shear": [5, 6, 10, 13, 16, 17, 23, 24, 26, 29, 30, 32, 42], "shell": 0, "shend": 42, "shift": [6, 10, 13, 17, 23, 29, 30, 31, 32], "shirai": 42, "short": [6, 7, 13, 15, 23, 24, 32, 40], "shorter": 5, "shortfal": [17, 20, 42], "shorthand": 38, "shot": 28, "should": [0, 4, 5, 8, 22, 23, 24, 28, 39], "show": [8, 13, 16, 26, 39], "shown": [10, 13, 16, 23, 28], "shrinkag": 39, "shumak": 42, "shut": 39, "side": 13, "sigma": [24, 38], "sigmar": [22, 24, 39], "sign": [10, 22, 23, 30, 32], "sign_bt": [17, 32], "sign_it": [17, 32], "signal": 39, "signific": [5, 13, 16], "significantli": [13, 16], "silent": 6, "silent_flag": [6, 17, 23, 24], "sim": 38, "sim_model": [17, 23, 24], "simeq": [26, 38], "similar": [13, 26, 28, 42], "simpl": [5, 8, 29, 31, 39], "simpli": 39, "simplif": 34, "simplifi": [13, 30], "simul": [5, 6, 7, 9, 11, 14, 17, 18, 22, 23, 25, 28, 29, 30, 33, 39, 40, 41, 42], "simultan": [13, 16, 39], "sin": [10, 24], "sinc": [13, 21, 28], "sine": 24, "singl": [0, 5, 6, 13, 26, 28, 30, 32], "singular": [5, 13], "size": [4, 6, 13, 16, 40, 41, 42], "sj": 24, "sk10": [9, 42], "sk_": [30, 32], "skw05": [13, 42], "skw07": [3, 9, 11, 13, 29, 30, 42], "slightli": [5, 13, 28], "slow": 16, "slowdown": 13, "slower": 5, "small": [5, 13, 26, 28], "smaller": [5, 13, 14, 16, 39], "smith": 42, "smoooth": 42, "smooth": 38, "snave": 42, "snyder": [13, 42], "so": [5, 6, 13, 16, 19, 22, 25, 27, 28, 30, 33, 38, 39], "soc": 42, "softwar": [9, 13, 19, 27], "solid": 16, "solomon": 42, "solut": [17, 22, 24, 29, 39, 42], "solv": [13, 17, 21, 22, 24, 29, 33, 38, 39], "solver": [3, 11, 17, 21, 22, 33, 42], "some": [11, 13, 17, 23, 28, 34], "sometim": 14, "somewhat": 13, "sonic": [5, 17, 21, 22, 24], "sort": [13, 30, 32], "sound": [3, 7, 13, 16], "sourc": [5, 6, 13, 17, 18, 19, 22, 25, 33, 38, 39, 41], "space": [3, 5, 11, 22, 23, 28, 30, 32, 42], "spain": 42, "span": [5, 13], "spars": 33, "spatial": [13, 16, 22], "speak": 13, "speci": [5, 11, 18, 21, 22, 26, 28, 30, 31, 39, 42], "species1": 22, "specif": [0, 3, 5, 18, 24, 26, 38], "specifi": [5, 18, 22, 23, 25, 39], "spectra": [13, 16, 31, 32], "spectral": [3, 13, 29, 30, 31, 32, 42], "spectral_shift": [17, 32], "spectroscopi": 16, "spectrum": [13, 30, 31, 32], "speed": [3, 5, 6, 7, 22, 24, 26], "spitzer": [22, 23], "spitzer_model": [17, 23], "split": [4, 25], "spot": 16, "spread": 13, "spring": 13, "sqrt": [3, 7, 16, 21, 22, 24], "squar": [5, 6, 10, 16, 18, 22, 23, 30, 32], "src": 8, "sreepathi": 42, "ss": 22, "stabil": [13, 29, 42], "stabl": 13, "staebler": 42, "staff": 13, "stage": 5, "standard": [3, 4, 5, 10, 13, 17, 22, 25, 26, 28, 30, 32, 39], "star": 42, "start": [13, 18, 28, 39], "startup": 39, "state": [13, 33, 38, 42], "statefil": 25, "static": [37, 39], "statist": [7, 13], "statu": 42, "steadi": [13, 33, 38, 42], "steep": 26, "steeper": [3, 11], "step": [4, 5, 13, 17, 27, 38, 39, 40], "stiff": 39, "still": [13, 38], "storag": 42, "store": [30, 32], "strategi": [17, 41], "strength": [10, 22], "stress": [31, 32], "strong": [13, 16, 22, 24, 26], "strongli": [8, 18, 28], "structur": 13, "student": 13, "studi": [13, 17, 26, 28, 42], "subdomin": 13, "subject": [9, 19, 26, 41], "submiss": 13, "submit": 8, "subroutin": [17, 21, 22], "subscript": 26, "substanti": [9, 19], "substitut": 26, "subtl": 26, "success": [0, 13, 16], "successfulli": [13, 16], "sudo": [1, 2], "suffer": 13, "suffici": [4, 18], "sugama": [5, 6, 17, 24, 26, 34, 42], "suggest": [3, 8, 13, 24, 33], "suit": [0, 13], "suitabl": [0, 3, 11, 25], "sum": [18, 26, 31, 32, 38], "sum_": [10, 24], "sum_a": [22, 34], "sum_flux_spectrum": [17, 32], "sum_p": 39, "summar": [13, 34], "summari": [11, 16, 28], "summer": 25, "sung": 42, "supercomput": [13, 42], "support": [13, 39], "suppress": [10, 26, 42], "surfac": [5, 13, 17, 18, 21, 22, 24, 26, 30, 32, 34, 42], "surprisingli": 29, "svpablo": 13, "swck13": [29, 30, 42], "switch": [7, 13, 30], "swnn11": [26, 42], "symbol": [10, 23], "symmetr": [5, 6, 10, 22], "symmetri": 6, "synchrotron": 18, "synopsi": 17, "synthet": [13, 28, 42], "system": [3, 5, 8, 10, 13, 22, 26, 29, 30, 32, 38, 41], "systemat": [13, 28], "t": [5, 7, 8, 10, 13, 16, 24, 26, 28, 30, 32, 34, 38, 41, 42], "t_": [5, 16, 21, 22, 24, 26, 30, 32, 38], "t_0": 16, "t_a": 22, "t_e": [3, 5, 7, 13, 16, 18, 24, 38, 39], "t_i": [13, 26, 38, 39], "ta": [22, 24], "tabl": [5, 14, 17, 22, 26, 29, 30, 31], "tabular": [3, 11, 17, 33], "tag": 7, "taguchi": 24, "tajima": 42, "take": [13, 23, 24], "taken": [16, 28, 38], "talk": [41, 42], "tang": 42, "tardini": 42, "target": [13, 38, 39], "task": [0, 7, 8], "tau": 13, "tau_": [22, 24], "taus_1": [17, 32], "tdg": [29, 42], "te": [4, 18, 22, 42], "te_ad": [17, 23], "team": 42, "tech": 42, "technic": [10, 13, 42], "tem": [13, 29, 30], "temp": [5, 22], "temp_": [6, 17, 23], "temp_1": [5, 22], "temp_2": 22, "temp_3": 22, "temp_para_": [17, 23], "temp_para_1": 22, "temp_para_2": 22, "temp_para_3": 22, "temp_perp_": [17, 23], "temp_perp_1": 22, "temp_perp_2": 22, "temp_perp_3": 22, "temperatur": [3, 5, 6, 13, 18, 21, 22, 23, 24, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 42], "temperature_spectrum": [17, 32], "temperaur": 23, "templat": [0, 8], "ten": 13, "tend": 13, "term": [5, 6, 13, 16, 21, 22, 24, 26, 30, 32, 38], "test": [0, 5, 6, 8, 9, 13, 16, 19, 22, 28], "text": [13, 26, 28, 29, 34, 38], "tftr": 29, "tg": 24, "tglf": [0, 3, 9, 11, 13, 17, 28, 33, 42], "tglf1": 39, "tglf2": 39, "tglf3": 39, "tglf4": 39, "tglf_adiabatic_elec_in": 32, "tglf_alpha_e_in": 32, "tglf_alpha_mach_in": 32, "tglf_alpha_p_in": 32, "tglf_alpha_quench_in": 32, "tglf_alpha_sa_in": 32, "tglf_as_in": 32, "tglf_b_model_sa_in": 32, "tglf_betae_in": 32, "tglf_debye_factor_in": 32, "tglf_debye_in": 32, "tglf_delta_loc_in": 32, "tglf_drmajdx_loc_in": 32, "tglf_drmindx_loc_in": 32, "tglf_dzmajdx_loc_in": 32, "tglf_elec_eflux_out": 32, "tglf_elec_mflux_out": 32, "tglf_elec_pflux_out": 32, "tglf_etg_factor_in": 32, "tglf_filter_in": 32, "tglf_find_width_in": 32, "tglf_ft_model_sa_in": 32, "tglf_gchat_in": 32, "tglf_geometry_flag_in": 32, "tglf_ghat_in": 32, "tglf_gradb_factor_in": 32, "tglf_ibranch_in": [30, 32], "tglf_iflux_in": 32, "tglf_ion1_eflux_out": 32, "tglf_ion1_mflux_out": 32, "tglf_ion1_pflux_out": 32, "tglf_ion2_eflux_out": 32, "tglf_ion2_mflux_out": 32, "tglf_ion2_pflux_out": 32, "tglf_kappa_loc_in": 32, "tglf_kx0_in": 32, "tglf_ky_in": 32, "tglf_kygrid_model_in": 32, "tglf_linsker_factor_in": 32, "tglf_mass_in": 32, "tglf_nbasis_max_in": 32, "tglf_nbasis_min_in": 32, "tglf_new_eikonal_in": [30, 32], "tglf_nky_in": 32, "tglf_nmodes_in": 32, "tglf_ns_in": 32, "tglf_nwidth_in": 32, "tglf_nxgrid_in": 32, "tglf_p_prime_loc_in": 32, "tglf_park_in": 32, "tglf_q_loc_in": 32, "tglf_q_prime_loc_in": 32, "tglf_q_sa_in": 32, "tglf_rlns_in": 32, "tglf_rlts_in": 32, "tglf_rmaj_loc_in": 32, "tglf_rmaj_sa_in": 32, "tglf_rmin_loc_in": 32, "tglf_rmin_sa_in": 32, "tglf_s_delta_loc_in": 32, "tglf_s_kappa_loc_in": 32, "tglf_s_zeta_loc_in": 32, "tglf_sat_rule_in": 32, "tglf_shat_sa_in": 32, "tglf_sign_bt_in": 32, "tglf_sign_it_in": 32, "tglf_taus_in": 32, "tglf_theta0_sa_in": 32, "tglf_theta_trapped_in": 32, "tglf_tm": 32, "tglf_use_bisection_in": 32, "tglf_use_bpar_in": 32, "tglf_use_bper_in": 32, "tglf_use_inboard_detrapped_in": 32, "tglf_use_mhd_rule_in": 32, "tglf_use_transport_model_in": 32, "tglf_vexb_in": 32, "tglf_vexb_shear_in": 32, "tglf_vpar_in": 32, "tglf_vpar_model_in": 32, "tglf_vpar_shear_in": 32, "tglf_vpar_shear_model_in": 32, "tglf_wd_zero_in": 32, "tglf_width_in": 32, "tglf_width_min_in": 32, "tglf_write_wavefunction_flag_in": 32, "tglf_xnu_factor_in": 32, "tglf_xnu_model_in": 32, "tglf_xnue_in": 32, "tglf_xwell_sa_in": 32, "tglf_zeff_in": 32, "tglf_zeta_loc_in": 32, "tglf_zmaj_loc_in": 32, "tglf_zs_in": 32, "tgyro": [9, 17, 18, 24, 27, 42], "tgyro_den_method": [17, 40], "tgyro_den_method0": 39, "tgyro_den_method1": 39, "tgyro_den_method2": 39, "tgyro_den_method3": 39, "tgyro_den_method4": 39, "tgyro_iteration_method": [17, 40], "tgyro_mod": [17, 40], "tgyro_neo_method": [17, 40], "tgyro_relax_iter": [17, 40], "tgyro_rmax": 39, "tgyro_therm_flag": [17, 40], "tgyro_therm_flag1": 39, "tgyro_write_profiles_flag": [17, 40], "than": [4, 5, 13, 26, 30, 32, 38, 39], "thank": 28, "thei": [13, 21], "them": 26, "themselv": 22, "theoret": [17, 34], "theori": [10, 13, 17, 21, 22, 27, 28, 34, 39, 42], "thermal": [13, 16, 18, 22, 24, 26, 39, 40, 42], "thermodiffus": 16, "thermonuclear": 39, "thermostat": 42, "thesi": [13, 16, 42], "theta": [5, 6, 7, 10, 16, 22, 24, 26, 30, 32, 34], "theta0_sa": [17, 32], "theta_0": [5, 41], "theta_i": 5, "theta_j": 24, "theta_r": 10, "theta_trap": [17, 32], "thi": [0, 3, 5, 8, 9, 10, 11, 13, 14, 16, 19, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 38, 39], "thing": 16, "third": [9, 19], "thome": 42, "those": [13, 21, 28], "though": 38, "thousand": [3, 11, 13], "thread": [0, 7], "three": [16, 38], "threed": 22, "threed_exb_dphi0dr": [17, 23], "threed_exb_model": [17, 23], "threed_model": [17, 23], "threshold": [13, 30, 32], "through": [17, 26], "throughout": 26, "thu": [5, 10, 13, 22, 26, 38], "thursdai": 41, "ti": [4, 13, 18, 42], "tild": 31, "tilt": [6, 10, 18], "tim": 29, "time": [3, 4, 5, 10, 13, 14, 16, 22, 24, 26, 27, 28, 30, 32, 33, 38, 41], "timer": 7, "timestamp": 7, "timestep": [4, 5, 13, 41], "tn": 42, "tobia": 28, "togeth": [5, 21], "toggl": [5, 6, 39, 40], "tokamak": [10, 13, 26, 28, 29, 42], "told": 42, "toler": [4, 5, 6], "tool": [2, 4, 13, 18, 21, 25, 27, 28, 42], "top": [0, 30, 32], "topic": [9, 16, 28, 42], "tor": [10, 28, 30, 32], "torodi": 22, "toroid": [3, 5, 6, 10, 13, 16, 18, 22, 23, 24, 26, 30, 31, 32, 42], "toroidals_per_proc": 6, "torqu": [18, 26], "tort": 19, "toru": [5, 22], "tot": [37, 39], "total": [0, 18, 22, 24, 31, 38, 39], "toward": [3, 11, 13], "transform": [24, 39], "transit": 13, "transp": 25, "transport": [3, 5, 9, 10, 11, 17, 19, 22, 25, 26, 28, 29, 32, 38, 39, 42], "transvers": [30, 32], "trap": [4, 13, 16, 26, 29, 30, 32, 42], "trap_grid": 28, "trapezoid": 38, "treat": [3, 5, 13, 21, 22, 26, 30], "treatment": [10, 42], "triangular": [5, 6, 10, 18, 22, 23, 30, 32], "trigger": [5, 13], "true": [13, 26, 30, 32, 38], "truli": 16, "truncat": 38, "truth": 13, "tsujii": 42, "tube": [13, 16], "tur": 34, "turb": 38, "turbul": [3, 11, 13, 19, 26, 28, 34, 38, 42], "turco": 42, "tutori": 28, "two": [3, 16, 28, 30, 32, 38, 42], "tynan": 42, "type": [0, 8, 18, 30, 31, 32], "typic": [5, 10, 13, 22, 25], "u": [6, 9, 13, 24, 26, 30, 42], "u_": [24, 26], "ubuntu": 0, "ucsd": 13, "udsymmetry_flag": 6, "uk": 42, "uncertainti": [13, 16], "unchang": [5, 13, 39], "under": [13, 26], "underestim": 16, "underli": [13, 26], "underpredict": [13, 16], "understand": [3, 11, 34], "unequ": 39, "unifi": 17, "unimport": [5, 14], "uniqu": [25, 38], "unit": [3, 4, 5, 7, 10, 17, 18, 21, 22, 24, 31, 32, 34], "uniti": 39, "units_in": 32, "univ": 16, "univers": [13, 42], "unless": 28, "unlik": [5, 33], "unperturb": 16, "unphys": 30, "unpublish": 13, "unsolv": 13, "unstabl": [5, 13, 30, 32], "unsubstanti": 13, "until": 13, "up": [0, 6, 16, 18, 21, 24, 28, 30, 32], "up_alpha": 6, "up_radi": 6, "up_theta": 6, "updat": [5, 6, 9, 28, 38, 40], "upgrad": 42, "upon": 13, "upper": 22, "upshift": 13, "upwind": [5, 6, 42], "upwind_single_flag": 6, "urban": 17, "urg": 28, "url": [12, 42], "us": [0, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42], "usag": [5, 7], "use_bisect": [17, 32], "use_bp": [17, 32], "use_bpar": [17, 32], "use_inboard_detrap": [17, 32], "use_lock": 0, "use_mhd_rul": [17, 32], "use_thread": 0, "use_transport_model": [17, 32], "user": [0, 3, 5, 17, 19, 30, 32, 33, 42], "usernam": 9, "usual": [5, 26], "util": 13, "v": [2, 21, 22, 23, 24, 26, 28, 34, 38, 42], "v_": [22, 24, 26, 30, 32], "v_a": 7, "v_i": 5, "valid": [11, 13, 17, 24, 26, 28, 42], "valu": [4, 5, 7, 13, 14, 16, 22, 23, 24, 28, 30, 32, 39, 42], "van": 42, "vanish": 13, "varepsilon": 22, "varepsilon_": [5, 24], "vari": [13, 16, 26], "variabl": [13, 17, 34, 38], "variant": [13, 38], "variat": [3, 11, 13, 24, 38, 39], "variou": [7, 13, 21, 28], "varphi": [5, 10, 22, 24, 26, 34], "vathd": [13, 42], "vector": [7, 13, 22, 24, 38], "veloc": [3, 5, 6, 18, 21, 22, 23, 26, 28, 30, 31, 32, 41, 42], "velocity_ord": 6, "veri": [5, 8, 16], "verif": [11, 13, 17, 28, 42], "verifi": [13, 16], "verner": 5, "version": [7, 9, 28, 30, 39], "versu": [7, 16, 41], "vertic": 16, "vetter": [13, 42], "vexb": [17, 32], "vexb_shear": [17, 32], "via": [10, 13, 16, 17, 22, 23, 42], "view": [5, 13, 22], "virtual": 41, "visual": 41, "vol": [24, 42], "voltag": 13, "volum": [34, 38], "vpar": [30, 32], "vpar_1": [17, 32], "vpar_model": [17, 32], "vpar_shear_1": [17, 32], "vpar_shear_model": [17, 32], "vpol": 18, "vtor": 18, "w": [8, 24, 27, 34, 42], "w_a": 34, "wa": [0, 3, 10, 11, 13, 16, 21, 25, 26, 33, 38], "wabc06": [13, 42], "wai": [26, 38], "wal05": [13, 42], "wall": [18, 27, 34], "waltz": [4, 12, 13, 42], "wan": 42, "warranti": 19, "wast": 13, "watanab": 42, "wathd": [13, 42], "wave": [13, 16, 30, 42], "wavelength": [5, 13, 26], "wavenumb": [3, 4, 5, 6, 11], "wc05": [13, 42], "wcc": [13, 42], "wcf07": [13, 42], "wch": [13, 42], "wcp06": [13, 42], "wcr02": [13, 42], "wd_zero": [17, 32], "we": [0, 4, 5, 7, 10, 11, 13, 16, 22, 24, 26, 27, 28, 29, 33, 34, 38], "weak": [5, 38], "weaker": 13, "weber": 18, "weight": [7, 29, 30, 31, 32], "welcom": [9, 19, 28], "well": [13, 16, 21, 26, 28, 30, 32], "were": [13, 16, 29], "wh08": [13, 42], "what": [0, 4, 6, 8, 13, 18], "whatsoev": 13, "when": [0, 3, 4, 5, 6, 11, 13, 21, 22, 24, 30, 31, 32, 38, 39], "where": [3, 4, 5, 10, 11, 13, 16, 22, 24, 26, 29, 30, 34, 38, 39], "wherea": [4, 10, 13, 26], "wherev": 13, "whether": [13, 19, 22, 23], "which": [3, 4, 5, 10, 11, 13, 16, 22, 25, 26, 28, 29, 31, 32, 38, 39], "while": [16, 22, 28, 38, 39], "white": [28, 42], "whiteros": 42, "who": 26, "whom": 19, "why": [4, 13], "wide": [13, 16, 21], "widehat": 38, "width": [13, 17], "width_min": [17, 32], "wiki": 13, "william": 42, "winter": 13, "within": [13, 16], "without": [16, 19, 26, 38], "wkm94": [13, 42], "wkmh95": [13, 42], "wolf": 42, "wong": [22, 26, 42], "word": 10, "work": [4, 13, 16, 17, 26, 28, 30, 41], "worker": 13, "workshop": [17, 20], "worldwid": 13, "worlei": [13, 42], "would": [5, 8, 10, 38], "write": [8, 26, 34, 39, 40], "write_wavefunction_flag": [17, 32], "written": [5, 13, 16, 22, 24, 38, 39], "wrote": 4, "ws08": [13, 42], "wsch07": [13, 42], "wsd": [13, 42], "wsm": [13, 28, 42], "wukitch": 42, "www": 2, "x": [30, 32, 34, 38, 42], "x1": [13, 42], "x_": 24, "x_a": [22, 24], "xcode": 2, "xd1": [13, 42], "xi": [5, 6, 22, 23, 24], "xi_i": 5, "xnu_factor": [17, 32], "xnu_model": [17, 32], "xnue": [17, 32], "xquartz": 2, "xt3": [13, 42], "xwell_sa": [17, 32], "y": [30, 32, 34, 42], "yann": 28, "year": [11, 13, 28], "yearli": 17, "yield": 13, "york": 42, "you": [0, 4, 8, 17, 30], "your": [8, 9, 17, 41], "z": [10, 22, 34, 38, 39, 42], "z0": 22, "z_": [6, 17, 18, 23, 24, 30, 32, 38, 39], "z_0": [5, 10, 18, 22], "z_1": [5, 22], "z_2": [5, 22], "z_3": [5, 22], "z_a": 26, "z_c": 16, "z_e": 38, "z_eff": 18, "z_i": 38, "zeeland": 42, "zeff": [17, 32], "zeng": 42, "zero": [5, 13, 22, 30, 32, 39], "zeroth": [22, 24, 26, 39], "zeta": [6, 10, 17, 18, 23, 30, 32], "zeta_loc": [17, 32], "zf": 30, "zf_test_mod": 6, "zhang": 42, "zhu": 42, "zmag": [6, 10, 18], "zmag_over_a": [10, 17, 23], "zmaj_loc": [17, 32], "zonal": [5, 6, 13, 30, 42], "zoom": 41, "zs_1": [17, 32], "\u03b1": 42}, "titles": ["Build on your laptop", "Ubuntu/Mint", "OSX Sonoma", "CGYRO", "FAQ", "Alphabetical list for input.cgyro", "Tabular list for input.cgyro", "CGYRO output files", "Running Cases", "Download and user agreement", "FLUX-SURFACE GEOMETRY", "GYRO", "Gallery of classic GYRO images (circa 2003)", "Gyrokinetic Simulation in the 2000s", "Alphabetical list for input.gyro", "Tabular list for input.gyro", "GYRO verification and validation (pre 2010)", "The General Atomics GACODE Suite", "input.gacode", "GACODE License", "Miscellaneous", "NEO", "Alphabetical list for input.neo", "Parameters for input.neo", "NEO Output Files", "profiles_gen", "PLASMA ROTATION THEORY", "Prebuilt Environments", "DIII-D L-mode shortfall", "TGLF", "Alphabetical list for input.tglf", "Alphabetical list for out.tglf files", "Table of inputs and outputs", "TGYRO", "Equations solved in TGYRO", "OUTPUT", "PLOT", "Scenarios and connection to energy sources", "TGYRO solver algorithm", "input.tgyro Alphabetical List", "input.tgyro Tabular List", "CGYRO Workshop 2022", "References"], "titleterms": {"": [5, 32], "2000": 13, "2001": 16, "2002": 13, "2003": [12, 13], "2004": [13, 16], "2005": 13, "2006": [13, 16], "2007": 13, "2008": 13, "2009": [13, 16], "2010": 16, "2013": 28, "2022": 41, "25": 28, "A": 13, "BES": 16, "The": [13, 17, 26], "_scale": 22, "abstract": 16, "access": 9, "acknowledg": 28, "ad": 28, "adiabat": 16, "adiabatic_elec": 30, "advanc": 6, "against": 29, "agenda": 41, "agreement": 9, "algorithm": 38, "alpha": 32, "alpha_": 30, "alpha_mach": 30, "alpha_p": 30, "alpha_quench": 30, "alpha_sa": 30, "alpha_zf": 30, "alphabet": [5, 14, 22, 30, 31, 39], "amp": 5, "amp0": 5, "amp_phi_n": 14, "aniso_model_": 22, "anomal": 16, "appropri": [9, 42], "ar": 13, "as_1": 30, "ask": 3, "atom": 17, "b_model_sa": 30, "balanc": 26, "base": 16, "basi": 26, "batch": 8, "benchmark": 28, "beta": 30, "beta_star": 22, "beta_star_scal": 5, "betae_unit": 5, "betae_unit_scal": 5, "bound": 10, "box": 10, "box_siz": 5, "brief": 3, "btccw": [5, 22], "build": 0, "c": 16, "can": 13, "case": [3, 8, 16], "cer": 16, "cgyro": [3, 5, 6, 7, 41], "chang": 32, "circa": 12, "classic": 12, "code": [0, 3, 9, 13, 17, 28], "coeffici": 16, "collis": 6, "collision_ene_diffus": 5, "collision_ene_restor": 5, "collision_field_model": 5, "collision_kperp": 5, "collision_model": [5, 22], "collision_mom_restor": 5, "collision_precision_mod": 5, "command": 8, "comment": 38, "common": 7, "comparison": 16, "compression": 16, "comput": [13, 38], "concept": 0, "connect": [26, 34, 37], "consider": 26, "consist": 26, "control": [6, 15, 32, 40], "coordin": 10, "correctli": 13, "cpu": 27, "cross": 28, "cyclon": 16, "d": [16, 28], "data": [3, 7, 16, 21, 26, 29, 33], "deby": 30, "debye_factor": 30, "delta": [5, 22], "delta_loc": 30, "delta_t": 5, "delta_t_method": 5, "dens_": [5, 22], "densiti": 34, "density_spectrum": 31, "depend": [7, 23], "descript": [3, 24], "design": 13, "detail": 24, "diagnost": 16, "differ": 13, "diii": [16, 28], "discret": 38, "dissip": 6, "dlnndr_": [5, 22], "dlnndre_ad": 22, "dlntdr_": [5, 22], "dlntdr_para_": 22, "dlntdr_perp_": 22, "dlntdre_ad": 22, "doppler": 16, "download": 9, "dphi0dr": 22, "dramat": 13, "drmajdx_loc": 30, "drmindx_loc": 30, "dzmag": 5, "dzmajdx_loc": 30, "e_max": 5, "effect": [10, 13, 23], "eigenvalue_spectrum": 31, "electromagnet": 16, "electron": 16, "energet": 16, "energi": [34, 37], "environ": [0, 27], "epar0": 22, "epar0_spitz": 22, "equat": [33, 34], "equil": 24, "equilibria": 10, "equilibrium": [17, 23], "equilibrium_model": [5, 22], "error_tol": 5, "etg_factor": 30, "eulerian": 13, "exampl": 8, "exp_norm": 24, "experiment": [24, 26, 28, 29], "extra": 23, "f": 24, "faq": 4, "fast": 16, "feedback": 40, "field": [6, 10], "field_print_flag": 5, "field_spectrum": 31, "file": [0, 6, 7, 18, 24, 31, 32], "filter": 30, "find_width": 30, "first": 0, "flux": [10, 34], "forc": 26, "formal": 26, "formul": 38, "freq_tol": 5, "frequent": 3, "from": 13, "ft_model_sa": 30, "full": 13, "futur": 3, "ga": 27, "gacod": [17, 18, 19], "galleri": 12, "gamma_": 5, "gamma_e_scal": 5, "gamma_p": 5, "gamma_p_scal": 5, "gaussian": 32, "gchat": 30, "gener": [17, 23], "geo_ni": 22, "geo_yin": 22, "geometri": [6, 10, 17, 23, 32], "geometry_flag": 30, "gflux_print_flag": 5, "ghat": 30, "gkw": 28, "global": [6, 13, 16], "gpu": 27, "gpu_bigmem_flag": 5, "gradb_factor": 30, "gradient": 16, "grid": [24, 38], "gyro": [11, 12, 14, 15, 16, 28], "gyrobohm": 13, "gyrokinet": [13, 16], "h_print_flag": 5, "have": 13, "high": 40, "histori": [13, 25], "ibranch": 30, "iflux": 30, "imag": [3, 12], "impur": 16, "inadequ": 13, "independ": 7, "input": [3, 5, 6, 14, 15, 18, 21, 22, 23, 26, 30, 32, 33, 39, 40], "intensity_spectrum": 31, "interfac": [23, 33], "ipccw": [5, 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": 5, "n_global": 5, "n_radial": [5, 22], "n_speci": [5, 22], "n_theta": [5, 22], "n_toroid": 5, "n_xi": [5, 22], "nbasis_max": 30, "nbasis_min": 30, "ne_ad": 22, "necessari": 13, "neo": [21, 22, 23, 24], "nersc": 27, "new_eikon": 30, "nky": 30, "nmode": 30, "nonaxisymmetr": 23, "nonlinear": 13, "nonlinear_flag": 5, "normal": [3, 7, 21], "nsts_crossphase_spectrum": 31, "nu_1": 22, "nu_e": 5, "nu_glob": 5, "numer": [6, 23], "nup_alpha": 5, "nup_radi": 5, "nup_theta": 5, "nwidth": 30, "nxgrid": 30, "omega": 27, "omega_rot": 22, "omega_rot_deriv": 22, "openbla": 0, "optim": 6, "orient": 10, "osx": 2, "out": [24, 31], "output": [3, 6, 7, 21, 24, 32, 33, 35], "overview": [11, 18, 25, 28, 29, 33], "own": 32, "p_prime_loc": 30, "parallel": 13, "paramet": [6, 10, 15, 23, 26, 32, 40], "park": 30, "particl": 16, "past": 3, "pci": 16, "perlmutt": 27, "perspect": 13, "perturb": 16, "phi": 24, "physic": [6, 17, 23, 26, 40], "plasma": [6, 17, 23, 26], "platform": 0, "plot": [3, 33, 36], "power": 34, "pre": 16, "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, "synthet": 16, "tabl": [10, 32], "tabular": [6, 15, 40], "taus_1": 30, "te_ad": 22, "temp_": [5, 22], "temp_para_": 22, "temp_perp_": 22, "temperatur": 16, "temperature_spectrum": 31, "tglf": [29, 30, 31, 32], "tgyro": [33, 34, 38, 39, 40], "tgyro_den_method": 39, "tgyro_iteration_method": 39, "tgyro_mod": 39, "tgyro_neo_method": 39, "tgyro_relax_iter": 39, "tgyro_therm_flag": 39, "tgyro_write_profiles_flag": 39, "theoret": 26, "theori": [24, 26], "theory_nclass": 24, "theta0_sa": 30, "theta_plot": 5, "theta_trap": 30, "threed_exb_dphi0dr": 22, "threed_exb_model": 22, "threed_model": 22, "time": [6, 7], "tokamak": 16, "tore": 16, "toroidals_per_proc": 5, "toru": 13, "transport": [13, 16, 24, 33, 34], "transport_exp": 24, "transport_flux": 24, "transport_gv": 24, "turbul": 16, "ubuntu": 1, "udsymmetry_flag": 5, "ul1": 13, "ul2": 13, "ul3": 13, "ul4": 13, "unit": [30, 38], "up_alpha": 5, "up_radi": 5, "up_theta": 5, "upwind_single_flag": 5, "urban": 13, "usag": 8, "use_bisect": 30, "use_bp": 30, "use_bpar": 30, "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
+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"]], "Alphabetical list for input.neo": [[22, "alphabetical-list-for-input-neo"]], "Alphabetical list for input.tglf": [[30, "alphabetical-list-for-input-tglf"]], "Alphabetical list for out.tglf files": [[31, "alphabetical-list-for-out-tglf-files"]], "Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation": [[16, "anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation"]], "Appropriate References": [[9, "id6"], [42, "id146"]], "BETAE": [[30, "betae"]], "BETAE_UNIT": [[5, "betae-unit"]], "BETAE_UNIT_SCALE": [[5, "betae-unit-scale"]], "BETA_STAR": [[22, "beta-star"]], "BETA_STAR_SCALE": [[5, "beta-star-scale"]], "BOX_SIZE": [[5, "box-size"]], "BTCCW": [[5, "btccw"], [22, "btccw"]], "B_MODEL_SA": [[30, "b-model-sa"]], "Batch submission": [[8, "batch-submission"]], "Bounding-box method": [[10, "bounding-box-method"]], "Brief description": [[3, "brief-description"]], "Build on your laptop": [[0, "build-on-your-laptop"]], "Building": [[0, "building"]], "CGYRO": [[3, "cgyro"]], "CGYRO Normalization": [[3, "id8"]], "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_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"]], "Clebsch coordinates": [[10, "clebsch-coordinates"]], "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"]], "Cross-code benchmarking results": [[28, "cross-code-benchmarking-results"]], "Cyclone Base Case with Adiabatic Electrons (2001)": [[16, "cyclone-base-case-with-adiabatic-electrons-2001"]], "DEBYE": [[30, "debye"]], "DEBYE_FACTOR": [[30, "debye-factor"]], "DELTA": [[5, "delta"], [22, "delta"]], "DELTA_LOC": [[30, "delta-loc"]], "DELTA_T": [[5, "delta-t"]], "DELTA_T_METHOD": [[5, "delta-t-method"]], "DENS_*": [[5, "dens"], [22, "dens"]], "DIII-D L-mode shortfall": [[28, "diii-d-l-mode-shortfall"]], "DLNNDRE_ADE": [[22, "dlnndre-ade"]], "DLNNDR_*": [[5, "dlnndr"], [22, "dlnndr"]], "DLNTDRE_ADE": [[22, "dlntdre-ade"]], "DLNTDR_*": [[5, "dlntdr"], [22, "dlntdr"]], "DLNTDR_PARA_*": [[22, "dlntdr-para"]], "DLNTDR_PERP_*": [[22, "dlntdr-perp"]], "DPHI0DR": [[22, "dphi0dr"]], "DRMAJDX_LOC": [[30, "drmajdx-loc"]], "DRMINDX_LOC": [[30, "drmindx-loc"]], "DZMAG": [[5, "dzmag"]], "DZMAJDX_LOC": [[30, "dzmajdx-loc"]], "Data input": [[3, "data-input"], [21, "data-input"], [33, "data-input"]], "Data output": [[21, "data-output"]], "Data output and plotting": [[3, "data-output-and-plotting"]], "Data output, python interface, and plotting": [[33, "data-output-python-interface-and-plotting"]], "Density Transport": [[34, "density-transport"]], "Density fluxes and sources": [[34, "id2"]], "Design History": [[13, "design-history"]], "Detailed description of NEO output files": [[24, "detailed-description-of-neo-output-files"]], "Download and user agreement": [[9, "download-and-user-agreement"]], "EPAR0": [[22, "epar0"]], "EPAR0_SPITZER": [[22, "epar0-spitzer"]], "EQUILIBRIUM_MODEL": [[5, "equilibrium-model"], [22, "equilibrium-model"]], "ERROR_TOL": [[5, "error-tol"]], "ETG_FACTOR": [[30, "etg-factor"]], "EXPERIMENTAL profiles": [[28, "experimental-profiles"]], "E_MAX": [[5, "e-max"]], "Effective field": [[10, "effective-field"]], "Electron Temperature Gradient Turbulence (2006)": [[16, "electron-temperature-gradient-turbulence-2006"]], "Energetic particle transport coefficients (2009)": [[16, "energetic-particle-transport-coefficients-2009"]], "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 orientation": [[10, "magnetic-field-orientation"]], "Miller geometry parameters": [[32, "id4"]], "Miscellaneous": [[20, "miscellaneous"]], "Momentum Transport": [[34, "momentum-transport"]], "Momentum fluxes and sources": [[34, "id4"]], "NBASIS_MAX": [[30, "nbasis-max"]], "NBASIS_MIN": [[30, "nbasis-min"]], "NEO": [[21, "neo"]], "NEO Output Files": [[24, "neo-output-files"]], "NERSC PERLMUTTER (CPU)": [[27, "nersc-perlmutter-cpu"]], "NERSC PERLMUTTER (GPU)": [[27, "nersc-perlmutter-gpu"]], "NEW_EIKONAL": [[30, "new-eikonal"]], "NE_ADE": [[22, "ne-ade"]], "NKY": [[30, "nky"]], "NMODES": [[30, "nmodes"]], "NONLINEAR_FLAG": [[5, "nonlinear-flag"]], "NS": [[30, "ns"]], "NUP_ALPHA": [[5, "nup-alpha"]], "NUP_RADIAL": [[5, "nup-radial"]], "NUP_THETA": [[5, "nup-theta"]], "NU_1": [[22, "nu-1"]], "NU_EE": [[5, "nu-ee"]], "NU_GLOBAL": [[5, "nu-global"]], "NWIDTH": [[30, "nwidth"]], "NXGRID": [[30, "nxgrid"]], "N_ENERGY": [[5, "n-energy"], [22, "n-energy"]], "N_FIELD": [[5, "n-field"]], "N_GLOBAL": [[5, "n-global"]], "N_RADIAL": [[5, "n-radial"], [22, "n-radial"]], "N_SPECIES": [[5, "n-species"], [22, "n-species"]], "N_THETA": [[5, "n-theta"], [22, "n-theta"]], "N_TOROIDAL": [[5, "n-toroidal"]], "N_XI": [[5, "n-xi"], [22, "n-xi"]], "Nonaxisymmetric effects": [[23, "id6"]], "Normalization": [[3, "normalization"], [21, "normalization"]], "Numerical Dissipation": [[6, "id6"]], "Numerical Resolution": [[6, "id5"]], "Numerical resolution": [[23, "id1"]], "OMEGA_ROT": [[22, "omega-rot"]], "OMEGA_ROT_DERIV": [[22, "omega-rot-deriv"]], "OSX Sonoma": [[2, "osx-sonoma"]], "OUTPUT": [[35, "output"]], "OpenBLAS": [[0, "openblas"]], "Optimization related parameters": [[6, "id13"]], "Output Normalization": [[7, "output-normalization"]], "Output file control": [[6, "id12"]], "Overview": [[11, "overview"], [18, "overview"], [28, "overview"], [29, "overview"], [33, "overview"]], "PARK": [[30, "park"]], "PLASMA ROTATION THEORY": [[26, "plasma-rotation-theory"]], "PLOT": [[36, "plot"]], "PRINT_STEP": [[5, "print-step"]], "PROFILE_DLNNDR_*_SCALE": [[22, "profile-dlnndr-scale"]], "PROFILE_DLNTDR_*_SCALE": [[22, "profile-dlntdr-scale"]], "PROFILE_EQUILIBRIUM_MODEL": [[22, "profile-equilibrium-model"]], "PROFILE_ERAD0_MODEL": [[22, "profile-erad0-model"]], "PROFILE_MODEL": [[5, "profile-model"], [22, "profile-model"]], "PX0": [[5, "px0"]], "P_PRIME_LOC": [[30, "p-prime-loc"]], "Parameters for input.neo": [[23, "parameters-for-input-neo"]], "Past and Future": [[3, "past-and-future"]], "Physical considerations": [[26, "physical-considerations"]], "Physics": [[17, null]], "Physics Control": [[40, "id4"]], "Plasma Rotation": [[17, "plasma-rotation"]], "Plasma equilibrium/geometry": [[23, "id2"]], "Plasma shape/geometry": [[6, "id1"]], "Prebuilt Environments": [[27, "prebuilt-environments"]], "Prehistory": [[13, "prehistory"]], "Profile Feedback Control": [[40, "id3"]], "Profile models": [[23, "id4"]], "Q": [[5, "q"], [22, "q"]], "QL_flux_spectrum": [[31, "ql-flux-spectrum"]], "QUASINEUTRAL_FLAG": [[5, "quasineutral-flag"]], "Q_LOC": [[30, "q-loc"]], "Q_PRIME_LOC": [[30, "q-prime-loc"]], "Q_SA": [[30, "q-sa"]], "Quick links": [[11, "quick-links"], [21, "quick-links"], [29, "quick-links"], [33, "quick-links"]], "Quick-start example": [[8, "quick-start-example"]], "RESTART_STEP": [[5, "restart-step"]], "RHO_STAR": [[22, "rho-star"]], "RLNS_1": [[30, "rlns-1"]], "RLTS_1": [[30, "rlts-1"]], "RMAJ": [[5, "rmaj"]], "RMAJ_LOC": [[30, "rmaj-loc"]], "RMAJ_OVER_A": [[22, "rmaj-over-a"]], "RMAJ_SA": [[30, "rmaj-sa"]], "RMIN": [[5, "rmin"]], "RMIN_LOC": [[30, "rmin-loc"]], "RMIN_OVER_A": [[22, "rmin-over-a"]], "RMIN_OVER_A_2": [[22, "rmin-over-a-2"]], "RMIN_SA": [[30, "rmin-sa"]], "ROTATION_MODEL": [[5, "rotation-model"], [22, "rotation-model"]], "References": [[42, "references"]], "References: TGLF saturation models": [[29, "id9"]], "References: TGLF validation against experimental data": [[29, "id10"]], "Repository access": [[9, "repository-access"]], "Restart data": [[7, "id3"]], "Rotation output files": [[24, "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, "silent-flag"], [22, "silent-flag"]], "SIM_MODEL": [[22, "sim-model"]], "SPITZER_MODEL": [[22, "spitzer-model"]], "S_DELTA": [[5, "s-delta"], [22, "s-delta"]], "S_DELTA_LOC": [[30, "s-delta-loc"]], "S_KAPPA": [[5, "s-kappa"], [22, "s-kappa"]], "S_KAPPA_LOC": [[30, "s-kappa-loc"]], "S_ZETA": [[5, "s-zeta"], [22, "s-zeta"]], "S_ZETA_LOC": [[30, "s-zeta-loc"]], "S_ZMAG": [[22, "s-zmag"]], "Scenarios and connection to energy sources": [[37, "scenarios-and-connection-to-energy-sources"]], "Simulation images": [[3, "simulation-images"]], "Software": [[17, null]], "Solution strategy": [[38, "solution-strategy"]], "Some comments regarding units": [[38, "some-comments-regarding-units"]], "Sonic rotation formalism": [[26, "sonic-rotation-formalism"]], "Source Code": [[3, "source-code"]], "Source code": [[0, "source-code"], [9, "source-code"]], "Species Parameters": [[40, "id5"]], "Species Vectors": [[32, "id2"]], "Species-dependent parameters": [[23, "id7"]], "Species-related parameters": [[6, "id8"]], "Standard output files": [[24, "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"]], "TOROIDALS_PER_PROC": [[5, "toroidals-per-proc"]], "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"]], "Toroidal and poloidal flux": [[10, "toroidal-and-poloidal-flux"]], "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 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"]], "UNITS": [[30, "units"]], "UPWIND_SINGLE_FLAG": [[5, "upwind-single-flag"]], "UP_ALPHA": [[5, "up-alpha"]], "UP_RADIAL": [[5, "up-radial"]], "UP_THETA": [[5, "up-theta"]], "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"]], "Ubuntu/Mint": [[1, "ubuntu-mint"]], "Urban Legends": [[13, "urban-legends"]], "VELOCITY_ORDER": [[5, "velocity-order"]], "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"]], "Verification Studies": [[16, "verification-studies"]], "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"]], "Yearly Publication Synopsis": [[13, "yearly-publication-synopsis"]], "ZEFF": [[30, "zeff"]], "ZETA": [[5, "zeta"], [22, "zeta"]], "ZETA_LOC": [[30, "zeta-loc"]], "ZF_TEST_MODE": [[5, "zf-test-mode"]], "ZMAG": [[5, "zmag"]], "ZMAG_OVER_A": [[22, "zmag-over-a"]], "ZMAJ_LOC": [[30, "zmaj-loc"]], "ZS_1": [[30, "zs-1"]], "Z_*": [[5, "z"], [22, "z"]], "Z_EFF": [[5, "z-eff"]], "Z_EFF_METHOD": [[5, "z-eff-method"]], "density_spectrum": [[31, "density-spectrum"]], "eigenvalue_spectrum": [[31, "eigenvalue-spectrum"]], "field_spectrum": [[31, "field-spectrum"]], "input.gacode": [[18, "input-gacode"]], "input.tgyro Alphabetical List": [[39, "input-tgyro-alphabetical-list"]], "input.tgyro Tabular List": [[40, "input-tgyro-tabular-list"]], "intensity_spectrum": [[31, "intensity-spectrum"]], "nsts_crossphase_spectrum": [[31, "nsts-crossphase-spectrum"]], "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.species": [[24, "out-neo-species"]], "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"]], "s-alpha geometry parameters": [[32, "id5"]], "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"]]}, "docnames": ["build", "build/pre_linux", "build/pre_osx", "cgyro", "cgyro/FAQ", "cgyro/cgyro_list", "cgyro/cgyro_table", "cgyro/outputs", "cgyro/running_cases", "download", "geometry", "gyro", "gyro/gyro_gallery", "gyro/gyro_history", "gyro/gyro_list", "gyro/gyro_table", "gyro/gyro_vv", "index", "input_gacode", "license", "misc", "neo", "neo/neo_list", "neo/neo_table", "neo/outputs", "prgen", "rotation", "setup", "shortfall", "tglf", "tglf/tglf_list", "tglf/tglf_output_list", "tglf/tglf_table", "tgyro", "tgyro/equations", "tgyro/output", "tgyro/plot", "tgyro/scenarios", "tgyro/solver", "tgyro/tgyro_list", "tgyro/tgyro_table", "workshop", "zreferences"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinxcontrib.bibtex": 9}, "filenames": ["build.rst", "build/pre_linux.rst", "build/pre_osx.rst", "cgyro.rst", "cgyro/FAQ.rst", "cgyro/cgyro_list.rst", "cgyro/cgyro_table.rst", "cgyro/outputs.rst", "cgyro/running_cases.rst", "download.rst", "geometry.rst", "gyro.rst", "gyro/gyro_gallery.rst", "gyro/gyro_history.rst", "gyro/gyro_list.rst", "gyro/gyro_table.rst", "gyro/gyro_vv.rst", "index.rst", "input_gacode.rst", "license.rst", "misc.rst", "neo.rst", "neo/neo_list.rst", "neo/neo_table.rst", "neo/outputs.rst", "prgen.rst", "rotation.rst", "setup.rst", "shortfall.rst", "tglf.rst", "tglf/tglf_list.rst", "tglf/tglf_output_list.rst", "tglf/tglf_table.rst", "tgyro.rst", "tgyro/equations.rst", "tgyro/output.rst", "tgyro/plot.rst", "tgyro/scenarios.rst", "tgyro/solver.rst", "tgyro/tgyro_list.rst", "tgyro/tgyro_table.rst", "workshop.rst", "zreferences.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [3, 4, 6, 7, 8, 9, 10, 11, 13, 16, 18, 19, 22, 24, 29, 30, 31, 34, 38, 42], "0": [0, 4, 5, 6, 7, 8, 10, 13, 15, 16, 18, 21, 22, 23, 24, 26, 28, 30, 31, 32, 38, 39, 40, 41], "00": [4, 8, 13, 42], "00035": 42, "00079": 42, "001": [5, 6, 22, 23], "0010": 42, "0029": 42, "005": 28, "00am": 41, "01": [4, 5, 6, 13], "012001": 42, "012008": 42, "012043": 42, "012502": 42, "014004": 42, "014505": 42, "015013": 42, "015015": 42, "016": 42, "02": [9, 39], "020": 42, "022305": 42, "022509": 42, "024004": 42, "03": [4, 13, 42], "032301": 42, "032310": 42, "036036": 42, "039": 42, "04": [39, 42], "042001": 42, "045001": 42, "045005": 42, "05": [13, 30, 39, 42], "052301": [28, 42], "055003": 42, "055013": 42, "055908": 42, "055909": 42, "056116": [28, 42], "06": [9, 16, 39, 42], "060704": 42, "060901": [28, 42], "062302": 42, "062518": 42, "066015": 42, "07": [9, 42], "072303": 42, "072304": 42, "072307": 42, "072505": 24, "0741": 42, "074501": 42, "074505": 42, "075018": 42, "08": [13, 28, 39, 42], "09": [8, 9, 13, 16, 28, 42], "095010": 42, "096005": 42, "0_": 38, "0a": 24, "0th": [5, 22], "1": [0, 4, 5, 6, 7, 8, 9, 10, 13, 16, 18, 21, 22, 23, 24, 26, 27, 30, 31, 32, 34, 37, 38, 39, 40, 42], "10": [3, 5, 6, 13, 18, 28, 39, 42], "100": [4, 5, 6, 28], "1000": 5, "1016": 42, "102301": 42, "102306": 42, "102508": 42, "1051": 42, "1063": 42, "1088": 42, "11": [9, 16, 22, 24, 41, 42], "110": 42, "1103": 42, "112007": 42, "1121": 42, "112303": 42, "112503": [28, 42], "113017": 42, "116007": 42, "11am": 41, "12": [30, 32, 42], "1209": 42, "122305": 42, "122306": 42, "122307": [28, 42], "122309": 42, "122503": 42, "122505": [28, 42], "122507": 42, "125": 42, "128": [13, 27, 42], "128913": 28, "13": [29, 42], "1361": 42, "14": [28, 42], "1477": 42, "1493": 24, "15": [5, 6, 28, 42], "1500": 28, "15th": 42, "16": [3, 5, 6, 11, 24, 27, 28, 30, 32, 42], "1695358": 42, "17": [22, 23, 24, 42], "1741": 42, "18": [28, 29, 42], "1800": 29, "186": 42, "1879": 42, "188": 42, "1897": 24, "19": [3, 18, 24, 29, 42], "1938": 42, "195004": 42, "1958": 42, "1973": 24, "1976": 24, "1977": 24, "1982": 24, "1985": 42, "1988": [24, 42], "1990": 13, "1991": 42, "1993": 42, "1994": [13, 42], "1995": 42, "1996": 42, "1997": [24, 42], "1998": 42, "1999": [13, 24, 42], "1_": 38, "1e": [5, 6, 14, 15], "1st": [5, 22], "1th": [5, 22], "2": [0, 4, 5, 6, 7, 8, 9, 10, 13, 16, 18, 21, 22, 23, 24, 26, 27, 30, 31, 32, 34, 37, 38, 39, 40, 42], "20": [24, 29, 30, 42], "2000": [11, 17, 42], "2001": [13, 42], "2002": 42, "2003": [11, 16, 17, 42], "2004": 42, "2005": [25, 42], "2006": 42, "2007": 42, "2008": [28, 42], "2009": [28, 42], "2010": [11, 17, 25, 42], "2011": [28, 42], "2012": [24, 28, 42], "2013": [9, 17, 42], "2014": [28, 42], "2016": [28, 42], "2017": 42, "2018": [9, 19, 42], "2019": [30, 42], "2020": 42, "2021": 42, "2022": [17, 20, 42], "21": [28, 29, 30, 32, 42], "2107": 42, "22": [29, 30, 42], "2229": 42, "23": [28, 42], "239": 24, "24": [3, 5, 6, 30, 41], "2408": 42, "2433": 42, "2436852": 42, "2482": 42, "25": [17, 24, 30, 32, 41, 42], "256": 27, "2560": 42, "26": 42, "265": 42, "27": [21, 22, 24, 28], "273": 42, "28": 42, "2834": 24, "2889008": 42, "2d": 22, "2m": 22, "2nd": [5, 6, 22, 32], "2t_e": 5, "2th": [5, 22], "3": [2, 3, 5, 6, 9, 10, 13, 16, 18, 21, 22, 23, 24, 30, 32, 34, 37, 38, 39, 42], "30": [24, 28, 42], "300": 13, "3082": 42, "310": 2, "32": [5, 22, 27], "3211": 42, "3230": 24, "324": 42, "32664": 42, "33": 42, "3335": 42, "3412": 42, "345": 3, "3452e": [21, 22], "356": 42, "384": 39, "3d": [22, 23], "3rd": [5, 6, 13, 22], "4": [0, 4, 5, 6, 9, 13, 14, 15, 16, 22, 23, 24, 27, 30, 32, 39, 42], "40": 42, "400": 16, "4018": 42, "4046": 42, "405": 24, "418": 24, "43": 42, "4326": 42, "44577e": 4, "448": 42, "45": 42, "45am": 41, "4655": 42, "47th": 42, "48": [24, 42], "49": 42, "4904301": 42, "4954905": 42, "4th": 22, "5": [5, 6, 9, 13, 16, 22, 23, 24, 28, 30, 32, 39, 42], "50": [28, 42], "500": 29, "51": 42, "512": 8, "53": 42, "54": 42, "545": 42, "5515": 42, "5579": 42, "56": 42, "58644e": 4, "59": [27, 42], "5th": [5, 28], "6": [4, 5, 13, 16, 22, 23, 24, 39, 42], "60": 16, "61": 42, "62": 42, "63": 42, "64": [0, 5], "65": [30, 32], "6587": 42, "667": 42, "6th": 13, "7": [4, 5, 16, 24, 30, 32], "71": 42, "724": 42, "724e": 5, "73": 42, "741": 42, "744": 42, "74754e": 4, "75": [13, 16, 28, 39], "77": 42, "78": 42, "8": [0, 4, 5, 6, 22, 24, 27, 42], "80": 42, "812": 42, "81550e": 4, "83": 29, "836": 24, "84003e": 4, "85": 42, "865350": 42, "88": 42, "9": [41, 42], "900": 16, "91": 42, "92020e": 4, "94": [13, 42], "95": 42, "96": 29, "97": [13, 42], "9991": 42, "9am": 41, "9i4": 42, "A": [3, 5, 8, 16, 17, 19, 21, 24, 28, 31, 38, 42], "AND": 19, "AS": [9, 19], "AT": 9, "As": [3, 13, 16, 26], "At": [13, 16], "BE": 19, "BES": 13, "BUT": 19, "By": [9, 10, 13, 25, 26, 29, 39], "FOR": 19, "For": [4, 5, 10, 11, 13, 14, 16, 18, 21, 22, 24, 26, 30, 32, 39], "IN": 19, "If": [0, 5, 9, 19, 22, 26, 38, 39], "In": [0, 5, 10, 13, 16, 21, 22, 24, 26, 29, 33, 38, 39, 42], "It": [0, 3, 5, 7, 8, 11, 16, 22, 26, 38, 39], "NO": 19, "NOT": [4, 19], "No": [5, 23, 39], "OF": 19, "ON": 5, "OR": 19, "Of": 22, "On": [5, 8, 13, 38], "One": 13, "THE": 19, "TO": 19, "The": [3, 4, 5, 8, 9, 10, 16, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 38, 39, 42], "Then": [4, 38], "There": [0, 5, 13, 16, 17, 18], "These": [4, 13, 18, 23, 24, 28], "To": [0, 4, 5, 8, 9, 12, 13, 18, 19, 27, 38, 39], "WITH": 19, "With": [13, 22, 29], "_": [5, 10, 21, 22, 24, 26, 30, 31, 32, 38], "_0": 26, "_1": [22, 26], "_ade": 22, "_deriv": 22, "_dlnndr": 22, "_dlntdr": 22, "_dphi0dr": 22, "_energi": 24, "_exb": 22, "_in": 21, "_model": 23, "_p": 39, "_para": 22, "_perp": 22, "_r": 22, "_radial": 24, "_relax": 39, "_rot": 22, "_rp": 22, "_scale": [17, 23], "_scenario": 37, "_size": 5, "_speci": 24, "_spitzer": 22, "_theta": 24, "_xi": 24, "_z": 22, "_zp": 22, "a_": [5, 7, 14, 24, 30, 32], "ab": [30, 32], "ab759c": 42, "abc63b": 42, "abc861": 42, "abil": [3, 13, 25, 33], "abl": 13, "about": [10, 13, 16, 17, 18, 22, 27], "abov": [5, 8, 9, 10, 19, 22, 26, 28, 38], "absenc": 5, "absent": 13, "absolut": [16, 30, 32], "absorb": [3, 11], "abstract": 17, "ac": 42, "ac243a": 42, "ac592b": 42, "ac7a4d": 42, "acb20": [10, 18, 42], "acceler": 5, "accept": 8, "access": 17, "accord": [10, 26], "accordingli": 8, "account": 9, "accur": [13, 28, 29, 38], "accuraci": [5, 13, 16, 21, 29, 42], "achiev": [13, 16], "acknowledg": 17, "acm": 42, "acquisit": 13, "across": [4, 13, 24, 28, 42], "action": 19, "activ": [5, 13, 22], "actual": [13, 16], "ad": [3, 8, 11, 13, 16, 17, 18, 22, 24], "adapt": [4, 5, 41], "add": 27, "addit": [8, 13, 21, 22, 24, 26, 30, 33], "address": 16, "adequ": 13, "adiabat": [13, 22, 23, 24, 28, 30, 32], "adiabatic_elec": [17, 32], "adjust": [30, 32, 39], "adopt": [3, 38], "advanc": [13, 16, 42], "advantag": 13, "ae": 13, "affect": [13, 22, 39], "after": [0, 5, 13, 16, 38], "against": [13, 16, 28], "agenda": 17, "agre": [9, 16], "agreement": [13, 16, 17, 19, 29], "agt": [29, 42], "al": [24, 28], "alam": 42, "alcat": [16, 42], "alfv\u00e9n": 13, "algorithm": [3, 11, 13, 17, 33], "align": [4, 10, 24, 26, 30, 37, 38], "alik": 13, "all": [3, 4, 5, 8, 9, 11, 13, 16, 18, 19, 22, 24, 26, 28, 30, 31, 32, 39, 40], "allow": [5, 13, 16, 18, 22, 23, 26, 30, 32, 39], "almost": 0, "along": [5, 10, 22, 29, 30], "alpha": [4, 5, 10, 13, 16, 22, 24, 29, 30, 34, 39, 42], "alpha_": [17, 31, 32], "alpha_mach": [17, 32], "alpha_p": [17, 32], "alpha_quench": [17, 31, 32], "alpha_sa": [17, 32], "alpha_zf": [17, 31, 32], "alphabet": [3, 11, 17, 21, 29, 33], "also": [5, 8, 10, 11, 13, 16, 17, 21, 22, 25, 28, 29, 33, 38], "altern": [26, 28], "although": [3, 13, 28, 33], "altix": 13, "alwai": [5, 13, 24, 26, 39], "am": 42, "ambigu": 13, "ambipolar": 24, "among": [13, 16], "amount": [13, 30, 39, 40], "amp": 6, "amp0": 6, "amp_phi_n": [15, 17], "amper": 13, "amplifi": 26, "amplitud": [5, 6, 13, 14, 15, 30, 31, 32], "an": [0, 3, 4, 5, 8, 13, 16, 18, 19, 21, 22, 25, 26, 29, 30, 38, 39, 42], "analog": 13, "analogi": 26, "analys": 26, "analysi": [13, 26, 28, 41, 42], "analyt": [21, 22, 23, 24], "analyz": 13, "angioni": [16, 42], "angl": [5, 6, 10, 22, 24, 26, 28], "angular": [13, 22, 23, 24, 26, 32, 34, 42], "ani": [5, 9, 19, 28, 30, 38, 39], "aniso": [23, 24], "aniso_model_": [17, 23], "aniso_model_1": 22, "aniso_model_2": 22, "aniso_model_3": 22, "anisotrop": [22, 23, 24], "anisotropi": 16, "anomal": 42, "anomali": 16, "anti": [10, 30], "antisymmetr": [5, 6, 22], "apart": 13, "app": [16, 42], "appar": 16, "appear": [13, 26], "append": 21, "appli": [5, 13, 26, 38], "applic": [13, 16, 28, 42], "approach": [3, 11], "appropri": 19, "approxim": [10, 13, 21, 26, 30, 38, 39], "apt": 1, "ar": [3, 4, 5, 8, 9, 10, 11, 16, 17, 18, 19, 21, 22, 23, 24, 26, 28, 29, 30, 33, 38, 39], "arash": 41, "arbitrari": [4, 18, 21, 22, 23, 38], "arbon": 42, "architechtur": 42, "area": [9, 34, 42], "aris": [19, 26, 39], "around": 26, "arrai": [5, 22, 23, 24, 30, 32], "arrow": 26, "articl": [9, 19, 28], "artifici": [4, 13], "artun": 42, "as_1": [17, 32], "ascii": [24, 28], "asdex": [29, 42], "ash": [13, 39, 42], "ashourvan": 41, "ask": 17, "aspect": [3, 11, 22, 29], "assess": 39, "associ": [16, 19, 22, 24, 28, 38], "assum": [22, 24, 30], "assumpt": [30, 38], "asymmetr": [18, 24], "asymmetri": [21, 22, 24, 26, 28], "asymptot": [13, 21], "atom": [3, 8, 12, 13, 27, 42], "attempt": [13, 16], "attend": 13, "attent": [8, 38], "attenu": 16, "attribut": 12, "austin": 42, "author": [9, 19], "auto": [8, 10], "autodetect": 4, "automat": 5, "aux": [34, 37], "auxiliari": [34, 39], "avail": [3, 5, 9, 13, 19, 22, 23, 28], "availbl": 28, "averag": [5, 13, 16, 22, 24, 26, 28, 34, 42], "avoid": 30, "axi": [31, 42], "axisymmetr": [22, 26, 42], "azevedo": 42, "b": [5, 6, 10, 13, 14, 16, 22, 24, 26, 30, 31, 32, 42], "b_": [4, 5, 7, 10, 14, 16, 22, 24, 30, 31, 32], "b_model_sa": [17, 32], "b_p": [5, 18, 22, 26], "b_t": [5, 22, 26], "balanc": [13, 17, 39, 40, 42], "ball": [8, 41], "balloon": [5, 29, 30, 32, 42], "banana": 26, "bar": [13, 16, 28], "barn": [28, 42], "barrier": [13, 25, 26, 29], "base": [5, 9, 13, 19, 22, 25, 28, 33, 39, 42], "baselin": 42, "bashrc": 27, "basi": [17, 22, 28, 30, 32, 38], "basic": 16, "bc08": [3, 9, 21, 26, 42], "bc09": [21, 26, 42], "bc12": [3, 9, 21, 42], "bc17": [3, 11, 42], "bc18": [3, 11, 42], "bcbh11": [28, 42], "beam": [16, 18, 26, 34, 42], "becam": 25, "becaus": [5, 26, 38, 39], "becom": [3, 10, 11, 26], "been": [10, 13, 16, 21, 28, 29, 38], "beer": [13, 42], "befor": 13, "began": 13, "begin": [4, 23, 24, 26, 37, 38], "begun": 13, "behav": 16, "behaviour": 39, "being": [5, 13, 31, 32], "believ": [13, 26], "belli": [3, 42], "below": [9, 10, 13, 16, 24, 26, 27, 28, 30, 34], "benchamark": 21, "benchmark": [13, 16, 17, 29], "berlin": 42, "beta": [5, 6, 13, 17, 22, 32, 39, 40, 42], "beta_": [4, 5, 10, 22], "beta_star": [10, 17, 23], "beta_star_scal": [6, 10], "betae_unit": [6, 10, 41], "betae_unit_scal": 6, "better": [5, 29], "between": [4, 5, 13, 16, 24, 25, 28, 29, 38], "beyond": 21, "bf": [10, 22], "bh96a": [13, 42], "bh96b": [13, 42], "bin": [0, 5, 7, 27], "binari": [0, 7], "binorm": [5, 6], "bisect": [30, 32], "bit": 5, "black": 16, "block": 38, "blue": [10, 16], "bogacki": 5, "bohm": [13, 16, 31, 32, 42], "bonanomi": 42, "bootstrap": [18, 24], "both": [5, 10, 13, 16, 25, 26, 29, 30, 32, 38, 41], "bottino": 42, "bounc": 42, "bound": [17, 22], "boundari": [3, 10, 11, 13, 22, 30, 32, 38], "box": [5, 17, 41], "box_siz": 6, "bpar": 30, "bracket": 26, "bravenec": [13, 28, 42], "breadth": 5, "break": 13, "bremsstrahlung": 18, "brief": [11, 17, 33], "bring": 16, "broad": 13, "broken": 42, "bt": 22, "btccw": [6, 10, 17, 23], "build": [13, 17, 30], "bull": 42, "bunit": 4, "burden": 8, "burrel": 42, "byer": 42, "c": [4, 7, 13, 18, 22, 24, 26, 28, 42], "c1": 39, "c2": 39, "c3": 39, "c4": 39, "c5": 39, "c6": 39, "c_": [3, 5, 7, 16, 24, 26, 28, 30, 32, 38, 39], "c_0": 10, "c_1": 10, "c_2": 10, "c_3": 10, "c_i": 26, "c_n": 10, "ca": 42, "cal": [26, 38], "calcul": [3, 13, 21, 24, 25, 28, 29, 34, 39, 40, 42], "calibr": [3, 11, 30], "call": [6, 13, 21, 25, 28, 30, 32, 33], "callen": 42, "camenen": 28, "can": [0, 4, 5, 8, 10, 16, 17, 18, 21, 22, 26, 28, 30, 38, 39], "can05": [13, 42], "cancel": [13, 26], "candi": [3, 12, 16, 28, 42], "cannot": [13, 26], "capabl": [13, 16, 38], "captur": [21, 30], "carbon": [5, 16], "carefulli": 13, "carri": [13, 16, 18, 26], "carrington": 42, "carter": 42, "casati": 16, "case": [5, 10, 11, 13, 17, 21, 22, 24, 26, 27, 28, 30, 38, 39], "cash": 5, "casson": 42, "cat": 18, "caus": [26, 30], "caution": 30, "cb10": [3, 10, 11, 42], "cb18": [3, 11, 42], "cbb16": [3, 4, 9, 11, 42], "cbs20": [3, 42], "cc": 13, "ccw": [30, 32], "cd": [0, 8], "cdot": [10, 22, 26], "cece": 13, "cell": [13, 28, 42], "center": [5, 13, 22, 24], "central": [28, 29], "centrifug": [21, 26, 42], "centroid": [30, 32], "cer": 28, "certain": 13, "cg": 38, "cgyro": [0, 4, 8, 9, 10, 11, 17, 18, 20, 21, 26, 27, 30, 33, 34, 39, 42], "cgyro_plot": 8, "ch": 24, "chain": 34, "challeng": 25, "chang": [5, 9, 19, 22, 24, 29, 30, 39], "character": [3, 11, 13, 42], "characterist": 28, "charg": [5, 6, 18, 19, 22, 23, 24, 30, 32], "chassi": 13, "check": [13, 22, 41], "chen": 42, "chi": [10, 29], "chi_": 16, "chi_e": [16, 29], "chi_i": 16, "chi_t": 10, "choic": [5, 22, 30, 39], "choos": [5, 7, 10], "chowdhuri": [28, 42], "chri": 28, "chw": [9, 42], "circa": [11, 17, 25], "circl": [10, 16], "circul": 13, "circular": [10, 29], "circumst": 26, "citat": [9, 29, 42], "cj": 24, "claim": [13, 19], "clarifi": [13, 16, 26], "classic": [5, 11, 17], "clean": 0, "clear": [13, 25], "clebsch": 17, "clock": 27, "clockwis": [5, 10, 22], "clone": [0, 9], "close": [8, 13, 16, 38], "closur": [30, 32], "cluster": 13, "cm": [34, 38], "cmat": 5, "co": [10, 13, 24], "coars": [13, 39], "code": [4, 11, 16, 19, 21, 22, 24, 25, 26, 27, 29, 33, 39, 41, 42], "coeffici": [7, 13, 22, 23, 24, 26, 30], "cohen": 42, "col": [24, 34], "collabor": 28, "collect": 17, "collis": [3, 4, 5, 13, 21, 22, 23, 24, 28, 30, 32, 42], "collision": [3, 5, 11, 13, 21, 24, 28, 34, 39, 42], "collision_ene_diffus": 6, "collision_ene_restor": 6, "collision_field_model": 6, "collision_kperp": 6, "collision_model": [6, 17, 23], "collision_mom_restor": 6, "collision_precision_mod": 6, "collisionless": 5, "colloc": 22, "colorado": 16, "column": [18, 31], "com": [0, 9, 19, 41], "combin": [13, 24, 26], "command": [0, 2, 18], "comment": [5, 14, 17, 18, 22, 23, 28, 30, 31, 39], "commment": [5, 22], "commod": 13, "common": [27, 28, 30, 32], "commonli": 13, "commun": [3, 5, 6, 11, 13, 16, 42], "compar": [13, 16, 28, 29, 33, 39, 42], "comparison": [13, 28, 42], "compars": 16, "compens": 29, "compfluid": 42, "compil": [0, 2, 9, 13, 19], "complement": [3, 11, 21], "complementari": 16, "complet": [0, 3, 11, 16, 21, 26, 27, 28], "complex": 26, "complic": 3, "compon": [6, 24, 38], "comprehens": [13, 34, 42], "compression": [30, 32], "comput": [5, 10, 16, 17, 22, 30, 32, 39, 42], "concentr": [10, 16], "concept": 17, "conceptu": 25, "conclus": 13, "concret": 10, "condit": [3, 9, 10, 11, 13, 16, 19, 22, 38], "conduct": [16, 18], "conf": 42, "confer": [13, 42], "configur": [8, 10], "confin": [28, 29, 42], "confirm": 13, "confront": 13, "connect": [13, 17, 18, 19, 33, 38, 39], "connor": [5, 22], "consequ": 42, "conserv": [5, 6, 13], "consid": 13, "consider": 17, "consist": [5, 6, 13, 17, 24, 39, 42], "constant": [5, 22, 26], "construct": 10, "consult": 10, "contact": 16, "contain": [7, 13, 16, 18, 21, 24, 26], "context": 13, "continu": [13, 39], "continuum": 28, "contour": 10, "contract": 19, "contrast": [16, 29, 42], "contribut": [13, 30, 32], "control": [4, 5, 13, 16, 39, 42], "convect": [16, 18, 24], "conveni": [18, 38], "convent": 10, "converg": [5, 13, 28, 38, 42], "coordin": [3, 5, 7, 17, 22, 42], "copi": [0, 5, 9, 19], "copyright": [9, 19], "core": [3, 8, 11, 13, 27, 28, 29, 42], "cori": 41, "corioli": [13, 26], "correct": 13, "correl": [13, 16], "correspond": [5, 10, 16, 21, 22, 39], "corrug": [13, 42], "cosin": [22, 24], "cost": 5, "could": [8, 13], "count": [5, 8], "counter": [5, 10, 22], "counterclockwis": 10, "coupl": [13, 21, 22, 30, 38, 42], "courant": 13, "courtesi": [3, 12], "cover": [3, 11, 16, 30], "cowlei": 42, "cpc": [13, 42], "cpu": [5, 17], "crai": [13, 42], "creat": [0, 13, 25], "crictic": 13, "critic": 26, "cross": [17, 21, 31, 32, 42], "crucial": [13, 16], "csb": [3, 42], "cum": 42, "curiou": 38, "current": [5, 6, 13, 18, 22, 23, 24, 28, 42], "curv": [13, 16], "curvatur": [26, 30, 32, 42], "custom": 41, "cut": [3, 11], "cutoff": [30, 32], "cw03a": [3, 11, 13, 42], "cw03b": [3, 9, 11, 13, 16, 42], "cw06": [13, 42], "cwc": [28, 42], "cwd04": [3, 11, 13, 16, 42], "cwfh07a": [13, 42], "cwfh07b": [13, 42], "cwpc06": [13, 42], "cwr04": [13, 42], "cyclon": 13, "cyclotron": 16, "cylindr": 10, "d": [3, 5, 10, 13, 17, 18, 20, 21, 22, 24, 26, 29, 30, 32, 34, 42], "dai": 41, "damag": 19, "damp": 13, "dannert": 42, "dash": 16, "data": [5, 6, 10, 13, 17, 18, 22, 24, 25, 28, 39], "databas": [3, 11, 13, 29], "dataset": 18, "date": [0, 13, 25, 28, 41], "dcd": [29, 30, 42], "deal": [19, 38], "deby": [6, 17, 32], "debye_factor": [17, 32], "decad": [3, 13], "decid": 25, "decoupl": [13, 39, 40], "decreas": [4, 5, 16], "decyk": 42, "dedic": 27, "deduc": [10, 26], "default": [4, 5, 6, 14, 15, 22, 23, 30, 32, 39, 40], "defin": [5, 10, 21, 22, 24, 26, 30, 32, 33, 38], "defind": 30, "definit": [4, 5, 10, 14, 18, 22, 23, 26, 30, 32, 34, 39], "deform": 10, "delai": 13, "delta": [4, 6, 7, 10, 13, 14, 16, 17, 18, 23, 28, 30, 31, 32, 38, 39, 42], "delta_": [22, 38], "delta_loc": [17, 32], "delta_t": [4, 6], "delta_t_method": [4, 6], "demand": 5, "demonstr": [13, 16, 29], "den": [5, 22], "denot": [13, 26, 38], "dens_": [6, 17, 23], "dens_1": [5, 22], "dens_2": 22, "dens_3": 22, "densiti": [3, 5, 6, 13, 16, 17, 18, 21, 22, 23, 24, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 42], "density_spectrum": [17, 32], "depart": 9, "departur": 13, "depend": [5, 13, 22, 26, 31, 32, 38, 42], "deprec": 32, "depress": 13, "depric": 30, "depth": 5, "deriv": [5, 10, 22, 26, 38], "describ": [13, 17, 26, 38], "descript": [6, 7, 13, 15, 17, 18, 21, 23, 26, 31, 32, 33, 40], "design": [3, 16, 17, 28, 33], "desir": [5, 38], "desktop": 17, "detail": [0, 13, 16, 17, 22, 26, 28, 34, 38, 39], "determin": [5, 22, 23, 38], "dettrick": 42, "deuterium": [3, 5, 21, 22, 24], "dev": 1, "develop": [2, 3, 9, 11, 13, 17, 21, 29, 39], "deviat": [13, 21, 28], "devic": 29, "dh93": [13, 42], "dh95": [16, 42], "dhaesel": 42, "dhcs91": [10, 42], "diagnos": 13, "diagnost": [8, 13, 22, 28, 41, 42], "diagon": [16, 38], "diamagnet": [16, 22, 24, 26], "dickinson": 42, "did": 13, "differ": [22, 24, 28, 30, 31, 32, 34, 38, 39], "differenti": [10, 13], "difficulti": [13, 16], "diffus": [5, 6, 13, 16], "diii": [5, 10, 13, 17, 20, 22, 29, 42], "dimens": [7, 22], "dimension": [13, 24], "dimensionless": [5, 18, 24, 25, 38, 39], "dimit": [13, 42], "dir": 39, "direct": [5, 13, 16, 22, 28, 30, 32, 42], "directli": [7, 22, 38], "directori": 0, "dirichlet": 13, "disabl": 5, "discharg": [13, 16, 28, 29, 42], "disclaim": [9, 19], "discontinu": [13, 42], "discover": 13, "discoveri": 13, "discret": [5, 13, 17, 28, 42], "discuss": [5, 16, 26], "dishcharg": 28, "dispar": 42, "displaystyl": [4, 5, 18, 24, 26, 38, 39], "dissimilar": 13, "dissip": [5, 13, 42], "distanc": 5, "distinct": [13, 38], "distinguish": 30, "distribut": [5, 6, 9, 13, 16, 17, 24], "divid": [5, 10, 26], "divisor": 5, "djkr00": [13, 42], "dke": [22, 23, 24], "dlnndr": [5, 22], "dlnndr_": [6, 17, 23], "dlnndr_1": 22, "dlnndr_2": 22, "dlnndr_3": 22, "dlnndre": 22, "dlnndre_ad": [17, 23], "dlntdr": [5, 22], "dlntdr_": [6, 17, 23], "dlntdr_1": 22, "dlntdr_2": 22, "dlntdr_3": 22, "dlntdr_para_": [17, 23], "dlntdr_para_1": 22, "dlntdr_para_2": 22, "dlntdr_para_3": 22, "dlntdr_perp_": [17, 23], "dlntdr_perp_1": 22, "dlntdr_perp_2": 22, "dlntdr_perp_3": 22, "dlntdre": 22, "dlntdre_ad": [17, 23], "dn": 34, "dn_": [30, 32], "do": [13, 19, 39], "document": [13, 19, 28], "doe": [4, 9, 13, 16, 22, 30, 39], "doi": 42, "domain": [6, 7, 13, 22], "domin": [3, 11, 13, 30], "done": [16, 22, 28], "dong": [16, 42], "dopper": 6, "doppler": [6, 30, 32], "dorland": [13, 42], "dot": 16, "doteq": [4, 5, 10, 22, 26, 38], "down": [6, 10, 16, 18, 21, 24, 28], "download": [2, 17, 28], "dp": 5, "dphi0dr": [17, 23], "dr": [5, 10, 22, 24, 26, 30, 32, 34], "draft": [9, 19], "drain": 13, "drastic": 5, "draw": 13, "drift": [13, 21, 22, 23, 26, 28, 30, 32, 42], "driftwav": [30, 32], "drive": 13, "driven": [18, 26, 42], "drmajdx_loc": [17, 32], "drmindx_loc": [17, 32], "dt": 39, "dt_": [30, 32], "du": 42, "dud": 42, "dud22": [29, 30, 42], "due": [5, 13, 16, 22, 26, 28, 29, 30, 42], "dunigan": 42, "dure": [5, 13], "dux": 42, "dv": [10, 34], "dwbc96": [13, 42], "dx": 38, "dynam": [13, 21, 37, 39, 42], "dynamo": 13, "dz": 39, "dzmag": [6, 10], "dzmajdx_loc": [17, 32], "e": [4, 5, 6, 7, 8, 10, 13, 14, 16, 18, 21, 22, 23, 24, 26, 28, 30, 32, 38, 42], "e0": 31, "e19": 24, "e_": [22, 24], "e_a": [5, 7], "e_max": 6, "e_r": [18, 22, 23, 26], "each": [0, 22, 24, 30, 31, 32, 39], "earli": [13, 42], "earliest": 13, "easiest": 8, "edg": [3, 11, 28], "edit": 0, "edlund": 42, "ee": 5, "eff": [5, 16, 18], "effect": [4, 5, 16, 17, 18, 22, 24, 26, 28, 29, 30, 32, 39, 42], "effici": [13, 39], "effort": [3, 13], "efit": [25, 28], "egrid": 7, "ei": [5, 30, 32, 37], "eigenmod": [29, 30, 32], "eigenvalu": [5, 30, 31, 32, 42], "eigenvalue_spectrum": [17, 32], "eikon": [30, 32], "either": [13, 27], "electon": 13, "electr": [5, 22, 23, 24, 26, 39, 40, 42], "electrion": 28, "electromagnet": [3, 6, 11, 13, 28, 29, 39, 42], "electron": [3, 5, 6, 11, 13, 18, 22, 23, 24, 26, 28, 29, 30, 32, 38, 39, 40, 42], "electrostat": [13, 24, 26, 28, 30], "element": [22, 34], "elev": [5, 6, 10, 18, 22, 23, 30, 32], "elimin": 39, "elit": [30, 32], "ell": 10, "elong": [5, 6, 10, 18, 22, 23, 29, 30, 32], "elsewher": 8, "em": 28, "email": [9, 19, 41], "emcw05": [11, 13, 16, 42], "emcw06a": [13, 16, 42], "emcw06b": [13, 42], "emf": 13, "emili": 3, "emiss": 16, "emphas": [13, 26, 38], "emploi": 38, "enabl": [5, 6], "encount": 16, "encourag": [7, 28], "end": [4, 13, 24, 26, 37, 38], "energet": [13, 39], "energi": [5, 6, 7, 9, 13, 16, 17, 18, 22, 24, 29, 31, 32, 33, 38, 39, 42], "energy_grid": 28, "enforc": [4, 5, 6, 13, 30, 38, 39], "enhanc": [26, 42], "enorm": 13, "enough": 30, "ensembl": 33, "ensur": [9, 19, 28], "enter": [0, 22], "entir": [0, 18], "entri": 24, "entropi": [13, 42], "env": [0, 27], "environ": [13, 17, 41], "envis": 38, "epar0": [17, 23], "epar0_spitz": [17, 23], "eq": 38, "equal": [13, 22, 23, 26, 30, 32, 39], "equat": [3, 4, 7, 11, 13, 17, 21, 22, 24, 26, 29, 38, 39, 42], "equilibria": [17, 18], "equilibrium": [5, 7, 10, 13, 16, 18, 22, 24, 25, 26, 28, 29, 42], "equilibrium_model": [6, 10, 17, 23], "equival": [5, 10, 13], "era": 11, "erg": [34, 38], "error": [4, 5, 6, 7, 13, 16, 28, 38, 39], "error_tol": [4, 6], "esl": 21, "esoter": 13, "especi": 29, "essenti": 16, "establish": [8, 13, 25], "estim": 5, "estrada": [16, 42], "et": [24, 28], "eta": 39, "eta_": 38, "etc": [13, 39, 41], "etg": [13, 16, 29, 30, 32], "etg_factor": [17, 32], "ethes": 42, "ethier": 42, "eulearian": 28, "eulerian": [3, 21, 42], "eurofus": 42, "european": 16, "evalu": [38, 42], "even": [5, 13, 38], "event": 19, "eventu": 13, "everi": [5, 18, 39], "evid": 16, "evolut": [5, 9, 28, 38, 39, 40, 42], "evolv": [5, 6, 13, 38, 39, 40], "exact": [38, 39], "exactli": [0, 22], "exam": 28, "examin": [13, 28], "exampl": [0, 10, 13, 26, 39], "exb": [23, 29, 30, 32], "exch": 39, "exchang": [18, 31, 32, 34, 37, 39, 42], "exclud": [30, 32], "exec": 0, "execut": 8, "exercis": 16, "exist": 0, "exp": 38, "expans": 22, "expect": [10, 13], "expens": 38, "experi": [13, 16, 26, 39, 42], "experiment": [5, 10, 13, 16, 17, 18, 21, 22, 23, 25], "explanatori": [30, 32], "explicit": [4, 5, 13, 38], "explicitli": 10, "explor": 13, "expon": [30, 32], "export": [0, 27], "express": [19, 26], "extens": 21, "extra": [17, 28], "extrem": 16, "extrema": 10, "f": [13, 28, 34, 39, 42], "f_": [24, 26], "f_c": 16, "f_i": 26, "f_p": 39, "fabl": 42, "fact": 13, "factor": [5, 6, 10, 13, 16, 18, 22, 23, 24, 30, 31, 32, 42], "fahei": [13, 42], "failur": 13, "faith": 34, "fals": [13, 30, 32], "faq": 3, "fast": [18, 39, 42], "faster": 5, "fastest": 5, "fc04": [13, 42], "featur": [13, 23, 38], "februari": [16, 41], "feedback": 13, "few": [8, 13, 39], "fftw": [1, 2], "field": [4, 5, 8, 16, 17, 22, 23, 24, 26, 30, 31, 32, 39, 40, 42], "field_print_flag": [6, 7], "field_spectrum": [17, 32], "fig": 16, "figur": [10, 12, 16, 28], "file": [5, 8, 10, 17, 19, 21, 22, 28, 29, 33, 39, 41], "filenam": [7, 24, 32], "filesystem": 13, "fill": 23, "filter": [17, 32], "final": [10, 25, 26, 39], "find": [0, 8, 16, 29, 30, 32, 39], "find_width": [17, 32], "fine": 13, "finit": [5, 13, 14, 22, 28, 29, 38, 39], "fior": 42, "first": [3, 5, 8, 11, 13, 17, 18, 21, 22, 24, 28, 29, 39, 42], "fit": [19, 29], "fix": [4, 5, 13, 24, 38, 39, 41], "flag": [5, 8, 22, 39], "flexibl": 38, "flow": [5, 6, 13, 16, 22, 24, 26, 30, 42], "flr": 6, "fluct": 41, "fluctuat": [5, 13, 16, 26, 28, 29, 30, 31, 32, 39, 42], "fluid": [24, 29, 42], "flutter": 30, "flux": [5, 6, 7, 13, 16, 17, 18, 21, 22, 24, 26, 28, 29, 30, 31, 32, 38, 39, 41, 42], "focus": [3, 13, 29], "fokker": [21, 22, 26, 42], "folder": 0, "follow": [0, 5, 9, 10, 13, 16, 19, 21, 24, 26, 27, 38], "forc": 17, "forgotten": 11, "form": [10, 13, 21, 22, 26, 34, 38], "formal": [13, 17], "format": [5, 13, 17, 24, 25, 26, 28, 42], "formul": [3, 11, 17, 26], "formula": [26, 39, 40], "fortran": [0, 1, 2], "forward": 38, "found": [0, 9, 13, 16, 28, 29, 38], "foundat": [13, 34], "fourier": [5, 22, 23, 24, 30, 32], "fp": 22, "frac": [4, 5, 7, 10, 13, 18, 22, 24, 26, 30, 31, 32, 34, 38, 39], "fraction": [13, 26, 30, 32], "francisco": 42, "frankli": 38, "free": [9, 13, 19, 26], "freq": [7, 31], "freq_tol": 6, "frequenc": [5, 6, 7, 16, 18, 22, 23, 24, 26, 30, 32], "frequent": 17, "fridai": 41, "friend": 41, "from": [0, 3, 5, 10, 11, 16, 17, 19, 21, 22, 24, 25, 26, 28, 29, 30, 32, 39], "ft_model_sa": [17, 32], "fu": [16, 37, 42], "full": [0, 5, 16, 21, 22, 26, 42], "fulli": 13, "function": [5, 13, 16, 22, 24, 26, 30, 32, 38], "fund": 9, "fundament": 4, "furnish": 19, "furth": 42, "further": 10, "fusion": [3, 9, 11, 13, 18, 19, 27, 41, 42], "futur": [13, 17, 28, 42], "g": [3, 8, 10, 18, 21, 22, 24, 42], "g_": 24, "ga": [13, 17], "gacod": [0, 3, 4, 5, 9, 10, 21, 25, 26, 27, 28, 33, 34, 39, 40, 41], "gacode_platform": [0, 27], "gacode_qsub": [8, 27], "gacode_root": [0, 27], "gacode_setup": [0, 27], "gafus": 0, "galleri": [11, 17], "gam": 13, "gamma": [22, 30, 31], "gamma_": [6, 7, 24, 26, 32, 39, 41], "gamma_1": 32, "gamma_2": 32, "gamma_a": [7, 34], "gamma_e_scal": 6, "gamma_p": [6, 26, 41], "gamma_p_scal": 6, "gamot": 42, "gap": 13, "gat": [9, 19, 41], "gauss": [30, 32], "gaussian": 30, "gb": [7, 24, 32, 38], "gcc": 2, "gcc13": 2, "gchat": [17, 32], "ge": 28, "gem": [16, 28], "gene": [16, 28], "gener": [3, 5, 8, 10, 12, 13, 18, 21, 22, 26, 28, 29, 30, 34, 38, 39, 41, 42], "geo": [7, 22, 28, 41], "geo_ni": [17, 23], "geo_yin": [17, 23], "geometr": [22, 30], "geometri": [3, 16, 22, 24, 25, 28, 29, 30, 31, 42], "geometry_flag": [17, 32], "georg": 42, "geqdsk": 28, "get": [9, 21, 30], "gfile": 25, "gflux_print_flag": 6, "gfortran": [0, 1], "ghat": [17, 32], "git": 0, "github": [0, 3, 9, 17], "give": [4, 10, 13, 26, 27, 31, 33], "given": [4, 5, 13, 22, 26, 38, 39], "gk": [3, 6, 7, 11, 13, 29, 30], "gkw": 17, "glf23": [13, 29], "global": [3, 5, 11, 22, 27, 28, 39, 42], "goal": [13, 38], "good": [13, 16, 39], "gpu": [5, 6, 17], "gpu_bigmem_flag": 6, "grad": [10, 22], "grad_r0": 30, "gradb": [30, 32], "gradb_factor": [17, 32], "gradient": [3, 5, 6, 11, 13, 22, 23, 24, 26, 29, 30, 32, 38, 39, 40, 42], "graduat": 13, "grain": 13, "grant": 19, "greater": 4, "greatli": [3, 11], "green": 16, "greenwald": 42, "grid": [5, 7, 13, 17, 18, 22, 30, 39], "gridpoint": [5, 6, 13, 18, 22, 23, 24, 38], "grierson": 42, "groebner": 42, "group": [13, 16, 17, 19, 28, 42], "grow": 13, "grown": 13, "growth": [13, 16, 28, 30, 32], "growthrat": [30, 32], "gs2": [13, 16, 28], "gss": [29, 42], "gstotal": 13, "gtc": 16, "guid": [5, 10, 42], "gv": 24, "gwt": [28, 42], "gyro": [3, 5, 9, 10, 13, 17, 21, 25, 26, 29, 30, 31, 32, 33, 39, 42], "gyroaverag": [3, 13], "gyrobohm": [7, 30, 32, 38, 39, 42], "gyrofluid": [13, 28, 42], "gyrokinet": [3, 4, 9, 11, 17, 21, 25, 26, 28, 29, 42], "gyroradii": 13, "gyroradiu": [4, 7, 13, 30, 32], "gyrovisc": 24, "gyroviscos": 24, "g\u00f6rler": [28, 42], "h": [13, 24, 28, 29, 42], "h_print_flag": 6, "ha": [3, 11, 13, 16, 21, 27, 28, 29, 30, 31, 32, 38, 39], "had": 13, "hahm": 42, "half": [7, 13], "hallatschek": 42, "hammett": [13, 42], "hamper": 13, "hand": [5, 10, 13, 22], "handl": 25, "hardwar": [5, 13], "harmon": [5, 6, 10], "harri": 42, "hat": [18, 22, 24, 38], "have": [3, 10, 11, 16, 26, 28, 29, 38, 39], "hazeltin": 24, "hazltin": 24, "hbc": [13, 42], "hcw": [13, 42], "he": 42, "he4": 39, "heat": [13, 16, 24, 34, 39, 42], "heavi": 26, "hein": 42, "helium": [13, 39, 42], "help": [0, 16], "henc": 26, "here": [4, 5, 10, 13, 18, 21, 26, 28, 38], "herebi": 19, "hermit": [30, 32], "heurist": [5, 42], "hh": 24, "hhw": [3, 11, 42], "hidden": 30, "hierarchi": 41, "high": [4, 5, 21, 29, 30, 32, 39, 42], "higher": [5, 13, 22, 23, 26, 39], "highli": [3, 13, 42], "hinton": [13, 17, 22, 24, 26, 42], "hirshman": [22, 24, 39], "histor": [10, 13], "histori": [11, 17], "hitchon": 42, "hoc": [3, 11, 22], "hol16": [28, 42], "hold": [13, 26, 39], "holder": 19, "holland": [13, 16, 28, 42], "home": 0, "homogen": 42, "horton": [24, 42], "host": 7, "hostnam": 7, "houlberg": 24, "how": [4, 5, 6, 18, 22, 39], "howard": [3, 42], "howev": [9, 10, 13, 16, 19], "hpc": [13, 17, 41], "hr": 24, "http": [0, 2, 42], "hu": 42, "huck": 42, "human": 7, "hw06": [13, 42], "hw85": [26, 42], "hwc04": [13, 42], "hwm": [28, 42], "hybrid": 42, "hybridtest": 0, "hypothesi": 13, "i": [0, 3, 4, 5, 7, 8, 9, 10, 11, 13, 14, 16, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42], "i0": 26, "i1": 26, "i_": [30, 32], "iaea": 42, "ibm": 13, "ibranch": [17, 32], "idea": 25, "ident": 13, "identifi": 13, "identit": 28, "idiosyncrat": 11, "ie": 24, "ieee": 42, "iflux": [17, 32], "ignor": [13, 18, 22, 26, 30, 32, 38], "igor": [3, 41], "iii": 42, "iiint": 10, "iint": 10, "imag": [11, 16, 17, 42], "imex": 13, "immedi": 30, "impact": 42, "implement": [13, 16, 26, 28, 42], "impli": 19, "implic": [41, 42], "implicit": [4, 13, 38], "import": [0, 3, 13, 26, 29, 30, 38], "impos": [13, 16], "improv": [13, 25, 29, 30], "impur": [13, 26, 39, 42], "inc": 0, "includ": [5, 9, 11, 12, 13, 16, 18, 19, 21, 22, 23, 24, 28, 30, 32, 38, 42], "inclus": [5, 26, 28], "incorpor": 16, "incorrect": 16, "increas": [5, 10, 13, 16, 26, 29, 39], "increasingli": [3, 11], "inde": 13, "independ": [5, 13, 22, 26, 33, 38, 39], "index": [7, 22, 31], "indic": 13, "individu": 28, "induc": [5, 13, 22, 26], "induct": [22, 23], "infer": [5, 10, 13, 22], "infinit": 29, "influenc": [26, 38], "info": [4, 5, 7], "inform": [3, 7, 10, 11, 18, 24, 27], "initi": [5, 6, 9, 13, 14, 15, 16, 25, 28, 39, 40, 42], "inject": 26, "inner": 5, "input": [4, 7, 8, 10, 11, 17, 24, 25, 28, 29, 31, 41], "insert": 10, "insid": 5, "insofar": 21, "instabl": [13, 30, 32, 42], "instal": [0, 1, 2, 17], "instanc": [26, 33, 39], "instead": [22, 33, 38], "instruct": 27, "instrument": 16, "int": 34, "int_": 22, "int_0": [10, 34, 38], "int_r": 38, "integ": [5, 22, 23], "integr": [3, 4, 5, 6, 10, 13, 22, 33, 38, 39], "intens": [5, 16, 29, 31, 32, 42], "intensity_spectrum": [17, 32], "interact": 8, "intercod": 16, "interconnect": 13, "interest": [11, 28, 38], "interestingli": 13, "interfac": [3, 7, 17, 21, 22, 32], "intern": [5, 6, 22, 42], "interpol": 24, "interpret": 24, "interprocess": 42, "interv": 6, "intev": 16, "introduc": 38, "invari": 4, "invent": 13, "investig": [13, 28], "invit": 42, "inward": [30, 32], "ion": [5, 6, 7, 13, 16, 18, 22, 24, 26, 28, 29, 30, 32, 38, 39, 40, 42], "ip": [5, 22], "ipccw": [6, 10, 17, 23], "ipm": 13, "irreduc": [30, 32], "isotop": 42, "isotrop": 22, "isotropi": 13, "issu": [0, 9, 13, 19, 28], "itb": 13, "iter": [38, 39, 42], "iterdb": 28, "iterdb2gyro": 25, "iterdb_read": 25, "itg": [13, 16, 29, 30], "itpa": 28, "its": [3, 5, 13, 16, 22, 29, 33], "ix": 24, "j": [10, 12, 16, 24, 28, 38, 42], "j_": 24, "j_r": 34, "jacobian": [10, 17, 34, 39, 40], "jan": 17, "jb": [18, 21], "jbstor": 18, "jcp": 42, "jeff": 3, "jenko": 42, "jet": [13, 29], "jift": 41, "jj": 38, "jnb": 18, "job": [8, 25, 27, 33, 39], "journal": 13, "jr": 42, "jrf": 18, "jt60": 13, "juli": 16, "june": [16, 42], "justifi": 26, "k": [22, 24, 29, 30, 32, 42], "k_": [5, 16, 24, 30, 32], "k_a": 26, "k_per": [30, 32], "k_r": 16, "k_x": [5, 6, 7, 31, 32], "k_y": [4, 5, 6, 7, 31, 32], "kaiser": 42, "kappa": [6, 10, 17, 18, 23, 30, 32], "kappa_loc": [17, 32], "karp": 5, "kay": 42, "kb": 29, "keep": 0, "kei": [3, 4, 13, 16, 17, 38], "kept": 5, "kerbel": 42, "kernel": [3, 7], "kev": [4, 18, 24], "kg": [21, 22, 24], "kh94": [13, 42], "kiefer": 42, "kim": 42, "kind": 19, "kinet": [3, 5, 11, 13, 21, 22, 23, 24, 28, 29, 39, 42], "kinsei": 42, "kishimoto": 42, "kk58": [10, 42], "kkh": [13, 42], "knolker": 42, "know": 10, "known": [13, 26], "knoxvil": 42, "koh": 24, "kojak": 13, "kone": 42, "kot88": [13, 42], "kotschenreuth": [13, 42], "kramer": 42, "kro99": [13, 42], "kromm": [13, 42], "krt95": [13, 42], "kruskal": 42, "ksw08": [29, 42], "kulsrud": 42, "kutta": 13, "kwc05": [3, 11, 13, 42], "kwc06": [3, 11, 13, 42], "kwc07": [3, 11, 13, 42], "kx": [31, 32], "kx0": [30, 32], "kx0_loc": [17, 32], "kx_e": [31, 32], "kx_phi": 41, "kxky_apar": [5, 7], "kxky_bpar": [5, 7], "kxky_e": 7, "kxky_n": 7, "kxky_phi": [5, 7], "kxky_v": 7, "ky": [4, 6, 17, 32], "ky_cflux": 7, "ky_flux": [7, 41], "ky_phi": 41, "kygrid_model": [17, 32], "kymin": 30, "l": [5, 13, 16, 17, 20, 22, 29, 42], "l11": 22, "l12": 22, "l21": 22, "l22": 22, "l25": 42, "l_": 24, "l_0": 5, "l_m": 22, "l_t": 16, "l_x": [5, 39], "label": 18, "lack": 29, "laguerr": [5, 22, 24], "lambda": [5, 22], "lambda_": 24, "lambda_deby": 6, "lambda_debye_scal": 6, "landau": [13, 29, 42], "landmark": 13, "langl": [26, 34], "languag": 13, "laptop": 17, "larg": [3, 4, 5, 8, 11, 13, 16, 22, 26, 30, 32, 39, 42], "larger": [3, 5, 11, 13, 16, 29], "larmor": [13, 16, 22, 23, 24, 29], "last": [0, 26, 30, 32, 39], "later": [13, 16], "latter": [10, 13, 16], "law": 42, "layer": [3, 11, 13], "layout": [13, 27], "lcf": 5, "ldot": [5, 13, 24, 26], "le": [5, 16, 22], "le3": 22, "lead": 26, "leav": [5, 26], "leboeuf": 42, "lebrun": 42, "led": 25, "lee": 42, "left": [4, 5, 10, 22, 23, 24, 26, 34, 37, 38, 39], "legaci": [4, 11], "legend": 17, "legendr": [5, 22, 24], "leht02": [13, 42], "length": [3, 5, 6, 13, 21, 22, 24, 30, 32, 39, 40], "less": [5, 13, 39], "lett": [16, 42], "letter": [9, 19], "level": [0, 16, 28, 39], "li": 42, "liabil": 19, "liabl": 19, "libfftw3": 1, "libmpich": 1, "librari": 1, "licens": 17, "like": [3, 8, 10, 11, 13, 16, 18], "limit": [19, 21, 22, 24, 26, 30, 31, 32, 42], "limits_": 10, "lin": [16, 42], "line": [0, 2, 13, 16, 18, 23, 27, 41], "linear": [5, 8, 13, 14, 16, 21, 22, 28, 29, 30, 41, 42], "link": [0, 17, 28, 41], "linsker": [30, 32], "linsker_factor": [17, 32], "linux": 0, "list": [3, 8, 9, 11, 17, 19, 21, 28, 29, 33], "littl": [13, 29, 38], "ll": [21, 26], "llnl": 16, "ln": [5, 16, 22, 24, 26], "loc": [37, 39], "loc_betae_scal": [17, 40], "loc_dx": [17, 40], "loc_dx_max": [17, 40], "loc_er_feedback_flag": [17, 40], "loc_evolve_grad_only_flag": [17, 40], "loc_he_feedback_flag": 17, "loc_iteration_method": 39, "loc_lock_profile_flag": [17, 40], "loc_rad": [4, 41], "loc_relax": [17, 40], "loc_residual_method": [17, 40], "loc_restart_flag": [17, 40], "loc_scenario": [17, 40], "loc_te_feedback_flag": [17, 40], "loc_ti_feedback_flag": [17, 40], "local": [5, 10, 17, 21, 22, 23, 24, 28, 38, 39, 42], "locat": [13, 16], "locpargen": 4, "log": 5, "logarithm": [23, 30], "logic": 27, "long": [5, 13, 26], "longrightarrow": 26, "look": [10, 18], "loop": 5, "lorentz": [5, 26], "loss": [5, 13, 26, 42], "lost": 13, "low": [3, 5, 11, 13, 16, 25, 29, 30, 32], "lower": [5, 13, 22], "lowest": [5, 22, 30], "lpe": [13, 42], "luda": 42, "lvert": [16, 30, 32], "m": [5, 18, 24, 26, 28, 42], "m2": 0, "m_": [3, 5, 21, 22, 24, 30, 32], "m_a": 34, "m_d": [4, 5, 7, 22, 24], "m_e": 5, "m_i": 26, "m_theta": 24, "ma": 18, "mac": 0, "mach": [6, 26, 30, 32], "mach_scal": 6, "machin": 0, "macport": 2, "made": [9, 13, 19, 21, 30, 32], "magnet": [4, 5, 6, 13, 16, 17, 22, 23, 24, 28, 30, 32, 42], "magnitud": [16, 22], "mahinthakumar": 42, "mai": [10, 16, 26, 28, 42], "main": [5, 25, 26, 32, 39], "maintain": [13, 17, 27], "maj": [30, 32], "major": [5, 6, 10, 13, 18, 22, 23, 24, 30, 32], "make": [0, 5, 9, 13, 19, 38, 39], "makefil": 0, "malonei": 42, "manag": [8, 13, 33, 39, 40], "mani": [6, 11, 13], "manner": 13, "manual": 13, "mar": 28, "margin": [13, 16], "marinoni": 42, "mark": 13, "mass": [3, 5, 6, 13, 21, 22, 23, 24, 26, 30, 32], "mass_": [6, 17, 23], "mass_1": [5, 17, 22, 32], "mass_2": [5, 22], "mass_3": [5, 22], "match": [4, 13, 28, 39, 42], "math": 22, "mathbf": [5, 10, 13, 14, 16, 22, 26, 30], "mathcal": 10, "mathrm": [3, 5, 10, 13, 16, 24, 34, 37, 39], "mathtt": [4, 24, 37], "matric": 38, "matrix": [26, 38], "max": [5, 23, 39], "max_": 10, "max_tim": 6, "maxim": [5, 30, 32], "maximum": [5, 6, 13, 22, 30, 32, 39, 40], "maxwel": 42, "maxwellian": [5, 16, 21, 22, 24, 30], "mbox": [10, 38], "mcclenaghan": 42, "mckee": 42, "md": [30, 32], "me": [30, 32], "mean": [10, 13, 22, 26, 42], "meaning": 24, "measur": [5, 13, 16, 22, 26, 28, 30, 32, 38, 42], "mechan": 30, "meet": 13, "memori": [5, 6, 7, 13], "merchant": 19, "mesh": [5, 7, 33], "meshpoint": 5, "method": [3, 4, 13, 16, 17, 29, 30, 32, 38, 39, 42], "metric": [28, 42], "mhd": [13, 30], "microst": [28, 42], "microturbul": 42, "mid": 13, "midplan": [4, 5, 22, 24, 30, 32], "mikkelsen": 42, "mila": [16, 42], "miller": [5, 22, 28, 29, 30], "milovich": 42, "min": [13, 23, 27], "min_": 10, "mine": 0, "minim": [33, 38, 39], "minimium": 5, "minimum": [5, 30, 32, 42], "minor": [3, 4, 5, 6, 10, 13, 18, 21, 22, 23, 24, 30, 32], "mint": 0, "miscellan": 17, "misunderstand": 13, "mit": [3, 13], "mix": 30, "mod": [13, 24, 42], "mode": [5, 6, 7, 8, 13, 14, 16, 17, 20, 21, 22, 23, 24, 29, 30, 31, 32, 39, 40, 42], "model": [3, 5, 6, 9, 10, 11, 13, 16, 22, 24, 26, 28, 30, 31, 32, 33, 39, 42], "modest": 13, "modif": [9, 19], "modifi": [3, 4, 5, 8, 11, 19, 24, 38], "modul": [21, 22], "modular": 13, "moment": [5, 6, 10, 22, 26, 29, 30], "moment_print_flag": [6, 7], "momentum": [5, 6, 7, 10, 13, 17, 18, 24, 32, 42], "monitor": 41, "monolith": [21, 24], "monomi": 22, "monoton": 13, "moor": 42, "more": [0, 3, 11, 13, 18, 22, 28, 29, 30, 38, 39], "moreov": [13, 16], "morph": 25, "most": [0, 5, 13, 16, 26, 28, 30, 32, 33, 34], "mostli": 13, "motiv": [3, 11, 13, 16, 25], "move": [3, 10, 11, 13], "mp": 2, "mpi": [0, 2, 5, 6, 7, 8, 27], "mpi_rank_ord": 6, "mpich": [1, 2], "mst1": 42, "much": [13, 22], "multi": [11, 13, 16, 21, 39, 42], "multipl": [3, 5, 13, 24, 28, 33, 38], "multipli": [5, 30, 32], "multiscal": [3, 42], "multistream": 13, "must": [0, 5, 10, 13, 22, 38], "mw": 18, "mxh": [10, 18], "mxh3": 10, "mynick": 42, "n": [0, 4, 5, 6, 8, 10, 14, 15, 16, 17, 18, 24, 27, 31, 32, 34, 39, 42], "n_": [5, 21, 22, 24, 30, 31, 32], "n_0": 16, "n_a": [5, 7, 22, 26, 34], "n_c": 16, "n_e": [3, 5, 7, 16, 18, 24, 38], "n_energi": [6, 17, 23, 41], "n_evolv": 39, "n_field": 6, "n_global": 6, "n_mpi": 39, "n_r": 22, "n_radial": [6, 17, 23, 24], "n_speci": [6, 17, 23], "n_theta": [6, 17, 23, 24, 41], "n_toroid": 6, "n_xi": [6, 17, 23, 41], "na": 10, "nabla": [10, 16, 22, 26, 34], "name": [9, 13, 16, 19, 21, 24], "nathan": 3, "natur": 13, "nbasis_max": [17, 32], "nbasis_min": [17, 32], "nbi": 39, "ncc": [16, 42], "nclass": [21, 22, 24], "ne": [18, 22], "ne_ad": [17, 23], "nearli": 13, "need": [0, 5, 8, 14, 25, 38], "neg": [5, 10, 22, 23], "neglect": [10, 13, 16], "neglig": [5, 13], "neo": [0, 3, 9, 10, 16, 17, 25, 26, 27, 33, 34, 38, 39, 40, 42], "neo_": 21, "neo_aniso_model_in": 22, "neo_dens_in": 22, "neo_dlnndr_in": 22, "neo_dlntdr_in": 22, "neo_dlntdr_para_in": 22, "neo_dlntdr_perp_in": 22, "neo_eflux_thchi_out": 24, "neo_eflux_thhhe_out": 24, "neo_eflux_thhhi_out": 24, "neo_eflux_ths_out": 24, "neo_efluxncv_dke_out": 24, "neo_efluxncv_gv_out": 24, "neo_efluxtot_dke_out": 24, "neo_efluxtot_gv_out": 24, "neo_efluxtot_nclass_out": 24, "neo_init": 21, "neo_interfac": [21, 24], "neo_jpar_dke_out": [21, 24], "neo_jpar_nclass_out": 24, "neo_jpar_ths_out": 24, "neo_jtor_dke_out": 24, "neo_jtor_ths_out": 24, "neo_mass_in": 22, "neo_mflux_dke_out": 24, "neo_mflux_gv_out": 24, "neo_n_species_in": 21, "neo_pflux_dke_out": 24, "neo_pflux_gv_out": 24, "neo_pflux_nclass_out": 24, "neo_pflux_thhh_out": 24, "neo_pflux_thhs_out": 24, "neo_profile_dlnndr_scale_in": 22, "neo_profile_dlntdr_scale_in": 22, "neo_rotation_model": 22, "neo_run": 21, "neo_temp_in": 22, "neo_temp_para_in": 22, "neo_temp_perp_in": 22, "neo_vpol_dke_out": 24, "neo_vpol_nclass_out": 24, "neo_vtor_dke_out": 24, "neo_vtor_nclass_out": 24, "neo_z_in": 22, "neoclass": [9, 13, 21, 22, 24, 25, 26, 34, 38, 39, 42], "nersc": [8, 17, 41], "net": 13, "netcdf": 2, "network": [22, 42], "neural": 22, "neutral": [22, 26], "nevin": [13, 42], "new": [0, 3, 10, 16, 18, 25, 29, 30, 32, 39, 42], "new_eikon": [17, 32], "newton": [38, 39, 40], "nexp": 18, "next": [13, 29], "nhd": [13, 42], "ni": 18, "nion": [18, 41], "nishimura": 42, "nky": [17, 31, 32], "nl": 30, "nl00": 8, "nl01": 8, "nl_flag": 41, "nm": 31, "nmode": [17, 31, 32], "no_cbla": 0, "no_lapack": 0, "no_shar": 0, "node": [5, 27, 30, 32], "nois": [13, 42], "nomin": 16, "nomp": [0, 8, 27], "non": [5, 13, 23, 24, 30, 32], "nonadiabat": 13, "nonaxisymmetr": [22, 42], "none": 24, "noninfring": 19, "nonlinear": [3, 5, 6, 8, 11, 14, 16, 28, 29, 41, 42], "nonlinear_flag": 6, "nonloc": [13, 42], "nonreson": 13, "nontherm": [39, 40], "nonuniform": 18, "nonuniformli": 26, "nonzero": [5, 24], "norm": [21, 22, 24, 26], "normal": [5, 6, 10, 13, 16, 17, 22, 23, 24, 30, 31, 32, 34, 38, 39], "normalzi": 38, "notat": [5, 34], "note": [5, 9, 17, 19, 22, 23, 24, 26, 28, 30, 31, 32, 38], "noth": 13, "notic": [9, 19], "nov": 30, "novel": 13, "now": 13, "nq": 4, "ns_in": 31, "nsts_crossphase_spectrum": [17, 32], "nstx": [13, 29, 30, 42], "nth": 39, "ntheta": 41, "nu": [10, 22], "nu_": 5, "nu_1": [17, 23], "nu_e": [6, 41], "nu_ei": 28, "nu_glob": 6, "nucl": 42, "nuclear": 42, "number": [5, 6, 8, 13, 16, 18, 21, 22, 23, 24, 26, 30, 32, 33, 38, 39, 40], "numer": [0, 3, 5, 8, 10, 11, 13, 17, 22, 24, 28, 41, 42], "nunami": 42, "nup_alpha": 6, "nup_radi": 6, "nup_theta": 6, "nwidth": [17, 32], "nx": 28, "nxgrid": [17, 32], "o": [5, 26], "observ": [13, 16, 26, 28], "obtain": [10, 13, 16, 19, 29, 33], "occur": 13, "octob": 42, "odd": 22, "off": [5, 39, 42], "offer": 11, "offload": [5, 6], "offset": [30, 32], "often": [0, 5, 8, 26, 30], "ohm": 42, "ohmic": [16, 18], "oint": 34, "old": 28, "older": 28, "omega": [17, 22, 34], "omega0": 18, "omega_": 26, "omega_0": [18, 22, 24, 26, 34], "omega_1": 26, "omega_intel": 27, "omega_rot": [17, 23, 26], "omega_rot_deriv": [17, 23, 26], "omp": [7, 27], "onc": [5, 27], "one": [5, 10, 13, 22, 30, 32, 38, 39], "ones": [0, 13], "onetwo": [13, 18, 25, 28], "onli": [5, 6, 11, 13, 16, 22, 23, 24, 26, 27, 28, 30, 38, 39], "open": [13, 16], "openbla": 17, "openmp": 0, "oper": [5, 13, 16, 21, 22, 33, 39, 40, 42], "operation": 38, "opposit": 13, "optim": [3, 5, 13, 42], "option": [21, 22, 41], "orbit_grid": 28, "order": [0, 4, 5, 6, 13, 16, 18, 21, 22, 23, 24, 26, 28, 30, 32, 33], "org": 2, "organ": 13, "orient": [5, 6, 17, 22], "orienti": [5, 22], "origin": [13, 28, 38, 39], "ornl": [8, 13, 42], "osx": 0, "other": [5, 10, 13, 16, 19, 22, 25, 28, 33, 39, 42], "otherwis": [9, 19, 22, 28, 30], "our": 13, "out": [5, 7, 8, 13, 16, 17, 18, 19, 22, 26, 29, 30, 32], "outboard": [5, 22, 24, 30, 32], "outer": 5, "output": [5, 8, 17, 22, 23, 25, 28, 29, 30, 31], "outward": 26, "oval": [6, 10], "over": [3, 13, 16, 18, 21, 28, 29, 31, 32], "overal": [4, 30], "overcom": 13, "overestim": 16, "overlin": 32, "overview": [13, 17], "ow": 13, "own": 0, "p": [5, 22, 26, 30, 32, 34, 38, 42], "p_": 24, "p_a": [22, 26], "p_l": 22, "p_prime_loc": [17, 32], "pa": 42, "pace": 42, "packag": 0, "page": 28, "pai": 8, "painstak": 13, "paper": [16, 34], "paradigm": [13, 42], "paradox": [13, 42], "parallel": [5, 7, 14, 18, 22, 23, 24, 26, 30, 31, 32, 33, 39, 42], "paramat": 16, "paramet": [4, 5, 13, 16, 17, 18, 21, 22, 24, 30, 31, 38, 39, 41], "parameter": [5, 10, 28, 42], "paramt": 22, "park": [17, 32], "parker": 42, "parser": 18, "part": [13, 16], "parti": [9, 19], "partial": [4, 5, 10, 22, 24, 26, 30, 32, 34, 38], "partial_t": 38, "particip": 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": 17, "patel": 42, "pathologi": 13, "pattern": 13, "pci": 13, "peak": [13, 30, 42], "pedest": [3, 11, 38, 41], "peebl": 42, "peeter": 42, "per": [6, 13, 27, 31, 32, 38], "perc": 13, "percent": 13, "pereverzev": 42, "perfect": 16, "perfectli": [13, 30], "perform": [3, 13, 16, 28, 39, 41, 42], "period": [13, 22, 25], "perlmutt": [17, 41], "perlmutter_cpu": 27, "perlmutter_gpu": 27, "permiss": 19, "permit": 19, "perp": [5, 22], "perpendicular": [16, 22, 23, 41], "persist": 13, "person": 19, "perspect": 17, "perturb": [5, 13], "petascal": 42, "petti": 42, "pfirsh": 26, "pg3eq": [13, 16], "ph": 16, "phase": [16, 29, 31, 32, 42], "phd": 42, "phenomena": [3, 11, 13], "phenomenon": 13, "phi": [5, 7, 10, 14, 18, 26, 31, 32], "phi_": [22, 24, 26], "phi_0": [22, 24, 26], "phi_1": [24, 26], "php": 2, "phy": [16, 24, 42], "physic": [4, 7, 9, 13, 16, 28, 30, 39, 41, 42], "physrevlett": 42, "pi": [5, 10, 18, 22, 26], "pi_": [7, 24, 32], "pi_1": 32, "pi_2": 32, "pi_a": [7, 34], "pi_e": 32, "pic": [13, 16], "pick": 30, "pictur": 13, "pinch": [13, 42], "pinsker": 42, "pioneer": [3, 11], "pip": 41, "pitch": [5, 6, 22, 24, 28], "pittsburgh": 42, "pivot": 39, "place": 29, "plai": [3, 11, 13, 16, 26, 29], "planck": [21, 26, 42], "plank": 22, "plasma": [3, 5, 11, 13, 16, 18, 21, 22, 24, 25, 28, 29, 39, 42], "platform": [8, 13, 17, 27, 41], "pleas": [0, 12, 18], "plot": [8, 16, 17, 28, 41], "plu": [6, 8], "pmac": 13, "pmatrix": 38, "point": [5, 13, 16, 18, 28, 38, 39], "poisson": 21, "pol": 10, "polflux": 18, "poloid": [5, 6, 13, 17, 18, 22, 23, 24, 26, 30, 32, 41, 42], "polynomi": [5, 22, 23, 24, 30, 32], "popul": 42, "popular": [3, 13, 38], "porkolab": 42, "port": [2, 13], "portion": [9, 19], "posit": [5, 10, 22], "possibl": [6, 13, 28, 38], "possibli": 11, "potenti": [5, 13, 22, 24, 26, 30], "power": [13, 16, 17, 18, 38, 39, 40], "ppc": 13, "ppcf": 24, "pppl": 41, "practic": [13, 21, 26, 34], "pre": [11, 17, 25], "prebuilt": 17, "precis": [5, 6], "predecessor": 29, "predict": [13, 16, 28, 29, 42], "prefer": [30, 38], "prehistori": 17, "prepend": 21, "presenc": [13, 26], "present": [9, 12, 13, 16, 17, 19, 22, 24, 26, 41], "preset": 30, "pressur": [3, 5, 6, 11, 18, 22, 23, 30, 32], "prevent": [30, 32], "previou": [10, 13, 26], "primari": [13, 21, 28, 33], "primarili": 3, "prime": [22, 34, 38], "principl": 13, "print": [5, 8, 22], "print_step": [4, 6], "prior": [13, 16], "priori": 26, "probabl": [13, 39], "problem": [5, 13, 22, 23, 38], "proce": 27, "proceed": 42, "process": [5, 6, 25, 39], "produc": [13, 24, 26], "product": [13, 42], "profil": [3, 5, 6, 9, 10, 11, 13, 16, 18, 21, 22, 25, 29, 33, 38, 39, 42], "profile_dlnndr_": [17, 23], "profile_dlnndr_1_scal": 22, "profile_dlnndr_2_scal": 22, "profile_dlnndr_3_scal": 22, "profile_dlntdr_": [17, 23], "profile_dlntdr_1_scal": 22, "profile_dlntdr_2_scal": 22, "profile_dlntdr_3_scal": 22, "profile_equilibrium_model": [10, 17, 23], "profile_erad0_model": [17, 23], "profile_model": [6, 17, 23, 24], "profiles_gen": [4, 17, 18, 41], "profiles_gen_plot": 41, "program": [0, 13], "progress": 13, "project": [0, 5, 13, 21, 27, 42], "pronounc": 13, "propag": 16, "proper": [10, 19], "properli": [10, 13], "properti": [5, 42], "provid": [3, 11, 13, 19, 25, 28], "pseudospectr": 5, "psfc": 41, "psi": [4, 10, 18, 22, 26, 34], "psi_": 10, "psi_p": 10, "psi_t": 10, "pst": 41, "ptot": 18, "public": [9, 12, 16, 17, 19], "publish": [9, 13, 16, 19], "pueschel": 42, "pull": [9, 19], "pure": [13, 16, 26], "purpos": [3, 5, 9, 19], "push": 26, "put": 38, "pygacod": 41, "python": [0, 2, 3, 7, 17], "python3": 2, "q": [4, 6, 10, 13, 17, 18, 23, 24, 26, 30, 32, 34, 38, 42], "q_": [7, 13, 24, 32, 37, 38, 39], "q_1": 32, "q_2": 32, "q_a": [7, 34], "q_e": [16, 32, 37, 38], "q_i": [37, 38], "q_loc": [17, 32], "q_prime_loc": [17, 32], "q_sa": [17, 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": [17, 32], "qline": [18, 37], "qmom": 18, "qohm": [18, 37], "qpar_beam": 18, "qpar_wal": 18, "qrfe": [18, 37], "qrfi": [18, 37], "qsync": [18, 37], "quad": [10, 26, 34, 38], "quadratur": [30, 32], "qualit": 28, "qualiti": 25, "quantit": 16, "quantiti": [3, 10, 16, 21, 22, 24, 26, 38], "quasi": [22, 26, 30, 42], "quasilinear": [16, 29, 30, 32, 42], "quasineutr": [4, 5, 6, 39], "quasineutral_flag": 6, "quench": [13, 29, 30, 32, 42], "queri": 0, "question": [13, 17, 28], "queue": 8, "quick": 17, "quit": 13, "r": [0, 4, 5, 10, 12, 13, 16, 18, 21, 22, 24, 26, 30, 32, 34, 38, 42], "r_": [30, 32, 38], "r_0": [5, 10, 18, 22, 24, 26], "r_1": 38, "r_2": 38, "r_3": 38, "r_j": [24, 38], "rad": [18, 34, 37], "radial": [3, 5, 6, 11, 13, 16, 22, 23, 24, 26, 33, 38, 39, 42], "radian": 18, "radiat": [18, 34, 39], "radii": [13, 39], "radiu": [3, 4, 5, 6, 10, 13, 16, 18, 21, 22, 23, 24, 29, 30, 32, 39, 42], "rais": 0, "rang": [13, 16, 21, 22], "rangl": [26, 34], "rank": [5, 6, 7, 30, 32], "rapid": 26, "rapidli": [38, 42], "rate": [5, 6, 13, 16, 22, 26, 28, 30, 32, 34], "rather": [7, 13, 26, 38, 39], "ratio": [5, 13, 21, 22, 24, 29, 39], "ration": 13, "rational": 25, "raw": 5, "rb_": [30, 32], "rbf": 28, "rc": 0, "rc_": [30, 32], "re": 22, "reach": 13, "reaction": 39, "reactor": [37, 39, 42], "read": [5, 7, 22, 25, 28, 34, 39], "readabl": 7, "reader": 11, "real": [3, 11, 13, 41], "realist": [13, 42], "realiti": 10, "realli": 26, "reason": [10, 26], "recent": [11, 13, 16, 28, 29, 30], "recipi": 9, "recombin": 18, "recommend": [0, 4, 5, 7, 30], "rectangular": 24, "red": 16, "redistribut": 26, "reduc": [3, 5, 6, 11, 13, 14, 26, 38], "reduct": 13, "reed": 42, "ref": [22, 38], "refer": [5, 13, 17, 19, 24, 28], "refin": [13, 30], "reflect": 10, "refus": 16, "reg08": 8, "reg14": 18, "regard": 17, "regardless": 22, "regim": [3, 13, 16, 26], "region": [3, 11, 13, 29], "regress": [0, 8], "regular": 8, "rel": [5, 6, 16, 22, 30], "relat": [13, 24, 26, 34], "relax": [13, 38, 39, 40], "relev": [13, 26, 42], "reliabl": 13, "remain": [13, 30], "remark": [10, 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": [3, 5, 9, 11, 13, 18, 22, 25, 26, 27, 29, 34, 42], "rescal": 16, "research": [3, 11, 13, 16, 28], "reset": 5, "residu": [13, 38, 39, 40], "resolut": [5, 22, 39, 41, 42], "resolv": [13, 30], "resourc": [13, 16, 28], "respect": [5, 10, 21, 22, 26, 30, 32], "respond": 30, "respons": [29, 42], "restart": [5, 6, 39, 40, 41], "restart_step": 6, "restrict": [9, 13, 19, 26, 38], "result": [5, 8, 9, 10, 11, 13, 17, 19, 26, 29, 30, 38, 42], "retain": [3, 5, 10, 13, 21], "return": [5, 14, 22, 30, 31], "rev": [16, 24, 42], "revers": [13, 42], "review": 13, "revis": 16, "rewoldt": 42, "rf": 18, "rh": [13, 22], "rh98": [13, 42], "rho": [4, 5, 16, 18, 30, 32, 42], "rho_": [4, 5, 7, 13, 16, 21, 22, 24, 28, 31, 38], "rho_i": [21, 26], "rho_ion": 30, "rho_star": [17, 23], "rhode": 42, "right": [4, 5, 10, 19, 22, 23, 24, 26, 34, 37, 38, 39], "rightarrow": [4, 5, 13, 22, 24, 38], "rigor": [13, 26], "rise": 13, "rk": 13, "rk4": 5, "rlns_1": [17, 32], "rlts_1": [17, 32], "rm": [4, 5, 7, 10, 16, 18, 21, 22, 23, 24, 26, 30, 32, 34, 38], "rmaj": [6, 10, 18], "rmaj_loc": [17, 32], "rmaj_over_a": [10, 17, 23], "rmaj_sa": [17, 32], "rmin": [6, 10, 18], "rmin_loc": [17, 32], "rmin_over_a": [10, 17, 23], "rmin_over_a_2": [17, 23], "rmin_sa": [17, 32], "roach": 42, "robust": [13, 16, 38, 39], "roger": 42, "role": [13, 16, 26, 29, 33, 42], "ron": 28, "root": [38, 39], "rosenbluth": [13, 24, 42], "rost": 42, "rotat": [3, 5, 18, 21, 22, 28, 33, 38, 39, 42], "rotation_model": [6, 17, 23, 24], "roth": 42, "rough": 16, "roughli": [10, 13, 16, 30], "routin": [13, 39], "row": 24, "rule": [0, 29, 30, 32, 38, 39, 40, 42], "run": [0, 5, 10, 13, 14, 21, 22, 24, 27, 29, 30, 39], "runawai": 13, "rung": 13, "runtim": 24, "s0021": 42, "s_": [5, 10, 22, 34], "s_1": 10, "s_2": 10, "s_3": 10, "s_delta": [6, 10, 17, 23], "s_delta_loc": [17, 32], "s_e": 38, "s_i": [26, 38], "s_kappa": [6, 10, 17, 23], "s_kappa_loc": [17, 32], "s_n": 10, "s_p": 10, "s_t": 10, "s_w": 34, "s_zeta": [6, 10, 17, 23], "s_zeta_loc": [17, 32], "s_zmag": [10, 17, 23], "safe": 39, "safeti": [0, 5, 6, 10, 13, 18, 22, 23, 24, 30, 32, 42], "sai": [0, 26], "same": [5, 11, 13, 16, 26, 28, 39], "sampl": [18, 27, 39], "san": 42, "santoro": 42, "sat0": [29, 30], "sat1": [29, 30, 32], "sat2": [29, 30], "sat3": [29, 30], "sat_geo_spectrum": [17, 32], "sat_rul": [17, 31, 32], "satur": [13, 16, 30, 31, 32, 42], "sauter": 24, "save": 5, "sbc": [29, 30, 42], "sc2004": 42, "scalar": [26, 31, 32], "scalar_saturation_paramet": [17, 32], "scale": [4, 5, 6, 10, 13, 16, 22, 23, 24, 26, 30, 39, 40, 42], "scan": [13, 16], "scatter": 28, "scb": [29, 30, 42], "scenario": [17, 18, 33, 39, 40, 42], "scheme": [5, 13, 22, 38, 39, 40], "schh16": [29, 30, 42], "schl\u00fcter": 26, "schmitz": 42, "schumak": 42, "sci": 42, "scidac": [13, 42], "scienc": 17, "scratch": [3, 11], "screen": 8, "script": 8, "scw": [29, 42], "sdsc": 3, "seamlessli": 13, "search": [30, 32], "second": [4, 24, 26, 28, 39], "section": [10, 26], "see": [4, 5, 9, 18, 22, 26, 29, 30, 32, 33, 39], "seem": 13, "seen": 28, "select": [2, 5, 6, 22], "selector": [5, 6, 23], "self": [5, 6, 13, 24, 30, 32, 39, 42], "selfupd": 2, "send": [9, 41], "sensit": 16, "separ": [13, 16, 25], "seri": [16, 24, 28, 42], "serial": [17, 39], "serv": 28, "set": [0, 2, 4, 5, 8, 13, 21, 22, 26, 28, 30, 31, 32, 39], "setup": [5, 27], "sever": 13, "sevil": 42, "sfiligoi": [3, 41, 42], "sgi": 13, "sh01": [13, 42], "sh98": [26, 34, 42], "shafer": 42, "shafranov": [5, 6, 10, 22, 23, 30], "shall": [9, 19], "shampin": 5, "shan": 42, "shape": [3, 5, 10, 13, 16, 18, 21, 22, 25, 29, 39, 42], "shape_cos0": [6, 10, 17, 18], "shape_cos1": [6, 10, 17, 18], "shape_cos2": [6, 10, 17, 18], "shape_cos3": [6, 10, 17, 18], "shape_s_cos0": [6, 10, 17], "shape_s_cos1": [6, 10, 17], "shape_s_cos2": [6, 10, 17], "shape_s_cos3": [6, 10, 17], "shape_s_sin3": [6, 10, 17], "shape_sin3": [6, 10, 17, 18], "share": [0, 27, 39], "shat_sa": [17, 32], "shear": [5, 6, 10, 13, 16, 17, 23, 24, 26, 29, 30, 32, 42], "shell": 0, "shend": 42, "shift": [6, 10, 13, 17, 23, 29, 30, 31, 32], "shirai": 42, "shohet": 42, "short": [6, 7, 13, 15, 23, 24, 32, 40], "shorter": 5, "shortfal": [17, 20, 42], "shorthand": 38, "shot": 28, "should": [0, 4, 5, 8, 22, 23, 24, 28, 39], "show": [8, 13, 16, 26, 39], "shown": [10, 13, 16, 23, 28], "shrinkag": 39, "shumak": 42, "shut": 39, "side": 13, "sigma": [24, 38], "sigmar": [22, 24, 39], "sign": [10, 22, 23, 30, 32], "sign_bt": [17, 32], "sign_it": [17, 32], "signal": 39, "signific": [5, 13, 16], "significantli": [13, 16], "silent": 6, "silent_flag": [6, 17, 23, 24], "sim": [10, 38], "sim_model": [17, 23, 24], "simeq": [26, 38], "similar": [13, 26, 28, 42], "simpl": [5, 8, 29, 31, 39], "simpli": 39, "simplif": 34, "simplifi": [13, 30], "simul": [5, 6, 7, 9, 11, 14, 17, 18, 22, 23, 25, 28, 29, 30, 33, 39, 40, 41, 42], "simultan": [13, 16, 39], "sin": [10, 24], "sinc": [10, 13, 21, 28], "sine": 24, "singl": [0, 5, 6, 13, 26, 28, 30, 32], "singular": [5, 13], "size": [4, 6, 13, 16, 40, 41, 42], "sj": 24, "sk10": [9, 42], "sk_": [30, 32], "skw05": [13, 42], "skw07": [3, 9, 11, 13, 29, 30, 42], "slightli": [5, 13, 28], "slow": 16, "slowdown": 13, "slower": 5, "small": [5, 13, 26, 28], "smaller": [5, 13, 14, 16, 39], "smith": 42, "smoooth": 42, "smooth": 38, "snave": 42, "snyder": [13, 42], "so": [5, 6, 13, 16, 19, 22, 25, 27, 28, 30, 33, 38, 39], "soc": 42, "softwar": [9, 13, 19, 27], "solid": 16, "solomon": 42, "solut": [17, 22, 24, 29, 39, 42], "solv": [13, 17, 21, 22, 24, 29, 33, 38, 39], "solver": [3, 11, 17, 21, 22, 33, 42], "some": [11, 13, 17, 23, 28, 34], "sometim": 14, "somewhat": 13, "sonic": [5, 17, 21, 22, 24], "sort": [13, 30, 32], "sound": [3, 7, 13, 16], "sourc": [5, 6, 13, 17, 18, 19, 22, 25, 33, 38, 39, 41], "space": [3, 5, 11, 22, 23, 28, 30, 32, 42], "spain": 42, "span": [5, 13], "spars": 33, "spatial": [13, 16, 22], "speak": 13, "speci": [5, 11, 18, 21, 22, 26, 28, 30, 31, 39, 42], "species1": 22, "specif": [0, 3, 5, 18, 24, 26, 38], "specifi": [5, 18, 22, 23, 25, 39], "spectra": [13, 16, 31, 32], "spectral": [3, 13, 29, 30, 31, 32, 42], "spectral_shift": [17, 32], "spectroscopi": 16, "spectrum": [13, 30, 31, 32], "speed": [3, 5, 6, 7, 22, 24, 26], "spitzer": [22, 23], "spitzer_model": [17, 23], "split": [4, 25], "spot": 16, "spread": 13, "spring": 13, "springer": 42, "sqrt": [3, 7, 16, 21, 22, 24], "squar": [5, 6, 10, 16, 18, 22, 23, 30, 32], "src": 8, "sreepathi": 42, "ss": 22, "stabil": [13, 29, 42], "stabl": 13, "staebler": 42, "staff": 13, "stage": 5, "standard": [3, 4, 5, 10, 13, 17, 22, 25, 26, 28, 30, 32, 39], "star": 42, "start": [10, 13, 18, 28, 39], "startup": 39, "state": [13, 33, 38, 42], "statefil": 25, "static": [37, 39], "statist": [7, 13], "statu": 42, "steadi": [13, 33, 38, 42], "steep": 26, "steeper": [3, 11], "step": [4, 5, 13, 17, 27, 38, 39, 40], "stiff": 39, "still": [13, 38], "storag": 42, "store": [30, 32], "strategi": [17, 41], "strength": [10, 22], "stress": [31, 32], "strong": [13, 16, 22, 24, 26], "strongli": [8, 18, 28], "structur": [13, 42], "student": 13, "studi": [13, 17, 26, 28, 42], "subdomin": 13, "subject": [9, 19, 26, 41], "submiss": 13, "submit": 8, "subroutin": [17, 21, 22], "subscript": 26, "substanti": [9, 19], "substitut": 26, "subtl": 26, "success": [0, 13, 16], "successfulli": [13, 16], "sudo": [1, 2], "suffer": 13, "suffici": [4, 18], "sugama": [5, 6, 17, 24, 26, 34, 42], "suggest": [3, 8, 13, 24, 33], "suit": [0, 13], "suitabl": [0, 3, 11, 25], "sum": [18, 26, 31, 32, 38], "sum_": [10, 24], "sum_a": [22, 34], "sum_flux_spectrum": [17, 32], "sum_p": 39, "summar": [13, 34], "summari": [11, 16, 28], "summer": 25, "sung": 42, "supercomput": [13, 42], "support": [13, 39], "suppress": [10, 26, 42], "surfac": [5, 13, 17, 18, 21, 22, 24, 26, 30, 32, 34, 42], "surprisingli": 29, "svpablo": 13, "swck13": [29, 30, 42], "switch": [7, 13, 30], "swnn11": [26, 42], "symbol": [10, 23], "symmetr": [5, 6, 10, 22], "symmetri": 6, "synchrotron": 18, "synopsi": 17, "synthet": [13, 28, 42], "system": [3, 5, 8, 10, 13, 22, 26, 29, 30, 32, 38, 41], "systemat": [13, 28], "t": [5, 7, 8, 10, 13, 16, 24, 26, 28, 30, 32, 34, 38, 41, 42], "t_": [5, 16, 21, 22, 24, 26, 30, 32, 38], "t_0": 16, "t_a": 22, "t_e": [3, 5, 7, 13, 16, 18, 24, 38, 39], "t_i": [13, 26, 38, 39], "ta": [22, 24], "tabl": [5, 14, 17, 22, 26, 29, 30, 31], "tabular": [3, 11, 17, 33], "tag": 7, "taguchi": 24, "tajima": 42, "take": [13, 23, 24], "taken": [16, 28, 38], "talk": [41, 42], "tang": 42, "tardini": 42, "target": [13, 38, 39], "task": [0, 7, 8], "tau": 13, "tau_": [22, 24], "taus_1": [17, 32], "tdg": [29, 42], "te": [4, 18, 22, 42], "te_ad": [17, 23], "team": 42, "tech": 42, "technic": [10, 13, 42], "tem": [13, 29, 30], "temp": [5, 22], "temp_": [6, 17, 23], "temp_1": [5, 22], "temp_2": 22, "temp_3": 22, "temp_para_": [17, 23], "temp_para_1": 22, "temp_para_2": 22, "temp_para_3": 22, "temp_perp_": [17, 23], "temp_perp_1": 22, "temp_perp_2": 22, "temp_perp_3": 22, "temperatur": [3, 5, 6, 13, 18, 21, 22, 23, 24, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 42], "temperature_spectrum": [17, 32], "temperaur": 23, "templat": [0, 8], "ten": 13, "tend": 13, "term": [5, 6, 13, 16, 21, 22, 24, 26, 30, 32, 38], "test": [0, 5, 6, 8, 9, 13, 16, 19, 22, 28], "text": [10, 13, 26, 28, 29, 34, 38], "tftr": 29, "tg": 24, "tglf": [0, 3, 9, 11, 13, 17, 28, 33, 42], "tglf1": 39, "tglf2": 39, "tglf3": 39, "tglf4": 39, "tglf_adiabatic_elec_in": 32, "tglf_alpha_e_in": 32, "tglf_alpha_mach_in": 32, "tglf_alpha_p_in": 32, "tglf_alpha_quench_in": 32, "tglf_alpha_sa_in": 32, "tglf_as_in": 32, "tglf_b_model_sa_in": 32, "tglf_betae_in": 32, "tglf_debye_factor_in": 32, "tglf_debye_in": 32, "tglf_delta_loc_in": 32, "tglf_drmajdx_loc_in": 32, "tglf_drmindx_loc_in": 32, "tglf_dzmajdx_loc_in": 32, "tglf_elec_eflux_out": 32, "tglf_elec_mflux_out": 32, "tglf_elec_pflux_out": 32, "tglf_etg_factor_in": 32, "tglf_filter_in": 32, "tglf_find_width_in": 32, "tglf_ft_model_sa_in": 32, "tglf_gchat_in": 32, "tglf_geometry_flag_in": 32, "tglf_ghat_in": 32, "tglf_gradb_factor_in": 32, "tglf_ibranch_in": [30, 32], "tglf_iflux_in": 32, "tglf_ion1_eflux_out": 32, "tglf_ion1_mflux_out": 32, "tglf_ion1_pflux_out": 32, "tglf_ion2_eflux_out": 32, "tglf_ion2_mflux_out": 32, "tglf_ion2_pflux_out": 32, "tglf_kappa_loc_in": 32, "tglf_kx0_in": 32, "tglf_ky_in": 32, "tglf_kygrid_model_in": 32, "tglf_linsker_factor_in": 32, "tglf_mass_in": 32, "tglf_nbasis_max_in": 32, "tglf_nbasis_min_in": 32, "tglf_new_eikonal_in": [30, 32], "tglf_nky_in": 32, "tglf_nmodes_in": 32, "tglf_ns_in": 32, "tglf_nwidth_in": 32, "tglf_nxgrid_in": 32, "tglf_p_prime_loc_in": 32, "tglf_park_in": 32, "tglf_q_loc_in": 32, "tglf_q_prime_loc_in": 32, "tglf_q_sa_in": 32, "tglf_rlns_in": 32, "tglf_rlts_in": 32, "tglf_rmaj_loc_in": 32, "tglf_rmaj_sa_in": 32, "tglf_rmin_loc_in": 32, "tglf_rmin_sa_in": 32, "tglf_s_delta_loc_in": 32, "tglf_s_kappa_loc_in": 32, "tglf_s_zeta_loc_in": 32, "tglf_sat_rule_in": 32, "tglf_shat_sa_in": 32, "tglf_sign_bt_in": 32, "tglf_sign_it_in": 32, "tglf_taus_in": 32, "tglf_theta0_sa_in": 32, "tglf_theta_trapped_in": 32, "tglf_tm": 32, "tglf_use_bisection_in": 32, "tglf_use_bpar_in": 32, "tglf_use_bper_in": 32, "tglf_use_inboard_detrapped_in": 32, "tglf_use_mhd_rule_in": 32, "tglf_use_transport_model_in": 32, "tglf_vexb_in": 32, "tglf_vexb_shear_in": 32, "tglf_vpar_in": 32, "tglf_vpar_model_in": 32, "tglf_vpar_shear_in": 32, "tglf_vpar_shear_model_in": 32, "tglf_wd_zero_in": 32, "tglf_width_in": 32, "tglf_width_min_in": 32, "tglf_write_wavefunction_flag_in": 32, "tglf_xnu_factor_in": 32, "tglf_xnu_model_in": 32, "tglf_xnue_in": 32, "tglf_xwell_sa_in": 32, "tglf_zeff_in": 32, "tglf_zeta_loc_in": 32, "tglf_zmaj_loc_in": 32, "tglf_zs_in": 32, "tgyro": [9, 17, 18, 24, 27, 42], "tgyro_den_method": [17, 40], "tgyro_den_method0": 39, "tgyro_den_method1": 39, "tgyro_den_method2": 39, "tgyro_den_method3": 39, "tgyro_den_method4": 39, "tgyro_iteration_method": [17, 40], "tgyro_mod": [17, 40], "tgyro_neo_method": [17, 40], "tgyro_relax_iter": [17, 40], "tgyro_rmax": 39, "tgyro_therm_flag": [17, 40], "tgyro_therm_flag1": 39, "tgyro_write_profiles_flag": [17, 40], "than": [4, 5, 13, 26, 30, 32, 38, 39], "thank": 28, "thei": [13, 21], "them": 26, "themselv": 22, "theoret": [17, 34], "theori": [10, 13, 17, 21, 22, 27, 28, 34, 39, 42], "thermal": [13, 16, 18, 22, 24, 26, 39, 40, 42], "thermodiffus": 16, "thermonuclear": 39, "thermostat": 42, "thesi": [13, 16, 42], "theta": [5, 6, 7, 10, 16, 22, 24, 26, 30, 32, 34], "theta0_sa": [17, 32], "theta_0": [5, 41], "theta_i": 5, "theta_j": 24, "theta_r": 10, "theta_trap": [17, 32], "thi": [0, 3, 5, 8, 9, 10, 11, 13, 14, 16, 19, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 38, 39], "thing": 16, "third": [9, 19], "thome": 42, "those": [13, 21, 28], "though": 38, "thousand": [3, 11, 13], "thread": [0, 7], "three": [16, 38], "threed": 22, "threed_exb_dphi0dr": [17, 23], "threed_exb_model": [17, 23], "threed_model": [17, 23], "threshold": [13, 30, 32], "through": [17, 26], "throughout": 26, "thu": [5, 10, 13, 22, 26, 38], "thursdai": 41, "ti": [4, 13, 18, 42], "tild": 31, "tilt": [6, 10, 18], "tim": 29, "time": [3, 4, 5, 10, 13, 14, 16, 22, 24, 26, 27, 28, 30, 32, 33, 38, 41], "timer": 7, "timestamp": 7, "timestep": [4, 5, 13, 41], "tn": 42, "tobia": 28, "togeth": [5, 21], "toggl": [5, 6, 39, 40], "tokamak": [10, 13, 26, 28, 29, 42], "told": 42, "toler": [4, 5, 6], "tool": [2, 4, 13, 18, 21, 25, 27, 28, 42], "top": [0, 30, 32], "topic": [9, 16, 28, 42], "tor": [10, 28, 30, 32], "torodi": 22, "toroid": [3, 5, 6, 13, 16, 17, 18, 22, 23, 24, 26, 30, 31, 32, 42], "toroidals_per_proc": 6, "torqu": [18, 26], "tort": 19, "toru": [5, 22], "tot": [37, 39], "total": [0, 18, 22, 24, 31, 38, 39], "toward": [3, 11, 13], "transform": [24, 39], "transit": 13, "transp": 25, "transport": [3, 5, 9, 10, 11, 17, 19, 22, 25, 26, 28, 29, 32, 38, 39, 42], "transvers": [30, 32], "trap": [4, 13, 16, 26, 29, 30, 32, 42], "trap_grid": 28, "trapezoid": 38, "treat": [3, 5, 13, 21, 22, 26, 30], "treatment": [10, 42], "triangular": [5, 6, 10, 18, 22, 23, 30, 32], "trigger": [5, 13], "true": [13, 26, 30, 32, 38], "truli": 16, "truncat": 38, "truth": 13, "tsujii": 42, "tube": [13, 16], "tur": 34, "turb": 38, "turbul": [3, 11, 13, 19, 26, 28, 34, 38, 42], "turco": 42, "tutori": 28, "two": [3, 16, 28, 30, 32, 38, 42], "tynan": 42, "type": [0, 8, 18, 30, 31, 32], "typic": [5, 10, 13, 22, 25], "u": [6, 9, 13, 24, 26, 30, 42], "u_": [24, 26], "ubuntu": 0, "ucsd": 13, "udsymmetry_flag": 6, "uk": 42, "uncertainti": [13, 16], "unchang": [5, 13, 39], "under": [13, 26], "underestim": 16, "underli": [13, 26], "underpredict": [13, 16], "understand": [3, 11, 34], "unequ": 39, "unifi": 17, "unimport": [5, 14], "uniqu": [25, 38], "unit": [3, 4, 5, 7, 10, 17, 18, 21, 22, 24, 31, 32, 34], "uniti": 39, "units_in": 32, "univ": 16, "univers": [13, 42], "unless": 28, "unlik": [5, 33], "unperturb": 16, "unphys": 30, "unpublish": 13, "unshift": 10, "unsolv": 13, "unstabl": [5, 13, 30, 32], "unsubstanti": 13, "until": 13, "up": [0, 6, 16, 18, 21, 24, 28, 30, 32], "up_alpha": 6, "up_radi": 6, "up_theta": 6, "updat": [5, 6, 9, 28, 38, 40], "upgrad": 42, "upon": 13, "upper": 22, "upshift": 13, "upwind": [5, 6, 42], "upwind_single_flag": 6, "urban": 17, "urg": 28, "url": [12, 42], "us": [0, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42], "usag": [5, 7], "use_bisect": [17, 32], "use_bp": [17, 32], "use_bpar": [17, 32], "use_inboard_detrap": [17, 32], "use_lock": 0, "use_mhd_rul": [17, 32], "use_thread": 0, "use_transport_model": [17, 32], "user": [0, 3, 5, 17, 19, 30, 32, 33, 42], "usernam": 9, "usual": [5, 26], "util": 13, "v": [2, 21, 22, 23, 24, 26, 28, 34, 38, 42], "v_": [22, 24, 26, 30, 32], "v_a": 7, "v_i": 5, "v_p": 10, "v_t": 10, "valid": [11, 13, 17, 24, 26, 28, 42], "valu": [4, 5, 7, 13, 14, 16, 22, 23, 24, 28, 30, 32, 39, 42], "van": 42, "vanish": 13, "varepsilon": 22, "varepsilon_": [5, 24], "vari": [13, 16, 26], "variabl": [13, 17, 34, 38], "variant": [13, 38], "variat": [3, 11, 13, 24, 38, 39], "variou": [7, 13, 21, 28], "varphi": [5, 10, 22, 24, 26, 34], "vathd": [13, 42], "vector": [7, 13, 22, 24, 38], "veloc": [3, 5, 6, 18, 21, 22, 23, 26, 28, 30, 31, 32, 41, 42], "velocity_ord": 6, "veri": [5, 8, 16], "verif": [11, 13, 17, 28, 42], "verifi": [13, 16], "verlag": 42, "verner": 5, "version": [7, 9, 28, 30, 39], "versu": [7, 16, 41], "vertic": 16, "vetter": [13, 42], "vexb": [17, 32], "vexb_shear": [17, 32], "via": [10, 13, 16, 17, 22, 23, 42], "view": [5, 13, 22], "virtual": 41, "visual": 41, "vol": [24, 42], "voltag": 13, "volum": [34, 38], "vpar": [30, 32], "vpar_1": [17, 32], "vpar_model": [17, 32], "vpar_shear_1": [17, 32], "vpar_shear_model": [17, 32], "vpol": 18, "vtor": 18, "w": [8, 24, 27, 34, 42], "w_a": 34, "wa": [0, 3, 10, 11, 13, 16, 21, 25, 26, 33, 38], "wabc06": [13, 42], "wai": [26, 38], "wal05": [13, 42], "wall": [18, 27, 34], "waltz": [4, 12, 13, 42], "wan": 42, "warranti": 19, "wast": 13, "watanab": 42, "wathd": [13, 42], "wave": [13, 16, 30, 42], "wavelength": [5, 13, 26], "wavenumb": [3, 4, 5, 6, 11], "wc05": [13, 42], "wcc": [13, 42], "wcf07": [13, 42], "wch": [13, 42], "wcp06": [13, 42], "wcr02": [13, 42], "wd_zero": [17, 32], "we": [0, 4, 5, 7, 10, 11, 13, 16, 22, 24, 26, 27, 28, 29, 33, 34, 38], "weak": [5, 38], "weaker": 13, "weber": 18, "weight": [7, 29, 30, 31, 32], "welcom": [9, 19, 28], "well": [13, 16, 21, 26, 28, 30, 32], "were": [13, 16, 29], "wh08": [13, 42], "what": [0, 4, 6, 8, 13, 18], "whatsoev": 13, "when": [0, 3, 4, 5, 6, 11, 13, 21, 22, 24, 30, 31, 32, 38, 39], "where": [3, 4, 5, 10, 11, 13, 16, 22, 24, 26, 29, 30, 34, 38, 39], "wherea": [4, 10, 13, 26], "wherev": 13, "whether": [13, 19, 22, 23], "which": [3, 4, 5, 10, 11, 13, 16, 22, 25, 26, 28, 29, 31, 32, 38, 39], "while": [16, 22, 28, 38, 39], "white": [28, 42], "whiteros": 42, "who": 26, "whom": 19, "why": [4, 13], "wide": [13, 16, 21], "widehat": 38, "width": [13, 17], "width_min": [17, 32], "wiki": 13, "william": 42, "winter": 13, "within": [13, 16], "without": [16, 19, 26, 38], "wkm94": [13, 42], "wkmh95": [13, 42], "wolf": 42, "wong": [22, 26, 42], "word": 10, "work": [4, 13, 16, 17, 26, 28, 30, 41], "worker": 13, "workshop": [17, 20], "worldwid": 13, "worlei": [13, 42], "would": [5, 8, 10, 38], "write": [8, 10, 26, 34, 39, 40], "write_wavefunction_flag": [17, 32], "written": [5, 13, 16, 22, 24, 38, 39], "wrote": 4, "ws08": [13, 42], "wsch07": [13, 42], "wsd": [13, 42], "wsm": [13, 28, 42], "wukitch": 42, "www": 2, "x": [30, 32, 34, 38, 42], "x1": [13, 42], "x_": 24, "x_a": [22, 24], "xcode": 2, "xd1": [13, 42], "xi": [5, 6, 22, 23, 24], "xi_i": 5, "xnu_factor": [17, 32], "xnu_model": [17, 32], "xnue": [17, 32], "xquartz": 2, "xt3": [13, 42], "xwell_sa": [17, 32], "y": [30, 32, 34, 42], "yann": 28, "year": [11, 13, 28], "yearli": 17, "yield": 13, "york": 42, "you": [0, 4, 8, 17, 30], "your": [8, 9, 17, 41], "z": [10, 22, 34, 38, 39, 42], "z0": 22, "z_": [6, 17, 18, 23, 24, 30, 32, 38, 39], "z_0": [5, 10, 18, 22], "z_1": [5, 22], "z_2": [5, 22], "z_3": [5, 22], "z_a": 26, "z_c": 16, "z_e": 38, "z_eff": 18, "z_i": 38, "zeeland": 42, "zeff": [17, 32], "zeng": 42, "zero": [5, 13, 22, 30, 32, 39], "zeroth": [22, 24, 26, 39], "zeta": [6, 10, 17, 18, 23, 30, 32], "zeta_loc": [17, 32], "zf": 30, "zf_test_mod": 6, "zhang": 42, "zhu": 42, "zmag": [6, 10, 18], "zmag_over_a": [10, 17, 23], "zmaj_loc": [17, 32], "zonal": [5, 6, 13, 30, 42], "zoom": 41, "zs_1": [17, 32], "\u03b1": 42}, "titles": ["Build on your laptop", "Ubuntu/Mint", "OSX Sonoma", "CGYRO", "FAQ", "Alphabetical list for input.cgyro", "Tabular list for input.cgyro", "CGYRO output files", "Running Cases", "Download and user agreement", "FLUX-SURFACE GEOMETRY", "GYRO", "Gallery of classic GYRO images (circa 2003)", "Gyrokinetic Simulation in the 2000s", "Alphabetical list for input.gyro", "Tabular list for input.gyro", "GYRO verification and validation (pre 2010)", "The General Atomics GACODE Suite", "input.gacode", "GACODE License", "Miscellaneous", "NEO", "Alphabetical list for input.neo", "Parameters for input.neo", "NEO Output Files", "profiles_gen", "PLASMA ROTATION THEORY", "Prebuilt Environments", "DIII-D L-mode shortfall", "TGLF", "Alphabetical list for input.tglf", "Alphabetical list for out.tglf files", "Table of inputs and outputs", "TGYRO", "Equations solved in TGYRO", "OUTPUT", "PLOT", "Scenarios and connection to energy sources", "TGYRO solver algorithm", "input.tgyro Alphabetical List", "input.tgyro Tabular List", "CGYRO Workshop 2022", "References"], "titleterms": {"": [5, 32], "2000": 13, "2001": 16, "2002": 13, "2003": [12, 13], "2004": [13, 16], "2005": 13, "2006": [13, 16], "2007": 13, "2008": 13, "2009": [13, 16], "2010": 16, "2013": 28, "2022": 41, "25": 28, "A": 13, "BES": 16, "The": [13, 17, 26], "_scale": 22, "abstract": 16, "access": 9, "acknowledg": 28, "ad": 28, "adiabat": 16, "adiabatic_elec": 30, "advanc": 6, "against": 29, "agenda": 41, "agreement": 9, "algorithm": 38, "alpha": 32, "alpha_": 30, "alpha_mach": 30, "alpha_p": 30, "alpha_quench": 30, "alpha_sa": 30, "alpha_zf": 30, "alphabet": [5, 14, 22, 30, 31, 39], "amp": 5, "amp0": 5, "amp_phi_n": 14, "aniso_model_": 22, "anomal": 16, "appropri": [9, 42], "ar": 13, "as_1": 30, "ask": 3, "atom": 17, "b_model_sa": 30, "balanc": 26, "base": 16, "basi": 26, "batch": 8, "benchmark": 28, "beta": 30, "beta_star": 22, "beta_star_scal": 5, "betae_unit": 5, "betae_unit_scal": 5, "bound": 10, "box": 10, "box_siz": 5, "brief": 3, "btccw": [5, 22], "build": 0, "c": 16, "can": 13, "case": [3, 8, 16], "cer": 16, "cgyro": [3, 5, 6, 7, 41], "chang": 32, "circa": 12, "classic": 12, "clebsch": 10, "code": [0, 3, 9, 13, 17, 28], "coeffici": 16, "collis": 6, "collision_ene_diffus": 5, "collision_ene_restor": 5, "collision_field_model": 5, "collision_kperp": 5, "collision_model": [5, 22], "collision_mom_restor": 5, "collision_precision_mod": 5, "command": 8, "comment": 38, "common": 7, "comparison": 16, "compression": 16, "comput": [13, 38], "concept": 0, "connect": [26, 34, 37], "consider": 26, "consist": 26, "control": [6, 15, 32, 40], "coordin": 10, "correctli": 13, "cpu": 27, "cross": 28, "cyclon": 16, "d": [16, 28], "data": [3, 7, 16, 21, 26, 29, 33], "deby": 30, "debye_factor": 30, "delta": [5, 22], "delta_loc": 30, "delta_t": 5, "delta_t_method": 5, "dens_": [5, 22], "densiti": 34, "density_spectrum": 31, "depend": [7, 23], "descript": [3, 24], "design": 13, "detail": 24, "diagnost": 16, "differ": 13, "diii": [16, 28], "discret": 38, "dissip": 6, "dlnndr_": [5, 22], "dlnndre_ad": 22, "dlntdr_": [5, 22], "dlntdr_para_": 22, "dlntdr_perp_": 22, "dlntdre_ad": 22, "doppler": 16, "download": 9, "dphi0dr": 22, "dramat": 13, "drmajdx_loc": 30, "drmindx_loc": 30, "dzmag": 5, "dzmajdx_loc": 30, "e_max": 5, "effect": [10, 13, 23], "eigenvalue_spectrum": 31, "electromagnet": 16, "electron": 16, "energet": 16, "energi": [34, 37], "environ": [0, 27], "epar0": 22, "epar0_spitz": 22, "equat": [33, 34], "equil": 24, "equilibria": 10, "equilibrium": [17, 23], "equilibrium_model": [5, 22], "error_tol": 5, "etg_factor": 30, "eulerian": 13, "exampl": 8, "exp_norm": 24, "experiment": [24, 26, 28, 29], "extra": 23, "f": 24, "faq": 4, "fast": 16, "feedback": 40, "field": [6, 10], "field_print_flag": 5, "field_spectrum": 31, "file": [0, 6, 7, 18, 24, 31, 32], "filter": 30, "find_width": 30, "first": 0, "flux": [10, 34], "forc": 26, "formal": 26, "formul": 38, "freq_tol": 5, "frequent": 3, "from": 13, "ft_model_sa": 30, "full": 13, "futur": 3, "ga": 27, "gacod": [17, 18, 19], "galleri": 12, "gamma_": 5, "gamma_e_scal": 5, "gamma_p": 5, "gamma_p_scal": 5, "gaussian": 32, "gchat": 30, "gener": [17, 23], "geo_ni": 22, "geo_yin": 22, "geometri": [6, 10, 17, 23, 32], "geometry_flag": 30, "gflux_print_flag": 5, "ghat": 30, "gkw": 28, "global": [6, 13, 16], "gpu": 27, "gpu_bigmem_flag": 5, "gradb_factor": 30, "gradient": 16, "grid": [24, 38], "gyro": [11, 12, 14, 15, 16, 28], "gyrobohm": 13, "gyrokinet": [13, 16], "h_print_flag": 5, "have": 13, "high": 40, "histori": [13, 25], "ibranch": 30, "iflux": 30, "imag": [3, 12], "impur": 16, "inadequ": 13, "independ": 7, "input": [3, 5, 6, 14, 15, 18, 21, 22, 23, 26, 30, 32, 33, 39, 40], "intensity_spectrum": 31, "interfac": [23, 33], "ipccw": [5, 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": 5, "n_global": 5, "n_radial": [5, 22], "n_speci": [5, 22], "n_theta": [5, 22], "n_toroid": 5, "n_xi": [5, 22], "nbasis_max": 30, "nbasis_min": 30, "ne_ad": 22, "necessari": 13, "neo": [21, 22, 23, 24], "nersc": 27, "new_eikon": 30, "nky": 30, "nmode": 30, "nonaxisymmetr": 23, "nonlinear": 13, "nonlinear_flag": 5, "normal": [3, 7, 21], "nsts_crossphase_spectrum": 31, "nu_1": 22, "nu_e": 5, "nu_glob": 5, "numer": [6, 23], "nup_alpha": 5, "nup_radi": 5, "nup_theta": 5, "nwidth": 30, "nxgrid": 30, "omega": 27, "omega_rot": 22, "omega_rot_deriv": 22, "openbla": 0, "optim": 6, "orient": 10, "osx": 2, "out": [24, 31], "output": [3, 6, 7, 21, 24, 32, 33, 35], "overview": [11, 18, 25, 28, 29, 33], "own": 32, "p_prime_loc": 30, "parallel": 13, "paramet": [6, 10, 15, 23, 26, 32, 40], "park": 30, "particl": 16, "past": 3, "pci": 16, "perlmutt": 27, "perspect": 13, "perturb": 16, "phi": 24, "physic": [6, 17, 23, 26, 40], "plasma": [6, 17, 23, 26], "platform": 0, "plot": [3, 33, 36], "poloid": 10, "power": 34, "pre": 16, "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, "synthet": 16, "tabl": [10, 32], "tabular": [6, 15, 40], "taus_1": 30, "te_ad": 22, "temp_": [5, 22], "temp_para_": 22, "temp_perp_": 22, "temperatur": 16, "temperature_spectrum": 31, "tglf": [29, 30, 31, 32], "tgyro": [33, 34, 38, 39, 40], "tgyro_den_method": 39, "tgyro_iteration_method": 39, "tgyro_mod": 39, "tgyro_neo_method": 39, "tgyro_relax_iter": 39, "tgyro_therm_flag": 39, "tgyro_write_profiles_flag": 39, "theoret": 26, "theori": [24, 26], "theory_nclass": 24, "theta0_sa": 30, "theta_plot": 5, "theta_trap": 30, "threed_exb_dphi0dr": 22, "threed_exb_model": 22, "threed_model": 22, "time": [6, 7], "tokamak": 16, "tore": 16, "toroid": 10, "toroidals_per_proc": 5, "toru": 13, "transport": [13, 16, 24, 33, 34], "transport_exp": 24, "transport_flux": 24, "transport_gv": 24, "turbul": 16, "ubuntu": 1, "udsymmetry_flag": 5, "ul1": 13, "ul2": 13, "ul3": 13, "ul4": 13, "unit": [30, 38], "up_alpha": 5, "up_radi": 5, "up_theta": 5, "upwind_single_flag": 5, "urban": 13, "usag": 8, "use_bisect": 30, "use_bp": 30, "use_bpar": 30, "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/docs/shortfall.html b/docs/shortfall.html
index fd5ada8..41643b6 100644
--- a/docs/shortfall.html
+++ b/docs/shortfall.html
@@ -123,7 +123,7 @@ <h2>Key publications and presentations<a class="headerlink" href="#key-publicati
 <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">
 <li><ol class="upperalpha simple">
-<li><p>E. White <em>et al.</em>, “Measurements of core electron temperature and density fluctuations in DIII-D and comparison to nonlinear gyrokinetic simulations”, <em>Physics of Plasmas</em> <strong>15</strong> 056116 (2008) <span id="id1">[<a class="reference internal" href="zreferences.html#id139" 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></p></li>
+<li><p>E. White <em>et al.</em>, “Measurements of core electron temperature and density fluctuations in DIII-D and comparison to nonlinear gyrokinetic simulations”, <em>Physics of Plasmas</em> <strong>15</strong> 056116 (2008) <span id="id1">[<a class="reference internal" href="zreferences.html#id143" 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></p></li>
 </ol>
 </li>
 </ul>
@@ -131,7 +131,7 @@ <h2>Key publications and presentations<a class="headerlink" href="#key-publicati
 <li><p>More detailed <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a> comparisons including documentation of synthetic diagnostic implementation.</p>
 <ul class="simple">
 <li><ol class="upperalpha simple" start="3">
-<li><p>Holland <em>et al.</em>, “Implementation and Application of Two Synthetic Diagnostics for Validating Simulations of Core Tokamak Turbulence”, <em>Physics of Plasmas</em> <strong>16</strong> 052301 (2009) <span id="id2">[<a class="reference internal" href="zreferences.html#id65" title="C. Holland, A.E. White, G.R. McKee, M.W. Shafer, J. Candy, R.E Waltz, L. Schmitz, and G.R Tynan. Implementation and application of two synthetic diagnostics for validating simulations of core tokamak turbulence. Phys. Plasmas, 16:052301, 2009.">HWM+09</a>]</span></p></li>
+<li><p>Holland <em>et al.</em>, “Implementation and Application of Two Synthetic Diagnostics for Validating Simulations of Core Tokamak Turbulence”, <em>Physics of Plasmas</em> <strong>16</strong> 052301 (2009) <span id="id2">[<a class="reference internal" href="zreferences.html#id66" title="C. Holland, A.E. White, G.R. McKee, M.W. Shafer, J. Candy, R.E Waltz, L. Schmitz, and G.R Tynan. Implementation and application of two synthetic diagnostics for validating simulations of core tokamak turbulence. Phys. Plasmas, 16:052301, 2009.">HWM+09</a>]</span></p></li>
 </ol>
 </li>
 </ul>
@@ -160,7 +160,7 @@ <h2>Key publications and presentations<a class="headerlink" href="#key-publicati
 <li><p>Analysis of this discharge using <a class="reference external" href="http://genecode.org"><cite>GENE</cite></a> code.</p>
 <ul class="simple">
 <li><ol class="upperalpha simple" start="20">
-<li><p>Görler <em>et al.</em>, “A flux-matched gyrokinetic analysis of DIII-D L-mode turbulence”, <em>Physics of Plasmas</em> <strong>21</strong> 122307 (2014) <span id="id5">[<a class="reference internal" href="zreferences.html#id57" title="T. Görler, A.E. White, D. Told, F. Jenko, C. Holland, and T.L. Rhodes. A flux-matched gyrokinetic analysis of diii-d l-mode turbulence. Phys. Plasmas, 21:122307, 2014. doi:10.1063/1.4904301.">GWT+14</a>]</span></p></li>
+<li><p>Görler <em>et al.</em>, “A flux-matched gyrokinetic analysis of DIII-D L-mode turbulence”, <em>Physics of Plasmas</em> <strong>21</strong> 122307 (2014) <span id="id5">[<a class="reference internal" href="zreferences.html#id59" title="T. Görler, A.E. White, D. Told, F. Jenko, C. Holland, and T.L. Rhodes. A flux-matched gyrokinetic analysis of diii-d l-mode turbulence. Phys. Plasmas, 21:122307, 2014. doi:10.1063/1.4904301.">GWT+14</a>]</span></p></li>
 </ol>
 </li>
 </ul>
@@ -168,7 +168,7 @@ <h2>Key publications and presentations<a class="headerlink" href="#key-publicati
 <li><p>Validation tutorial article documenting systematic near-edge shortfall observations with <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a> for multiple DIII-D L-mode discharges (including shot #128913)</p>
 <ul class="simple">
 <li><ol class="upperalpha simple" start="3">
-<li><p>Holland, “Validation metrics for turbulent plasma transport”, <em>Physics of Plasmas</em> <strong>23</strong> 060901 (2016) <span id="id6">[<a class="reference internal" href="zreferences.html#id68" title="C. Holland. Validation metrics for turbulent plasma transport. Phys. Plasmas, 23:060901, 2016.">Hol16</a>]</span></p></li>
+<li><p>Holland, “Validation metrics for turbulent plasma transport”, <em>Physics of Plasmas</em> <strong>23</strong> 060901 (2016) <span id="id6">[<a class="reference internal" href="zreferences.html#id69" title="C. Holland. Validation metrics for turbulent plasma transport. Phys. Plasmas, 23:060901, 2016.">Hol16</a>]</span></p></li>
 </ol>
 </li>
 </ul>
@@ -192,7 +192,7 @@ <h2>EXPERIMENTAL profiles<a class="headerlink" href="#experimental-profiles" tit
 <li><p><a class="reference download internal" download="" href="_downloads/9daeaf332c0cb6235779280cce7f1ca0/old.input.profiles.geo.128913_shortfall.txt"><code class="xref download docutils literal notranslate"><span class="pre">OLD</span> <span class="pre">input.profiles.geo</span></code></a></p></li>
 </ul>
 </li>
-<li><p>Note that there may be small numerical (but not qualitative) differences between the profiles in these files and the values reported in <span id="id7">[<a class="reference internal" href="zreferences.html#id65" title="C. Holland, A.E. White, G.R. McKee, M.W. Shafer, J. Candy, R.E Waltz, L. Schmitz, and G.R Tynan. Implementation and application of two synthetic diagnostics for validating simulations of core tokamak turbulence. Phys. Plasmas, 16:052301, 2009.">HWM+09</a>]</span> due to 10 years of code evolution since the original publication.  We <strong>strongly</strong> urge all future work use the most recent <a class="reference internal" href="input_gacode.html#input-gacode"><span class="std std-ref">input.gacode</span></a> file for future studies, to ensure a common starting point and basis for comparison.</p></li>
+<li><p>Note that there may be small numerical (but not qualitative) differences between the profiles in these files and the values reported in <span id="id7">[<a class="reference internal" href="zreferences.html#id66" title="C. Holland, A.E. White, G.R. McKee, M.W. Shafer, J. Candy, R.E Waltz, L. Schmitz, and G.R Tynan. Implementation and application of two synthetic diagnostics for validating simulations of core tokamak turbulence. Phys. Plasmas, 16:052301, 2009.">HWM+09</a>]</span> due to 10 years of code evolution since the original publication.  We <strong>strongly</strong> urge all future work use the most recent <a class="reference internal" href="input_gacode.html#input-gacode"><span class="std std-ref">input.gacode</span></a> file for future studies, to ensure a common starting point and basis for comparison.</p></li>
 </ul>
 </section>
 <section id="gyro-results">
diff --git a/docs/tglf.html b/docs/tglf.html
index 36d7961..a4f201e 100644
--- a/docs/tglf.html
+++ b/docs/tglf.html
@@ -134,19 +134,19 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 </thead>
 <tbody>
 <tr class="row-even"><td><p>SAT0</p></td>
-<td><p><span id="id1">[<a class="reference internal" href="zreferences.html#id84" title="J. E. Kinsey, G. M. Staebler, and R. E. Waltz. The first transport code simulations using the trapped gyro-Landau-fluid model. Phys. Plasmas, 15(5):055908, 2008. doi:10.1063/1.2889008.">KSW08</a>, <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></p></td>
+<td><p><span id="id1">[<a class="reference internal" href="zreferences.html#id86" title="J. E. Kinsey, G. M. Staebler, and R. E. Waltz. The first transport code simulations using the trapped gyro-Landau-fluid model. Phys. Plasmas, 15(5):055908, 2008. doi:10.1063/1.2889008.">KSW08</a>, <a class="reference internal" href="zreferences.html#id100" 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></p></td>
 </tr>
 <tr class="row-odd"><td><p>Spectral Shift</p></td>
-<td><p><span id="id2">[<a class="reference internal" href="zreferences.html#id102" title="G. M. Staebler, R. E. Waltz, J. Candy, and J. E. Kinsey. New paradigm for suppression of gyrokinetic turbulence by velocity shear. Phys. Rev. Lett., 110:055003, 2013. doi:10.1103/PhysRevLett.110.055003.">SWCK13</a>, <a class="reference internal" href="zreferences.html#id103" title="G.M. Staebler, J. Candy, R.E. Waltz, J.E. Kinsey, and W.M. Solomon. A new paradigm for ExB velocity shear suppression of gyro-kinetic turbulence and the momentum pinch. Nuclear Fusion, 53(11):113017, 2013. doi:10.1088/0029-5515/53/11/113017.">SCW+13</a>]</span></p></td>
+<td><p><span id="id2">[<a class="reference internal" href="zreferences.html#id105" title="G. M. Staebler, R. E. Waltz, J. Candy, and J. E. Kinsey. New paradigm for suppression of gyrokinetic turbulence by velocity shear. Phys. Rev. Lett., 110:055003, 2013. doi:10.1103/PhysRevLett.110.055003.">SWCK13</a>, <a class="reference internal" href="zreferences.html#id106" title="G.M. Staebler, J. Candy, R.E. Waltz, J.E. Kinsey, and W.M. Solomon. A new paradigm for ExB velocity shear suppression of gyro-kinetic turbulence and the momentum pinch. Nuclear Fusion, 53(11):113017, 2013. doi:10.1088/0029-5515/53/11/113017.">SCW+13</a>]</span></p></td>
 </tr>
 <tr class="row-even"><td><p>SAT1</p></td>
-<td><p><span id="id3">[<a class="reference internal" href="zreferences.html#id104" title="G. M. Staebler, J. Candy, N. T. Howard, and C. Holland. The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence. Phys. Plasmas, 23(6):062518, 2016. doi:10.1063/1.4954905.">SCHH16</a>]</span></p></td>
+<td><p><span id="id3">[<a class="reference internal" href="zreferences.html#id108" title="G. M. Staebler, J. Candy, N. T. Howard, and C. Holland. The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence. Phys. Plasmas, 23(6):062518, 2016. doi:10.1063/1.4954905.">SCHH16</a>]</span></p></td>
 </tr>
 <tr class="row-odd"><td><p>SAT2</p></td>
-<td><p><span id="id4">[<a class="reference internal" href="zreferences.html#id105" title="G M Staebler, J Candy, E A Belli, J E Kinsey, N Bonanomi, and B Patel. Geometry dependence of the fluctuation intensity in gyrokinetic turbulence. Plasma Physics and Controlled Fusion, 63(1):015013, 2020. doi:10.1088/1361-6587/abc861.">SCB+20</a>, <a class="reference internal" href="zreferences.html#id106" title="G.M. Staebler, E. A. Belli, J. Candy, J.E. Kinsey, H. Dudding, and B. Patel. Verification of a quasi-linear model for gyrokinetic turbulent transport. Nuclear Fusion, 61(11):116007, 2021. doi:10.1088/1741-4326/ac243a.">SBC+21</a>]</span></p></td>
+<td><p><span id="id4">[<a class="reference internal" href="zreferences.html#id107" title="G M Staebler, J Candy, E A Belli, J E Kinsey, N Bonanomi, and B Patel. Geometry dependence of the fluctuation intensity in gyrokinetic turbulence. Plasma Physics and Controlled Fusion, 63(1):015013, 2020. doi:10.1088/1361-6587/abc861.">SCB+20</a>, <a class="reference internal" href="zreferences.html#id109" title="G.M. Staebler, E. A. Belli, J. Candy, J.E. Kinsey, H. Dudding, and B. Patel. Verification of a quasi-linear model for gyrokinetic turbulent transport. Nuclear Fusion, 61(11):116007, 2021. doi:10.1088/1741-4326/ac243a.">SBC+21</a>]</span></p></td>
 </tr>
 <tr class="row-even"><td><p>SAT3</p></td>
-<td><p><span id="id5">[<a class="reference internal" href="zreferences.html#id51" title="H.G. Dudding, F.J. Casson, D. Dickinson, B.S. Patel, C.M. Roach, E.A. Belli, and G.M. Staebler. A new quasilinear saturation rule for tokamak turbulence with application to the isotope scaling of transport. Nuclear Fusion, 62(9):096005, 2022. doi:10.1088/1741-4326/ac7a4d.">DCD+22</a>, <a class="reference internal" href="zreferences.html#id52" title="Harry George Dudding. A new quasilinear saturation rule for tokamak turbulence. PhD thesis, University of York, October 2022. URL: https://etheses.whiterose.ac.uk/32664/.">Dud22</a>]</span></p></td>
+<td><p><span id="id5">[<a class="reference internal" href="zreferences.html#id52" title="H.G. Dudding, F.J. Casson, D. Dickinson, B.S. Patel, C.M. Roach, E.A. Belli, and G.M. Staebler. A new quasilinear saturation rule for tokamak turbulence with application to the isotope scaling of transport. Nuclear Fusion, 62(9):096005, 2022. doi:10.1088/1741-4326/ac7a4d.">DCD+22</a>, <a class="reference internal" href="zreferences.html#id53" title="Harry George Dudding. A new quasilinear saturation rule for tokamak turbulence. PhD thesis, University of York, October 2022. URL: https://etheses.whiterose.ac.uk/32664/.">Dud22</a>]</span></p></td>
 </tr>
 </tbody>
 </table>
@@ -163,10 +163,10 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 </thead>
 <tbody>
 <tr class="row-even"><td><p>DIII-D</p></td>
-<td><p><span id="id6">[<a class="reference internal" href="zreferences.html#id58" title="B.A. Grierson, G.M. Staebler, W.M. Solomon, G.R. McKee, C. Holland, M. Austin, A. Marinoni, L. Schmitz, R.I. Pinsker, and DIII-D Team. Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER. Phys. Plasmas, 25(2):022509, 2018.">GSS+18</a>, <a class="reference internal" href="zreferences.html#id142" title="K.E. Thome, X.D. Du, B.A. Grierson, G.J. Kramer, C.C. Petty, C. Holland, M. Knolker, G.R. McKee, J. McClenaghan, D.C. Pace, T.L. Rhodes, S.P. Smith, C. Sung, F. Turco, M.A. Van Zeeland, L. Zeng, and Y.B. Zhu. Response of thermal and fast-ion transport to beam ion population, rotation and Te/Ti in the DIII-D steady state hybrid scenario. Nucl. Fusion, 61:036036, 2021.">TDG+21</a>]</span></p></td>
+<td><p><span id="id6">[<a class="reference internal" href="zreferences.html#id58" title="B.A. Grierson, G.M. Staebler, W.M. Solomon, G.R. McKee, C. Holland, M. Austin, A. Marinoni, L. Schmitz, R.I. Pinsker, and DIII-D Team. Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER. Phys. Plasmas, 25(2):022509, 2018.">GSS+18</a>, <a class="reference internal" href="zreferences.html#id118" title="K.E. Thome, X.D. Du, B.A. Grierson, G.J. Kramer, C.C. Petty, C. Holland, M. Knolker, G.R. McKee, J. McClenaghan, D.C. Pace, T.L. Rhodes, S.P. Smith, C. Sung, F. Turco, M.A. Van Zeeland, L. Zeng, and Y.B. Zhu. Response of thermal and fast-ion transport to beam ion population, rotation and Te/Ti in the DIII-D steady state hybrid scenario. Nucl. Fusion, 61:036036, 2021.">TDG+21</a>]</span></p></td>
 </tr>
 <tr class="row-odd"><td><p>NSTX</p></td>
-<td><p><span id="id7">[<a class="reference internal" href="zreferences.html#id143" title="S.M. Kaye and others. NSTX/NSTX-U theory, modeling and analysis results. Nucl. Fusion, 59:112007, 2019.">K+19</a>]</span></p></td>
+<td><p><span id="id7">[<a class="reference internal" href="zreferences.html#id81" title="S.M. Kaye and others. NSTX/NSTX-U theory, modeling and analysis results. Nucl. Fusion, 59:112007, 2019.">K+19</a>]</span></p></td>
 </tr>
 <tr class="row-even"><td><p>ASDEX</p></td>
 <td><p><span id="id8">[<a class="reference internal" href="zreferences.html#id8" title="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. Nucl. Fusion, 62:066015, 2022. doi:10.1088/1741-4326/ac592b.">AGT+22</a>]</span></p></td>
diff --git a/docs/tglf/tglf_list.html b/docs/tglf/tglf_list.html
index 0afaf30..faae098 100644
--- a/docs/tglf/tglf_list.html
+++ b/docs/tglf/tglf_list.html
@@ -210,7 +210,7 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <section id="alpha-e">
 <span id="tglf-alpha-e"></span><h2>ALPHA_E<a class="headerlink" href="#alpha-e" title="Link to this heading"></a></h2>
 <p><strong>Definition</strong></p>
-<p>Multiplies ExB velocity shear for spectral shift model <span id="id1">[<a class="reference internal" href="../zreferences.html#id102" title="G. M. Staebler, R. E. Waltz, J. Candy, and J. E. Kinsey. New paradigm for suppression of gyrokinetic turbulence by velocity shear. Phys. Rev. Lett., 110:055003, 2013. doi:10.1103/PhysRevLett.110.055003.">SWCK13</a>]</span>.</p>
+<p>Multiplies ExB velocity shear for spectral shift model <span id="id1">[<a class="reference internal" href="../zreferences.html#id105" title="G. M. Staebler, R. E. Waltz, J. Candy, and J. E. Kinsey. New paradigm for suppression of gyrokinetic turbulence by velocity shear. Phys. Rev. Lett., 110:055003, 2013. doi:10.1103/PhysRevLett.110.055003.">SWCK13</a>]</span>.</p>
 <p><strong>Comments</strong></p>
 <ul class="simple">
 <li><p>DEFAULT = 1.0</p></li>
@@ -738,10 +738,10 @@ <h1>Alphabetical list for input.tglf<a class="headerlink" href="#alphabetical-li
 <span id="tglf-sat-rule"></span><h2>SAT_RULE<a class="headerlink" href="#sat-rule" title="Link 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 <span id="id2">[<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>.</p></li>
-<li><p>SAT_RULE = 1 finds dominant saturation mechanism (ZF mixing rate or drift-wave growth rate) and includes ky-coupling <span id="id3">[<a class="reference internal" href="../zreferences.html#id104" title="G. M. Staebler, J. Candy, N. T. Howard, and C. Holland. The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence. Phys. Plasmas, 23(6):062518, 2016. doi:10.1063/1.4954905.">SCHH16</a>]</span>.</p></li>
-<li><p>SAT_RULE = 2 builds on SAT1 with refined geometric effects (due to Shafranov shift and elongation), improved TEM physics, simplified spectral shift <span id="id4">[<a class="reference internal" href="../zreferences.html#id105" title="G M Staebler, J Candy, E A Belli, J E Kinsey, N Bonanomi, and B Patel. Geometry dependence of the fluctuation intensity in gyrokinetic turbulence. Plasma Physics and Controlled Fusion, 63(1):015013, 2020. doi:10.1088/1361-6587/abc861.">SCB+20</a>, <a class="reference internal" href="../zreferences.html#id106" title="G.M. Staebler, E. A. Belli, J. Candy, J.E. Kinsey, H. Dudding, and B. Patel. Verification of a quasi-linear model for gyrokinetic turbulent transport. Nuclear Fusion, 61(11):116007, 2021. doi:10.1088/1741-4326/ac243a.">SBC+21</a>]</span>.</p></li>
-<li><p>SAT_RULE = 3 builds on SAT2, captures anti-gyroBohm scaling of fluxes, treats saturation of ITG and TEM differently, has quasi-linear model approximations to align quasi-linear weights with NL GK simulations <span id="id5">[<a class="reference internal" href="../zreferences.html#id51" title="H.G. Dudding, F.J. Casson, D. Dickinson, B.S. Patel, C.M. Roach, E.A. Belli, and G.M. Staebler. A new quasilinear saturation rule for tokamak turbulence with application to the isotope scaling of transport. Nuclear Fusion, 62(9):096005, 2022. doi:10.1088/1741-4326/ac7a4d.">DCD+22</a>, <a class="reference internal" href="../zreferences.html#id52" title="Harry George Dudding. A new quasilinear saturation rule for tokamak turbulence. PhD thesis, University of York, October 2022. URL: https://etheses.whiterose.ac.uk/32664/.">Dud22</a>]</span>.</p></li>
+<li><p>SAT_RULE = 0 finds zonal flow shear at each ky <span id="id2">[<a class="reference internal" href="../zreferences.html#id100" 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>.</p></li>
+<li><p>SAT_RULE = 1 finds dominant saturation mechanism (ZF mixing rate or drift-wave growth rate) and includes ky-coupling <span id="id3">[<a class="reference internal" href="../zreferences.html#id108" title="G. M. Staebler, J. Candy, N. T. Howard, and C. Holland. The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence. Phys. Plasmas, 23(6):062518, 2016. doi:10.1063/1.4954905.">SCHH16</a>]</span>.</p></li>
+<li><p>SAT_RULE = 2 builds on SAT1 with refined geometric effects (due to Shafranov shift and elongation), improved TEM physics, simplified spectral shift <span id="id4">[<a class="reference internal" href="../zreferences.html#id107" title="G M Staebler, J Candy, E A Belli, J E Kinsey, N Bonanomi, and B Patel. Geometry dependence of the fluctuation intensity in gyrokinetic turbulence. Plasma Physics and Controlled Fusion, 63(1):015013, 2020. doi:10.1088/1361-6587/abc861.">SCB+20</a>, <a class="reference internal" href="../zreferences.html#id109" title="G.M. Staebler, E. A. Belli, J. Candy, J.E. Kinsey, H. Dudding, and B. Patel. Verification of a quasi-linear model for gyrokinetic turbulent transport. Nuclear Fusion, 61(11):116007, 2021. doi:10.1088/1741-4326/ac243a.">SBC+21</a>]</span>.</p></li>
+<li><p>SAT_RULE = 3 builds on SAT2, captures anti-gyroBohm scaling of fluxes, treats saturation of ITG and TEM differently, has quasi-linear model approximations to align quasi-linear weights with NL GK simulations <span id="id5">[<a class="reference internal" href="../zreferences.html#id52" title="H.G. Dudding, F.J. Casson, D. Dickinson, B.S. Patel, C.M. Roach, E.A. Belli, and G.M. Staebler. A new quasilinear saturation rule for tokamak turbulence with application to the isotope scaling of transport. Nuclear Fusion, 62(9):096005, 2022. doi:10.1088/1741-4326/ac7a4d.">DCD+22</a>, <a class="reference internal" href="../zreferences.html#id53" title="Harry George Dudding. A new quasilinear saturation rule for tokamak turbulence. PhD thesis, University of York, October 2022. URL: https://etheses.whiterose.ac.uk/32664/.">Dud22</a>]</span>.</p></li>
 </ul>
 <p><strong>Comments</strong></p>
 <ul class="simple">
diff --git a/docs/tgyro/equations.html b/docs/tgyro/equations.html
index abc578f..3719d70 100644
--- a/docs/tgyro/equations.html
+++ b/docs/tgyro/equations.html
@@ -124,7 +124,7 @@
 <span id="tgyro-equations"></span><h1>Equations solved in TGYRO<a class="headerlink" href="#equations-solved-in-tgyro" title="Link 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#id110" 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
+transport theory of Sugama <span id="id1">[<a class="reference internal" href="../zreferences.html#id113" 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
 detailed understanding of the theoretical foundations of GACODE.  Below we summarize
 Sugama’s form of the transport equations, with some practical simplifications and
 notational differences.</p>
diff --git a/docs/zreferences.html b/docs/zreferences.html
index 77a9e73..c581f82 100644
--- a/docs/zreferences.html
+++ b/docs/zreferences.html
@@ -99,8 +99,8 @@
   <section id="references">
 <h1>References<a class="headerlink" href="#references" title="Link to this heading"></a></h1>
 <p class="rubric">References</p>
-<table class="docutils align-default" id="id144">
-<caption><span class="caption-text"><strong>Appropriate References</strong></span><a class="headerlink" href="#id144" title="Link to this table"></a></caption>
+<table class="docutils align-default" id="id146">
+<caption><span class="caption-text"><strong>Appropriate References</strong></span><a class="headerlink" href="#id146" title="Link to this table"></a></caption>
 <colgroup>
 <col style="width: 27.3%" />
 <col style="width: 36.4%" />
@@ -127,7 +127,7 @@ <h1>References<a class="headerlink" href="#references" title="Link to this headi
 </tr>
 <tr class="row-odd"><td><p>TGLF</p></td>
 <td><p>transport model</p></td>
-<td><p><span id="id4">[<a class="reference internal" href="#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>, <a class="reference internal" href="#id100" title="G.M. Staebler and J.E. Kinsey. Electron collisions in the trapped gyro-landau fluid transport model. Phys. Plasmas, 17:122309, 2010.">SK10</a>]</span></p></td>
+<td><p><span id="id4">[<a class="reference internal" href="#id100" 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>, <a class="reference internal" href="#id103" title="G.M. Staebler and J.E. Kinsey. Electron collisions in the trapped gyro-landau fluid transport model. Phys. Plasmas, 17:122309, 2010.">SK10</a>]</span></p></td>
 </tr>
 <tr class="row-even"><td><p>TGYRO</p></td>
 <td><p>profile evolution</p></td>
@@ -239,7 +239,7 @@ <h1>References<a class="headerlink" href="#references" title="Link to this headi
 </div>
 <div class="citation" id="id28" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>CWR04<span class="fn-bracket">]</span></span>
-<p>J. Candy, R.E. Waltz, and M.N. Rosenbluth. Smooothness of turbulent transport across a minimum-$q$ surface. <em>Phys. Plasmas</em>, 11:1879, 2004.</p>
+<p>J. Candy, R.E. Waltz, and M.N. Rosenbluth. Smooothness of turbulent transport across a minimum-q surface. <em>Phys. Plasmas</em>, 11:1879, 2004.</p>
 </div>
 <div class="citation" id="id45" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>CPC+03<span class="fn-bracket">]</span></span>
@@ -250,42 +250,46 @@ <h1>References<a class="headerlink" href="#references" title="Link to this headi
 <p>J. Chowdhury, W. Wan, Y. Chen, S.E. Parker, R.J. Groebner, C. Holland, and N.T. Howard. Study of the l-mode tokamak plasma “shortfall” with local and global nonlinear gyrokinetic $\delta f$ particle-in-cell simulation. <em>Phys. Plasmas</em>, 21:112503, 2014.</p>
 </div>
 <div class="citation" id="id47" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span>DHCS91<span class="fn-bracket">]</span></span>
+<p>W.D. Dhaeseleer, W.N.G. Hitchon, J.D. Callen, and J.L. Shohet. <em>Flux coordinates and magnetic field structure</em>. Springer-Verlag, Berlin, 1991.</p>
+</div>
+<div class="citation" id="id48" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>DWBC96<span class="fn-bracket">]</span></span>
 <p>A.M. Dimits, T.J. Williams, J.A. Byers, and B.I. Cohen. Scalings of ion-temperature-gradient-driven anomalous transport in tokamaks. <em>Phys. Rev. Lett.</em>, 77:71, 1996.</p>
 </div>
-<div class="citation" id="id48" role="doc-biblioentry">
+<div class="citation" id="id49" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>DH95<span class="fn-bracket">]</span></span>
 <p>J.Q. Dong and W. Horton. Study of impurity mode and ion temperature gradient mode in toroidal plasmas. <em>Phys. Plasmas</em>, 2:3412, 1995.</p>
 </div>
-<div class="citation" id="id49" role="doc-biblioentry">
+<div class="citation" id="id50" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>DH93<span class="fn-bracket">]</span></span>
 <p>W. Dorland and G.W. Hammett. Gyrofluid turbulence models with kinetic effects. <em>Phys. Fluids B</em>, 5:812, 1993.</p>
 </div>
-<div class="citation" id="id50" role="doc-biblioentry">
+<div class="citation" id="id51" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>DJKR00<span class="fn-bracket">]</span></span>
 <p>W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers. Electron temperature gradient turbulence. <em>Phys. Rev. Lett.</em>, 85:5579, 2000.</p>
 </div>
-<div class="citation" id="id51" role="doc-biblioentry">
+<div class="citation" id="id52" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>DCD+22<span class="fn-bracket">]</span></span>
 <p>H.G. Dudding, F.J. Casson, D. Dickinson, B.S. Patel, C.M. Roach, E.A. Belli, and G.M. Staebler. A new quasilinear saturation rule for tokamak turbulence with application to the isotope scaling of transport. <em>Nuclear Fusion</em>, 62(9):096005, 2022. <a class="reference external" href="https://doi.org/10.1088/1741-4326/ac7a4d">doi:10.1088/1741-4326/ac7a4d</a>.</p>
 </div>
-<div class="citation" id="id52" role="doc-biblioentry">
+<div class="citation" id="id53" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>Dud22<span class="fn-bracket">]</span></span>
 <p>Harry George Dudding. <em>A new quasilinear saturation rule for tokamak turbulence</em>. PhD thesis, University of York, October 2022. URL: <a class="reference external" href="https://etheses.whiterose.ac.uk/32664/">https://etheses.whiterose.ac.uk/32664/</a>.</p>
 </div>
-<div class="citation" id="id53" role="doc-biblioentry">
+<div class="citation" id="id54" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>EMCW05<span class="fn-bracket">]</span></span>
 <p>C. Estrada-Mila, J. Candy, and R.E. Waltz. Gyrokinetic simulations of ion and impurity transport. <em>Phys. Plasmas</em>, 12:022305, 2005.</p>
 </div>
-<div class="citation" id="id54" role="doc-biblioentry">
+<div class="citation" id="id55" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>EMCW06a<span class="fn-bracket">]</span></span>
 <p>C. Estrada-Mila, J. Candy, and R.E. Waltz. Density peaking and turbulent pinch in DIII-D discharges. <em>Phys. Plasmas</em>, 13:074505, 2006.</p>
 </div>
-<div class="citation" id="id55" role="doc-biblioentry">
+<div class="citation" id="id56" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>EMCW06b<span class="fn-bracket">]</span></span>
 <p>C. Estrada-Mila, J. Candy, and R.E. Waltz. Turbulent transport of alpha particles and helium ash in reactor plasmas. <em>Phys. Plasmas</em>, 13:112303, 2006.</p>
 </div>
-<div class="citation" id="id56" role="doc-biblioentry">
+<div class="citation" id="id57" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>FC04<span class="fn-bracket">]</span></span>
 <p>M.R. Fahey and J. Candy. GYRO: A 5-D gyrokinetic-Maxwell solver. In <em>ACM/IEEE Proceedings of SC2004: High Performance Computing, Networking and Storage (Pittsburgh, PA)</em>. 2004.</p>
 </div>
@@ -293,215 +297,219 @@ <h1>References<a class="headerlink" href="#references" title="Link to this headi
 <span class="label"><span class="fn-bracket">[</span>GSS+18<span class="fn-bracket">]</span></span>
 <p>B.A. Grierson, G.M. Staebler, W.M. Solomon, G.R. McKee, C. Holland, M. Austin, A. Marinoni, L. Schmitz, R.I. Pinsker, and DIII-D Team. Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER. <em>Phys. Plasmas</em>, 25(2):022509, 2018.</p>
 </div>
-<div class="citation" id="id57" role="doc-biblioentry">
+<div class="citation" id="id59" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>GWT+14<span class="fn-bracket">]</span></span>
 <p>T. Görler, A.E. White, D. Told, F. Jenko, C. Holland, and T.L. Rhodes. A flux-matched gyrokinetic analysis of diii-d l-mode turbulence. <em>Phys. Plasmas</em>, 21:122307, 2014. <a class="reference external" href="https://doi.org/10.1063/1.4904301">doi:10.1063/1.4904301</a>.</p>
 </div>
-<div class="citation" id="id59" role="doc-biblioentry">
+<div class="citation" id="id60" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HBC+94<span class="fn-bracket">]</span></span>
 <p>G.W. Hammett, M.A. Beer, J.C. Cummings, W. Dorland, W.W. Lee, H.E. Mynick, S.E. Parker, R.A. Santoro, M. Artun, H.P. Furth, T.S. Hahm, G. Rewoldt, W.M. Tang, R.E. Waltz, G.D. Kerbel, and J.L. Milovich. Advances in simulating tokamak turbulent transport. In <em>Proceedings of the 15th IAEA Fusion Energy Conference, Seville, Spain, 1994</em>, Vol III, p. 273. 1994.</p>
 </div>
-<div class="citation" id="id62" role="doc-biblioentry">
+<div class="citation" id="id63" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HW06<span class="fn-bracket">]</span></span>
 <p>F.L. Hinton and R.E. Waltz. Gyrokinetic turbulent heating. <em>Phys. Plasmas</em>, 13:102301, 2006.</p>
 </div>
-<div class="citation" id="id61" role="doc-biblioentry">
+<div class="citation" id="id62" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HWC04<span class="fn-bracket">]</span></span>
 <p>F.L. Hinton, R.E. Waltz, and J. Candy. Effect of electromagnetic turbulence in the neoclassical Ohm's law. <em>Phys. Plasmas</em>, 11:2433, 2004.</p>
 </div>
-<div class="citation" id="id60" role="doc-biblioentry">
+<div class="citation" id="id61" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HW85<span class="fn-bracket">]</span></span>
 <p>F.L. Hinton and S.K. Wong. Neoclassical ion transport in rotating axisymmetric plasmas. <em>Phys. Fluids</em>, 28:3082, 1985. <a class="reference external" href="https://doi.org/10.1063/1.865350">doi:10.1063/1.865350</a>.</p>
 </div>
-<div class="citation" id="id68" role="doc-biblioentry">
+<div class="citation" id="id69" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>Hol16<span class="fn-bracket">]</span></span>
 <p>C. Holland. Validation metrics for turbulent plasma transport. <em>Phys. Plasmas</em>, 23:060901, 2016.</p>
 </div>
-<div class="citation" id="id64" role="doc-biblioentry">
+<div class="citation" id="id65" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HCW+08<span class="fn-bracket">]</span></span>
 <p>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. <em>J. Phys: Conf. Series</em>, 125:012043, 2008.</p>
 </div>
-<div class="citation" id="id65" role="doc-biblioentry">
+<div class="citation" id="id66" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HWM+09<span class="fn-bracket">]</span></span>
 <p>C. Holland, A.E. White, G.R. McKee, M.W. Shafer, J. Candy, R.E Waltz, L. Schmitz, and G.R Tynan. Implementation and application of two synthetic diagnostics for validating simulations of core tokamak turbulence. <em>Phys. Plasmas</em>, 16:052301, 2009.</p>
 </div>
-<div class="citation" id="id78" role="doc-biblioentry">
+<div class="citation" id="id79" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>HHW+16<span class="fn-bracket">]</span></span>
 <p>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. <em>Nucl. Fusion</em>, 56(1):014004, 2016. <a class="reference external" href="https://doi.org/10.1088/0029-5515/56/1/014004">doi:10.1088/0029-5515/56/1/014004</a>.</p>
 </div>
-<div class="citation" id="id143" role="doc-biblioentry">
+<div class="citation" id="id81" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>K+19<span class="fn-bracket">]</span></span>
 <p>S.M. Kaye and others. NSTX/NSTX-U theory, modeling and analysis results. <em>Nucl. Fusion</em>, 59:112007, 2019.</p>
 </div>
-<div class="citation" id="id84" role="doc-biblioentry">
+<div class="citation" id="id86" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KSW08<span class="fn-bracket">]</span></span>
 <p>J. E. Kinsey, G. M. Staebler, and R. E. Waltz. The first transport code simulations using the trapped gyro-Landau-fluid model. <em>Phys. Plasmas</em>, 15(5):055908, 2008. <a class="reference external" href="https://doi.org/10.1063/1.2889008">doi:10.1063/1.2889008</a>.</p>
 </div>
-<div class="citation" id="id81" role="doc-biblioentry">
+<div class="citation" id="id83" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KWC05<span class="fn-bracket">]</span></span>
 <p>J.E. Kinsey, R.E. Waltz, and J. Candy. Nonlinear gyrokinetic turbulence simulations of E×B shear quenching of transport. <em>Phys. Plasmas</em>, 12:062302, 2005.</p>
 </div>
-<div class="citation" id="id82" role="doc-biblioentry">
+<div class="citation" id="id84" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KWC06<span class="fn-bracket">]</span></span>
 <p>J.E. Kinsey, R.E. Waltz, and J. Candy. The effect of safety factor and magnetic shear on turbulent transport in nonlinear gyrokinetic simulations. <em>Phys. Plasmas</em>, 13:022305, 2006.</p>
 </div>
-<div class="citation" id="id83" role="doc-biblioentry">
+<div class="citation" id="id85" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KWC07<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 14:102306, 2007.</p>
 </div>
-<div class="citation" id="id86" role="doc-biblioentry">
+<div class="citation" id="id88" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KKH+00<span class="fn-bracket">]</span></span>
 <p>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. <em>Nucl. Fusion</em>, 40:667, 2000.</p>
 </div>
-<div class="citation" id="id87" role="doc-biblioentry">
+<div class="citation" id="id89" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>Kot88<span class="fn-bracket">]</span></span>
 <p>M. Kotschenreuther. Invited talk 9I4. <em>Bull. Am. Phys. Soc.</em>, 33:2107, 1988.</p>
 </div>
-<div class="citation" id="id88" role="doc-biblioentry">
+<div class="citation" id="id90" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KRT95<span class="fn-bracket">]</span></span>
 <p>M. Kotschenreuther, G. Rewoldt, and W.M. Tang. Comparison of initial value and eigenvalue codes for kinetic toroidal plasma instabilities. <em>Comput. Phys. Commun.</em>, 88:128, 1995. <a class="reference external" href="https://doi.org/10.1016/0010-4655(95)00035-E">doi:10.1016/0010-4655(95)00035-E</a>.</p>
 </div>
-<div class="citation" id="id90" role="doc-biblioentry">
+<div class="citation" id="id92" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>Kro99<span class="fn-bracket">]</span></span>
-<p>J.A. Krommes. Thermostatted $\delta f$. <em>Phys. Plasmas</em>, 6:1477, 1999.</p>
+<p>J.A. Krommes. Thermostatted delta-f. <em>Phys. Plasmas</em>, 6:1477, 1999.</p>
 </div>
-<div class="citation" id="id89" role="doc-biblioentry">
+<div class="citation" id="id91" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>KH94<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 1:3211, 1994.</p>
 </div>
-<div class="citation" id="id92" role="doc-biblioentry">
+<div class="citation" id="id93" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span>KK58<span class="fn-bracket">]</span></span>
+<p>M.D. Kruskal and R.M. Kulsrud. Equilibrium of a magnetically confined plasma in a toroid. <em>Phys. Fluids</em>, 1:265, 1958.</p>
+</div>
+<div class="citation" id="id95" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>LPE+09<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 16:012502, 2009.</p>
 </div>
-<div class="citation" id="id91" role="doc-biblioentry">
+<div class="citation" id="id94" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>LEHT02<span class="fn-bracket">]</span></span>
 <p>Z. Lin, S. Ethier, T.S. Hahm, and W.M. Tang. Size scaling of turbulent transport in magnetically confined plasmas. <em>Phys. Rev. Lett.</em>, 88:195004, 2002.</p>
 </div>
-<div class="citation" id="id94" role="doc-biblioentry">
+<div class="citation" id="id97" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>NCC+06<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 13:122306, 2006.</p>
 </div>
-<div class="citation" id="id93" role="doc-biblioentry">
+<div class="citation" id="id96" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>NHD+05<span class="fn-bracket">]</span></span>
 <p>W.M. Nevins, G.W. Hammett, A.M. Dimits, W. Dorland, and D.E. Shumaker. Discrete particle noise in particle-in-cell simulations of plasma microturbulence. <em>Phys. Plasmas</em>, 12:122305, 2005.</p>
 </div>
-<div class="citation" id="id95" role="doc-biblioentry">
+<div class="citation" id="id98" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>RH98<span class="fn-bracket">]</span></span>
 <p>M.N. Rosenbluth and F.L. Hinton. Poloidal flow driven by ion-temperature-gradient turbulence in tokamaks. <em>Phys. Rev. Lett.</em>, 80:724, 1998.</p>
 </div>
-<div class="citation" id="id96" role="doc-biblioentry">
+<div class="citation" id="id99" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SH01<span class="fn-bracket">]</span></span>
 <p>P.B. Snyder and G.W. Hammett. Electromagnetic effects on plasma microturbulence and transport. <em>Phys. Plasmas</em>, 8:744, 2001.</p>
 </div>
-<div class="citation" id="id105" role="doc-biblioentry">
+<div class="citation" id="id107" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SCB+20<span class="fn-bracket">]</span></span>
 <p>G M Staebler, J Candy, E A Belli, J E Kinsey, N Bonanomi, and B Patel. Geometry dependence of the fluctuation intensity in gyrokinetic turbulence. <em>Plasma Physics and Controlled Fusion</em>, 63(1):015013, 2020. <a class="reference external" href="https://doi.org/10.1088/1361-6587/abc861">doi:10.1088/1361-6587/abc861</a>.</p>
 </div>
-<div class="citation" id="id104" role="doc-biblioentry">
+<div class="citation" id="id108" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SCHH16<span class="fn-bracket">]</span></span>
 <p>G. M. Staebler, J. Candy, N. T. Howard, and C. Holland. The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence. <em>Phys. Plasmas</em>, 23(6):062518, 2016. <a class="reference external" href="https://doi.org/10.1063/1.4954905">doi:10.1063/1.4954905</a>.</p>
 </div>
-<div class="citation" id="id98" role="doc-biblioentry">
+<div class="citation" id="id100" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id4">SKW07</a><span class="fn-bracket">]</span></span>
 <p>G. M. Staebler, J. E. Kinsey, and R. E. Waltz. A theory-based transport model with comprehensive physics. <em>Phys. Plasmas</em>, 14(5):055909, 2007. <a class="reference external" href="https://doi.org/10.1063/1.2436852">doi:10.1063/1.2436852</a>.</p>
 </div>
-<div class="citation" id="id102" role="doc-biblioentry">
+<div class="citation" id="id105" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SWCK13<span class="fn-bracket">]</span></span>
 <p>G. M. Staebler, R. E. Waltz, J. Candy, and J. E. Kinsey. New paradigm for suppression of gyrokinetic turbulence by velocity shear. <em>Phys. Rev. Lett.</em>, 110:055003, 2013. <a class="reference external" href="https://doi.org/10.1103/PhysRevLett.110.055003">doi:10.1103/PhysRevLett.110.055003</a>.</p>
 </div>
-<div class="citation" id="id106" role="doc-biblioentry">
+<div class="citation" id="id109" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SBC+21<span class="fn-bracket">]</span></span>
 <p>G.M. Staebler, E. A. Belli, J. Candy, J.E. Kinsey, H. Dudding, and B. Patel. Verification of a quasi-linear model for gyrokinetic turbulent transport. <em>Nuclear Fusion</em>, 61(11):116007, 2021. <a class="reference external" href="https://doi.org/10.1088/1741-4326/ac243a">doi:10.1088/1741-4326/ac243a</a>.</p>
 </div>
-<div class="citation" id="id103" role="doc-biblioentry">
+<div class="citation" id="id106" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SCW+13<span class="fn-bracket">]</span></span>
 <p>G.M. Staebler, J. Candy, R.E. Waltz, J.E. Kinsey, and W.M. Solomon. A new paradigm for ExB velocity shear suppression of gyro-kinetic turbulence and the momentum pinch. <em>Nuclear Fusion</em>, 53(11):113017, 2013. <a class="reference external" href="https://doi.org/10.1088/0029-5515/53/11/113017">doi:10.1088/0029-5515/53/11/113017</a>.</p>
 </div>
-<div class="citation" id="id100" role="doc-biblioentry">
+<div class="citation" id="id103" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id4">SK10</a><span class="fn-bracket">]</span></span>
 <p>G.M. Staebler and J.E. Kinsey. Electron collisions in the trapped gyro-landau fluid transport model. <em>Phys. Plasmas</em>, 17:122309, 2010.</p>
 </div>
-<div class="citation" id="id97" role="doc-biblioentry">
+<div class="citation" id="id101" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SKW05<span class="fn-bracket">]</span></span>
 <p>G.M. Staebler, J.E. Kinsey, and R.E. Waltz. Gyro-Landau fluid equations for trapped and passing particles. <em>Phys. Plasmas</em>, 12:102508, 2005.</p>
 </div>
-<div class="citation" id="id110" role="doc-biblioentry">
+<div class="citation" id="id113" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SH98<span class="fn-bracket">]</span></span>
 <p>H. Sugama and W. Horton. Nonlinear electromagnetic gyrokinetic equation for plasmas with large mean flows. <em>Phys. Plasmas</em>, 5:2560, 1998.</p>
 </div>
-<div class="citation" id="id114" role="doc-biblioentry">
+<div class="citation" id="id117" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>SWNN11<span class="fn-bracket">]</span></span>
 <p>H. Sugama, T.-H. Watanabe, M. Nunami, and S. Nishimura. Momentum balance and radial electric fields in axisymmetric and nonaxisymmetric toroidal plasmas. <em>Plasma Phys. Control. Fusion</em>, 53:024004, 2011.</p>
 </div>
-<div class="citation" id="id142" role="doc-biblioentry">
+<div class="citation" id="id118" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>TDG+21<span class="fn-bracket">]</span></span>
 <p>K.E. Thome, X.D. Du, B.A. Grierson, G.J. Kramer, C.C. Petty, C. Holland, M. Knolker, G.R. McKee, J. McClenaghan, D.C. Pace, T.L. Rhodes, S.P. Smith, C. Sung, F. Turco, M.A. Van Zeeland, L. Zeng, and Y.B. Zhu. Response of thermal and fast-ion transport to beam ion population, rotation and Te/Ti in the DIII-D steady state hybrid scenario. <em>Nucl. Fusion</em>, 61:036036, 2021.</p>
 </div>
-<div class="citation" id="id115" role="doc-biblioentry">
+<div class="citation" id="id119" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>VATHD+05<span class="fn-bracket">]</span></span>
 <p>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 <em>Proceedings of the 47th Cray User Group Conference, Knoxville, TN, May 16-19</em>. 2005.</p>
 </div>
-<div class="citation" id="id129" role="doc-biblioentry">
+<div class="citation" id="id133" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>Wal05<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz. Rho-star scaling and physically realistic gyrokinetic simulations of transport in DIII-D. <em>Fus. Sci. Tech.</em>, 48:1051, 2005.</p>
 </div>
-<div class="citation" id="id131" role="doc-biblioentry">
+<div class="citation" id="id135" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WABC06<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, M.E. Austin, K.H. Burrell, and J. Candy. Gyrokinetic simulations of off-axis minimum-q profile corrugations. <em>Phys. Plasmas</em>, 12:052301, 2006.</p>
 </div>
-<div class="citation" id="id128" role="doc-biblioentry">
+<div class="citation" id="id132" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WC05<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz and J. Candy. Heuristic theory of nonlocally broken gyrobohm scaling. <em>Phys. Plasmas</em>, 12:072303, 2005.</p>
 </div>
-<div class="citation" id="id132" role="doc-biblioentry">
+<div class="citation" id="id136" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WCF07<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, J. Candy, and M. Fahey. Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations. <em>Phys. Plasmas</em>, 14:056116, 2007.</p>
 </div>
-<div class="citation" id="id127" role="doc-biblioentry">
+<div class="citation" id="id131" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WCH+05<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, J. Candy, F.L. Hinton, C. Estrada-Mila, and J.E. Kinsey. Advances in comprehensive simulations of transport in tokamaks. <em>Nucl. Fusion</em>, 45:741, 2005.</p>
 </div>
-<div class="citation" id="id130" role="doc-biblioentry">
+<div class="citation" id="id134" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WCP06<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 13:072304, 2006.</p>
 </div>
-<div class="citation" id="id126" role="doc-biblioentry">
+<div class="citation" id="id130" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WCR02<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, J. Candy, and M.N. Rosenbluth. Gyrokinetic turbulence simulation of profile shear stabilization and broken gyrobohm scaling. <em>Phys. Plasmas</em>, 9:1938, 2002.</p>
 </div>
-<div class="citation" id="id135" role="doc-biblioentry">
+<div class="citation" id="id139" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WH08<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz and C. Holland. Numerical experiments on the drift wave-zonal flow paradigm for nonlinear saturation. <em>Phys. Plasmas</em>, 15:122503, 2008.</p>
 </div>
-<div class="citation" id="id121" role="doc-biblioentry">
+<div class="citation" id="id125" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WKM94<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 1:2229, 1994.</p>
 </div>
-<div class="citation" id="id122" role="doc-biblioentry">
+<div class="citation" id="id126" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WKMH95<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, G.R. Kerbel, J. Milovich, and G.W. Hammett. Advances in the simulation of toroidal gyro-landau fluid model turbulence. <em>Phys. Plasmas</em>, 2:2408, 1995.</p>
 </div>
-<div class="citation" id="id134" role="doc-biblioentry">
+<div class="citation" id="id138" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WS08<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz and G.M. Staebler. Gyrokinetic theory and simulation of turbulent energy exchange. <em>Phys. Plasmas</em>, 15:014505, 2008.</p>
 </div>
-<div class="citation" id="id133" role="doc-biblioentry">
+<div class="citation" id="id137" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WSCH07<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, G.M. Staebler, J. Candy, and F.L. Hinton. Gyrokinetic theory and simulation of angular momentum transport. <em>Phys. Plasmas</em>, 14:122507, 2007.</p>
 </div>
-<div class="citation" id="id123" role="doc-biblioentry">
+<div class="citation" id="id127" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WSD+97<span class="fn-bracket">]</span></span>
 <p>R.E. Waltz, G.M. Staebler, W. Dorland, G.W. Hammett, M. Kotschenreuther, and J.A. Konings. A gyro-landau fluid transport model. <em>Phys. Plasmas</em>, 4:2482, 1997.</p>
 </div>
-<div class="citation" id="id139" role="doc-biblioentry">
+<div class="citation" id="id143" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WSM+08<span class="fn-bracket">]</span></span>
 <p>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. <em>Phys. Plasmas</em>, 15(5):056116, 2008.</p>
 </div>
-<div class="citation" id="id141" role="doc-biblioentry">
+<div class="citation" id="id145" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WATHD+05<span class="fn-bracket">]</span></span>
 <p>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 <em>Proceedings of the 47th Cray User Group Conference, Knoxville, TN, May 16-19</em>. 2005.</p>
 </div>
-<div class="citation" id="id140" role="doc-biblioentry">
+<div class="citation" id="id144" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>WCC+05<span class="fn-bracket">]</span></span>
 <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>
 </div>
diff --git a/html/src/geometry.rst b/html/src/geometry.rst
index 55b6c4b..a27ecbb 100644
--- a/html/src/geometry.rst
+++ b/html/src/geometry.rst
@@ -1,27 +1,67 @@
+.. |exb| mathmacro:: \mathbf{E}\times\mathbf{B}
+.. |B| mathmacro:: \mathbf{B}
+.. |jp|	mathmacro:: {\mathcal J}_\psi
+	     
 FLUX-SURFACE GEOMETRY
 =====================
 
-Coordinates
------------
+Clebsch coordinates
+-------------------
 
 GYRO/CGYRO/NEO use a right-handed (positively-oriented), field-aligned coordinate system
-:math:`(r,\theta,\alpha)` and the Clebsch field representation
+:math:`(r,\theta,\alpha)` and the Clebsch field representation :cite:`kruskal:1958`
 
 .. math::
 
-   \mathbf{B} =\nabla \alpha \times \nabla \psi (r) \; ,
+   \B = \nabla\alpha\times\nabla\psi \quad \text{such that} \quad\B\cdot\nabla\alpha = \B\cdot\nabla\psi = 0 
+
 
 where :math:`\psi` is the poloidal flux divided by :math:`2\pi` and
 
 .. math::
    
-    \alpha =\varphi +\nu (r,\theta ) 
+    \alpha =\varphi +\nu (r,\theta) 
 
 is the Clebsch angle. Here, :math:`\varphi` is the **toroidal angle**, oriented as shown
 in the figure below, and :math:`\theta` is the **poloidal angle** which increases as one
-moves counterclockwise along the flux-surface (shown in blue).
+moves counterclockwise along the flux-surface (shown in blue). In these coordinates, the Jacobian is 
+
+.. math::
+
+   \jp \doteq \frac{1}{\nabla\psi\times\nabla\theta\cdot\nabla\alpha} = \frac{1}{\nabla\psi\times\nabla\theta\cdot\nabla\varphi} \; . 
+
+Since the coordinates :math:`(\psi,\theta,\alpha)` and :math:`(\psi,\theta,\varphi)` form right-handed systems, the Jacobian :math:`\jp` is positive-definite.  In the latter coordinates, the magnetic field becomes
+
+.. math::
+   \B = \nabla\varphi\times\nabla\psi + \frac{\partial \nu}{\partial \theta} \nabla\theta\times\nabla\psi
+
+Using the definition of the safety factor, :math:`q(\psi)`, we may deduce
+
+.. math::
+
+   q(\psi) \doteq \frac{1}{2\pi} \int_0^{2\pi} \frac{\B\cdot\nabla\varphi}{\B\cdot\nabla\theta} \, d\theta = \frac{1}{2\pi} \int_0^{2\pi} \left( -\frac{\partial \nu}{\partial \theta} \right) \, d\theta = \frac{\nu(\psi,0)-\nu(\psi,2\pi)}{2\pi} \; .
+
+.. math::
+   
+For concreteness, we choose the following boundary conditions for :math:`\nu`:
+
+.. math::
+   \nu(\psi,2\pi) = &~-2\pi \, q(\psi) \; , \\
+    \nu(\psi,0)   = &~0 \; .
+
+By writing :math:`\B` in the standard form
+
+.. math::
+   
+   \B = \nabla\varphi\times\nabla\psi + I(\psi) \nabla\varphi \; ,
+
+we can derive the following integral for :math:`\nu`:
 
-The coordinate systems :math:`(R,Z,\varphi)` and :math:`(r,\theta,\varphi)` are positively oriented.
+.. math::
+   \nu(\psi,\theta) = -I(\psi)\int_0^\theta \jp \left|\nabla\varphi\right|^2 d\theta\; .
+   
+In the case of concentric (unshifted) circular flux surfaces, one will obtain the approximate result 
+:math:`\nu(\psi,\theta) \sim -q(\psi)\theta`.  Finally, we remark that the coordinate systems :math:`(R,Z,\varphi)` and :math:`(r,\theta,\varphi)` are positively oriented.
 		
 Bounding-box method
 -------------------
@@ -173,3 +213,35 @@ This corresponds to :ref:`cgyro_ipccw` = 1 and :ref:`cgyro_btccw` =-1.  Thus, in
 - sign(:math:`q`) = -1
 
  In other words, the safety factor and poloidal flux are negative in the typical case. This will be reflected in a properly-constructed :doc:`input.gacode <input_gacode>` file. 
+
+Toroidal and poloidal flux
+--------------------------
+
+We can start from the general forms of the toroidal and poloidal fluxes :cite:`dhaeseleer:1991`
+
+.. math::
+   \Psi_t \doteq &~\iint\limits_{S_t} \B \cdot d{\bf S} = \frac{1}{2\pi} \iiint\limits_{V_t} \B \cdot \nabla\varphi \, dV \; , \\
+   \Psi_p \doteq &~\iint\limits_{S_p} \B \cdot d{\bf S} = \frac{1}{2\pi} \iiint\limits_{V_p} \B \cdot \nabla\theta \, dV \; .
+
+Explicitly inserting the field-aligned coordinate system of the previous section, and differentiating these with respect to :math:`\psi`, gives
+
+.. math::
+   \frac{d\Psi_t}{d\psi} = &~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta \,\, \B\cdot\nabla\varphi \, \jp \; , \\
+   = &~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta \,\, \frac{\B\cdot\nabla\varphi}{\B\cdot\nabla\theta} \; , \\
+   = &~2 \pi \, q(\psi) \; ,
+
+.. math::
+   \frac{d\Psi_p}{d\psi} = &~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta 
+  \,\, \B\cdot\nabla\theta \, \jp \; , \\
+   = &~\frac{1}{2\pi} \int_0^{2\pi} d\varphi \int_0^{2\pi} d\theta \; , \\
+   = &~2 \pi \; .
+
+Thus, :math:`\psi` is the poloidal flux divided by :math:`2\pi`.  For this reason, it is useful to also define the toroidal flux divided by :math:`2\pi`:
+
+.. math::
+   \chi_t \doteq \frac{1}{2\pi} \Psi_t\; .
+
+According to these conventions, 
+
+.. math::
+   d\Psi_t = q \, d\Psi_p \quad \mbox{and} \quad d\chi_t = q \, d\psi \; .
diff --git a/html/src/references.bib b/html/src/references.bib
index b9a985b..64870ca 100644
--- a/html/src/references.bib
+++ b/html/src/references.bib
@@ -21,7 +21,6 @@ @STRING{prl
 @STRING{rmp	= "Rev. Mod. Phys." }
 @STRING{tps	= "IEEE Trans. Plasma Sci." }
 
-
 @Article{	  angioni:2009a,
   author =	 {C. Angioni and A.G. Peeters and G.V. Pereverzev and
                   A. Bottino and J. Candy and R. Dux and E. Fable and
@@ -36,23 +35,29 @@ @Article{	  angioni:2009a
 }
 
 @Article {angioni:2022,
-	doi = {10.1088/1741-4326/ac592b},
-	year = 2022,
-	volume = {62},
-	pages = {066015},
-	author = {C. Angioni and T. Gamot and G. Tardini and E. Fable and T. Luda and N. Bonanomi and C.K. Kiefer and G.M. Staebler and the ASDEX Upgrade Team and the EUROfusion MST1 Team},
-	title = {{Confinement properties of L-mode plasmas in ASDEX Upgrade and full-radius predictions of the TGLF transport model}},
-	journal = nf
+  doi =		 {10.1088/1741-4326/ac592b},
+  year =	 2022,
+  volume =	 62,
+  pages =	 066015,
+  author =	 {C. Angioni and T. Gamot and G. Tardini and E. Fable
+                  and T. Luda and N. Bonanomi and C.K. Kiefer and
+                  G.M. Staebler and the ASDEX Upgrade Team and the
+                  EUROfusion MST1 Team},
+  title =	 {{Confinement properties of L-mode plasmas in ASDEX
+                  Upgrade and full-radius predictions of the TGLF
+                  transport model}},
+  journal =	 nf
 }
 
 @Article{	  arbon:2020,
   author =	 {R. Arbon and J. Candy and E.A. Belli},
-  title =	 {Rapidly-convergent flux-surface shape parameterization},
+  title =	 {Rapidly-convergent flux-surface shape
+                  parameterization},
   journal =	 ppcf,
   volume =	 63,
   pages =	 012001,
   year =	 2020,
-  doi =          {10.1088/1361-6587/abc63b}
+  doi =		 {10.1088/1361-6587/abc63b}
 }
 
 @Article{	  beer:1996,
@@ -74,6 +79,7 @@ @Article{	  beer:1996b
   pages =	 4046,
   year =	 1996
 }
+
 @Article{	  belli:2005,
   author =	 {E.A. Belli and G.W. Hammett},
   title =	 {{{A numerical instability in an ADI algorithm for
@@ -86,13 +92,14 @@ @Article{	  belli:2005
 
 @Article{	  belli:2008,
   author =	 {E.A. Belli and J. Candy},
-  title =	 {Kinetic Calculation of Neoclassical Transport Including Self-Consistent
-                  Electron and Impurity Dynamics},
+  title =	 {Kinetic Calculation of Neoclassical Transport
+                  Including Self-Consistent Electron and Impurity
+                  Dynamics},
   journal =	 ppcf,
   volume =	 50,
   pages =	 095010,
   year =	 2008,
-  doi = {10.1088/0741-3335/50/9/095010}
+  doi =		 {10.1088/0741-3335/50/9/095010}
 }
 
 @Article{	  belli:2008b,
@@ -166,7 +173,8 @@ @Article{         belli:2015
 
 @Article{         belli:2017,
   author =	 {E.A. Belli and J. Candy},
-  title =	 {Implications of advanced collision operators for gyrokinetic simulation},
+  title =	 {Implications of advanced collision operators for
+                  gyrokinetic simulation},
   journal =	 ppcf,
   volume =	 59,
   pages =	 045005,
@@ -175,7 +183,8 @@ @Article{         belli:2017
 
 @Article{         belli:2018,
   author =	 {E.A. Belli and J. Candy},
-  title =	 {Impact of centrifugal drifts on ion turbulent transport},
+  title =	 {Impact of centrifugal drifts on ion turbulent
+                  transport},
   journal =	 pop,
   volume =	 25,
   pages =	 032301,
@@ -211,18 +220,18 @@ @Article{	  candy:2003
   volume =	 186,
   pages =	 545,
   year =	 2003,
-  doi = {10.1016/S0021-9991(03)00079-2}
+  doi =		 {10.1016/S0021-9991(03)00079-2}
 }
 
 @Article{	  candy:2003b,
   author =	 {J. Candy and R.E. Waltz},
-  title =	 {Anomalous Transport Scaling in the {{DIII-D}} Tokamak
-                  Matched by Supercomputer Simulation},
+  title =	 {Anomalous Transport Scaling in the {{DIII-D}}
+                  Tokamak Matched by Supercomputer Simulation},
   journal =	 prl,
   volume =	 91,
   pages =	 045001,
   year =	 2003,
-  doi = {10.1103/PhysRevLett.91.045001}
+  doi =		 {10.1103/PhysRevLett.91.045001}
 }
 
 @Article{	  candy:2004a,
@@ -232,13 +241,13 @@ @Article{	  candy:2004a
   volume =	 11,
   pages =	 {L25},
   year =	 2004,
-  doi = {10.1063/1.1695358} 
+  doi =		 {10.1063/1.1695358}
 }
 
 @Article{	  candy:2004b,
   author =	 {J. Candy and R.E. Waltz and M.N. Rosenbluth},
   title =	 {Smooothness of turbulent transport across a
-                  {{minimum-$q$}} surface},
+                  {{minimum-q}} surface},
   journal =	 pop,
   volume =	 11,
   pages =	 1879,
@@ -285,7 +294,8 @@ @TechReport{	  candy:2006c
 }
 
 @Article{	  candy:2007,
-  author =	 {J. Candy and R.E. Waltz and M.R. Fahey and C. Holland},
+  author =	 {J. Candy and R.E. Waltz and M.R. Fahey and
+                  C. Holland},
   title =	 {The effect of ion-scale dynamics on
                   electron-temperature-gradient turbulence},
   journal =	 ppcf,
@@ -295,9 +305,10 @@ @Article{	  candy:2007
 }
 
 @Article{	  candy:2007b,
-  author =	 {J. Candy and R.E. Waltz and M.R. Fahey and C. Holland},
-  title =	 {Plasma microturbulence simulation of instabilities at highly
-                 disparate scales},
+  author =	 {J. Candy and R.E. Waltz and M.R. Fahey and
+                  C. Holland},
+  title =	 {Plasma microturbulence simulation of instabilities
+                  at highly disparate scales},
   journal =	 jpcon,
   volume =	 78,
   pages =	 012008,
@@ -370,17 +381,17 @@ @Article{	  candy:2016
   volume =	 324,
   pages =	 73,
   year =	 2016,
-  doi =          {10.1016/j.jcp.2016.07.039}
+  doi =		 {10.1016/j.jcp.2016.07.039}
 }
 
 @Article{	  candy:2018,
   author =	 {J. Candy and E.A. Belli},
   title =	 {{{Spectral treatment of gyrokinetic shear flow}}},
   journal =	 jcp,
-  volume =       356,
+  volume =	 356,
   pages =	 448,
   year =	 2018,
-  doi =  {10.1016/j.jcp.2017.12.020}
+  doi =		 {10.1016/j.jcp.2017.12.020}
 }
 
 @Article{	  candy:2019,
@@ -392,7 +403,7 @@ @Article{	  candy:2019
   journal =	 cf,
   volume =	 188,
   pages =	 125,
-  doi		= {10.1016/j.compfluid.2019.04.016},
+  doi =		 {10.1016/j.compfluid.2019.04.016},
   year =	 2019
 }
 
@@ -402,11 +413,10 @@ @Article{	  candy:2020
   journal =	 ppcf,
   volume =	 62,
   pages =	 042001,
-  doi		= {10.1088/1361-6587/ab759c},
+  doi =		 {10.1088/1361-6587/ab759c},
   year =	 2020
 }
 
-
 @Article{	  chen:2003,
   author =	 {Y. Chen and S.E. Parker and B.I. Cohen and
                   A.M. Dimits and W.M. Nevins and D. Schumaker and
@@ -420,17 +430,26 @@ @Article{	  chen:2003
 }
 
 @Article{	  chowdhury:2014,
-  author =	 {J. Chowdhury and W. Wan and Y. Chen and S.E. Parker and
-                  R.J. Groebner and C. Holland and N.T. Howard},
-  title =	 {Study of the L-mode tokamak plasma “shortfall” with local
-                  and global nonlinear gyrokinetic $\delta f$ particle-in-cell
-		  simulation},
+  author =	 {J. Chowdhury and W. Wan and Y. Chen and S.E. Parker
+                  and R.J. Groebner and C. Holland and N.T. Howard},
+  title =	 {Study of the L-mode tokamak plasma “shortfall” with
+                  local and global nonlinear gyrokinetic $\delta f$
+                  particle-in-cell simulation},
   journal =	 pop,
   volume =	 21,
   pages =	 112503,
   year =	 2014
 }
 
+@Book{		  dhaeseleer:1991,
+  author =	 {W.D. Dhaeseleer and W.N.G. Hitchon and J.D. Callen
+                  and J.L. Shohet},
+  title =	 {Flux coordinates and magnetic field structure},
+  publisher =	 {Springer-Verlag},
+  address =	 {Berlin},
+  year =	 1991
+}
+
 @Article{	  dimits:1996,
   author =	 {A.M. Dimits and T.J. Williams and J.A. Byers and
                   B.I.  Cohen},
@@ -452,7 +471,6 @@ @Article{	  dong:1995
   year =	 1995
 }
 
-
 @Article{	  dorland:1993,
   author =	 {W. Dorland and G.W. Hammett},
   title =	 {Gyrofluid turbulence models with kinetic effects},
@@ -473,23 +491,28 @@ @Article{	  dorland:2000
 }
 
 @Article{dudding:2022a,
-	author = {H.G. Dudding and F.J. Casson and D. Dickinson and B.S. Patel and C.M. Roach and E.A. Belli and G.M. Staebler},
-	doi = {10.1088/1741-4326/ac7a4d},
-	journal = {Nuclear Fusion},
-	number = {9},
-	pages = {096005},
-	title = {A new quasilinear saturation rule for tokamak turbulence with application to the isotope scaling of transport},
-	volume = {62},
-	year = {2022}
+  author =	 {H.G. Dudding and F.J. Casson and D. Dickinson and
+                  B.S. Patel and C.M. Roach and E.A. Belli and
+                  G.M. Staebler},
+  doi =		 {10.1088/1741-4326/ac7a4d},
+  journal =	 {Nuclear Fusion},
+  number =	 9,
+  pages =	 096005,
+  title =	 {A new quasilinear saturation rule for tokamak
+                  turbulence with application to the isotope scaling
+                  of transport},
+  volume =	 62,
+  year =	 2022
 }
 
 @phdthesis{dudding:2022b,
-	author = {Harry George Dudding},
-	month = {October},
-	school = {University of York},
-	title = {A new quasilinear saturation rule for tokamak turbulence},
-	url = {https://etheses.whiterose.ac.uk/32664/},
-	year = {2022}
+  author =	 {Harry George Dudding},
+  month =	 {October},
+  school =	 {University of York},
+  title =	 {A new quasilinear saturation rule for tokamak
+                  turbulence},
+  url =		 {https://etheses.whiterose.ac.uk/32664/},
+  year =	 2022
 }
 
 @Article{	  estrada:2005,
@@ -530,26 +553,31 @@ @InProceedings{	  fahey:2004
   year =	 2004
 }
 
+@Article{	  grierson:2018,
+  title =	 {{Multi-scale transport in the DIII-D ITER baseline
+                  scenario with direct electron heating and projection
+                  to ITER}},
+  author =	 {B.A. Grierson and G.M. Staebler and W.M. Solomon and
+                  G.R. McKee and C. Holland and M. Austin and
+                  A. Marinoni and L. Schmitz and R.I. Pinsker and
+                  DIII-D Team},
+  journal =	 pop,
+  number =	 2,
+  pages =	 022509,
+  volume =	 25,
+  year =	 2018
+}
+
 @Article{	  görler:2014,
-  author =	 {T. Görler and A.E. White and D. Told and F. Jenko and
-                  C. Holland and T.L. Rhodes},
+  author =	 {T. Görler and A.E. White and D. Told and F. Jenko
+                  and C. Holland and T.L. Rhodes},
   title =	 {A flux-matched gyrokinetic analysis of DIII-D L-mode
                   turbulence},
   journal =	 pop,
   volume =	 21,
   pages =	 122307,
   year =	 2014,
-  doi = {10.1063/1.4904301}
-}
-
-@Article{	  grierson:2018,
-  title =	 {{Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER}},
-  author =	 {B.A. Grierson and G.M. Staebler and W.M. Solomon and G.R. McKee and C. Holland and M. Austin and A. Marinoni and L. Schmitz and R.I. Pinsker and DIII-D Team},
-  journal =	 pop,
-  number =	 2,
-  pages =	 022509,
-  volume =	 25,
-  year =	 2018
+  doi =		 {10.1063/1.4904301}
 }
 
 @InProceedings{	  hammett:1994,
@@ -573,7 +601,7 @@ @Article{	  hinton:1985
   volume =	 28,
   pages =	 3082,
   year =	 1985,
-  doi = {10.1063/1.865350}
+  doi =		 {10.1063/1.865350}
 }
 
 @Article{	  hinton:2004,
@@ -595,7 +623,6 @@ @Article{	  hinton:2006
   year =	 2006
 }
 
-
 @Article{	  holland:2004,
   author =	 {C. Holland and P.H. Diamond},
   title =	 {A simple model of interactions between electron
@@ -670,7 +697,8 @@ @Article{	  holland:2016
 
 @Article{	  holland:2017,
   author =	 {C. Holland and N.T. Howard and B.A. Grierson},
-  title =	 {Gyrokinetic predictions of multiscale transport in a {{DIII-D ITER}} baseline discharge},
+  title =	 {Gyrokinetic predictions of multiscale transport in a
+                  {{DIII-D ITER}} baseline discharge},
   journal =	 nf,
   volume =	 57,
   pages =	 066043,
@@ -710,7 +738,7 @@ @Article{	  houlberg:1997
 @Article{	  howard:2012,
   author =	 {N.T. Howard and M. Greenwald and D.R. Mikkelsen and
                   M.L.  Reinke and A.E. White and D. Ernst and
-                  Y. Podpaly and J.  Candy},
+                  Y. Podpaly and J. Candy},
   title =	 {Quantitative comparison of experimental impurity
                   transport with nonlinear gyrokinetic simulation in
                   an {{Alcator C-Mod L-mode}} plasma},
@@ -721,8 +749,9 @@ @Article{	  howard:2012
 }
 
 @Article{	  howard:2013,
-  author =	 {N.T. Howard and A.E. White and M. Greenwald and M.L. Reinke
-                  and J. Walk and C. Holland and J. Candy and T. G\"orler},
+  author =	 {N.T. Howard and A.E. White and M. Greenwald and
+                  M.L. Reinke and J. Walk and C. Holland and J. Candy
+                  and T. G\"orler},
   title =	 {Investigation of the transport shortfall in Alcator
                   C-Mod L-mode plasmas},
   journal =	 pop,
@@ -733,7 +762,7 @@ @Article{	  howard:2013
 
 @Article{	  howard:2014a,
   author =	 {N.T. Howard and A.E. White and M. Greenwald and
-                  C. Holland and J. Candy and J. E. Rice},
+                  C. Holland and J. Candy and J.E. Rice},
   title =	 {Impurity transport, turbulence transitions, and
                   intrinsic rotation in Alcator {{C-Mod}} plasmas},
   journal =	 ppcf,
@@ -756,9 +785,9 @@ @Article{	  howard:2014b
 @Article{	  howard:2016,
   author =	 {N.T. Howard and C. Holland and A.E. White and
                   M. Greenwald and J. Candy and A.J. Creely},
-  title =	 {Multi-scale gyrokinetic simulations: Comparison 
-                  with experiment and implications for predicting 
-                 turbulence and transport},
+  title =	 {Multi-scale gyrokinetic simulations: Comparison with
+                  experiment and implications for predicting
+                  turbulence and transport},
   journal =	 pop,
   volume =	 23,
   pages =	 056109,
@@ -766,22 +795,23 @@ @Article{	  howard:2016
 }
 
 @Article{	  howard:2016b,
-  author	= {N.T. Howard and C. Holland and A.E. White and M. Greenwald
-		  and J. Candy},
-  title		= {Multi-scale gyrokinetic simulation of tokamak plasmas:
-		  enhanced heat loss due to cross-scale coupling of plasma
-		  turbulence},
-  journal	= nf,
-  volume	= 56,
-  number	= 1,
-  pages		= 014004,
-  year		= 2016,
-  doi		= {10.1088/0029-5515/56/1/014004}
+  author =	 {N.T. Howard and C. Holland and A.E. White and
+                  M. Greenwald and J. Candy},
+  title =	 {Multi-scale gyrokinetic simulation of tokamak
+                  plasmas: enhanced heat loss due to cross-scale
+                  coupling of plasma turbulence},
+  journal =	 nf,
+  volume =	 56,
+  number =	 1,
+  pages =	 014004,
+  year =	 2016,
+  doi =		 {10.1088/0029-5515/56/1/014004}
 }
 
 @Article{	  howard:2017,
-  author =	 {N.T. Howard and C. Holland and A.E. White and M. Greenwald
-                  and P. Rodriguez-Fernandez and J. Candy and A.J. Creely},
+  author =	 {N.T. Howard and C. Holland and A.E. White and
+                  M. Greenwald and P. Rodriguez-Fernandez and J. Candy
+                  and A.J. Creely},
   title =	 {{{Multi-scale gyrokinetic simulations of an Alcator
                   C-Mod, ELM-y H-mode plasma}}},
   journal =	 ppcf,
@@ -790,6 +820,15 @@ @Article{	  howard:2017
   year =	 2017
 }
 
+@Article{	 kaye:2019,
+  title =	 {{NSTX/NSTX-U theory, modeling and analysis results}},
+  author =	 {S.M. Kaye and others},
+  journal =	 nf,
+  pages =	 112007,
+  volume =	 59,
+  year =	 2019
+}
+
 @Article{	  kinsey:2003,
   author =	 {J.E. Kinsey and G. Bateman and T. Onjun and
                   A.H. Kritz and A. Pankin and G.M. Staebler and
@@ -836,14 +875,15 @@ @Article{	  kinsey:2007
 }
 
 @Article{kinsey:2008,
-	author = {Kinsey,J. E. and Staebler,G. M. and Waltz,R. E.},
-	doi = {10.1063/1.2889008},
-	journal = pop,
-	number = {5},
-	pages = {055908},
-	title = {{The first transport code simulations using the trapped gyro-Landau-fluid model}},
-	volume = {15},
-	year = {2008}
+  author =	 {Kinsey,J. E. and Staebler,G. M. and Waltz,R. E.},
+  doi =		 {10.1063/1.2889008},
+  journal =	 pop,
+  number =	 5,
+  pages =	 055908,
+  title =	 {{The first transport code simulations using the
+                  trapped gyro-Landau-fluid model}},
+  volume =	 15,
+  year =	 2008
 }
 
 @Article{	  kinsey:2011,
@@ -903,13 +943,23 @@ @Article{	  krommes:1994
 
 @Article{	  krommes:1999,
   author =	 {J.A. Krommes},
-  title =	 {Thermostatted $\delta f$},
+  title =	 {Thermostatted delta-f},
   journal =	 pop,
   volume =	 6,
   pages =	 1477,
   year =	 1999
 }
 
+@Article{	  kruskal:1958,
+  author =	 {M.D. Kruskal and R.M. Kulsrud},
+  title =	 {Equilibrium of a magnetically confined plasma in a
+                  toroid},
+  journal =	 pf,
+  volume =	 1,
+  pages =	 265,
+  year =	 1958
+}
+
 @Article{	  lin:2002,
   author =	 {Z. Lin and S. Ethier and T.S. Hahm and W.M. Tang},
   title =	 {Size Scaling of Turbulent Transport in Magnetically
@@ -977,17 +1027,6 @@ @Article{	  snyder:2001
   year =	 2001
 }
 
-@Article{	  staebler:2005,
-  author =	 {G.M. Staebler and J.E. Kinsey and R.E. Waltz},
-  title =	 {{{Gyro-Landau}} fluid equations for trapped and
-                  passing particles},
-  journal =	 pop,
-  volume =	 12,
-  pages =	 102508,
-  year =	 2005
-}
-
-
 @Article{staebler:2007,
 	author = {Staebler,G. M. and Kinsey,J. E. and Waltz,R. E.},,
 	doi = {10.1063/1.2436852},
@@ -999,6 +1038,16 @@ @Article{staebler:2007
 	year = {2007}
 }
 
+@Article{	  staebler:2005,
+  author =	 {G.M. Staebler and J.E. Kinsey and R.E. Waltz},
+  title =	 {{{Gyro-Landau}} fluid equations for trapped and
+                  passing particles},
+  journal =	 pop,
+  volume =	 12,
+  pages =	 102508,
+  year =	 2005
+}
+
 @Article{	  staebler:2008,
   author =	 {G.M. Staebler and G. Colyer and S. Kaye and
                   J.E. Kinsey and R.E. Waltz},
@@ -1030,42 +1079,34 @@ @Article{	  staebler:2011
   year =	 2011
 }
 
-
 @Article{staebler:2013,
-	author = {Staebler, G. M. and Waltz, R. E. and Candy, J. and Kinsey, J. E.},
-	doi = {10.1103/PhysRevLett.110.055003},
-	issue = {5},
-	journal = {Phys. Rev. Lett.},
-	numpages = {5},
-	pages = {055003},
-	title = {New Paradigm for Suppression of Gyrokinetic Turbulence by Velocity Shear},
-	volume = {110},
-	year = {2013}
+  author =	 {Staebler, G. M. and Waltz, R. E. and Candy, J. and
+                  Kinsey, J. E.},
+  doi =		 {10.1103/PhysRevLett.110.055003},
+  issue =	 5,
+  journal =	 {Phys. Rev. Lett.},
+  numpages =	 5,
+  pages =	 055003,
+  title =	 {New Paradigm for Suppression of Gyrokinetic
+                  Turbulence by Velocity Shear},
+  volume =	 110,
+  year =	 2013
 }
 
 @Article{staebler:2013b,
-	author = {G.M. Staebler and J. Candy and R.E. Waltz and J.E. Kinsey and W.M. Solomon},
-	doi = {10.1088/0029-5515/53/11/113017},
-	journal = {Nuclear Fusion},
-	number = {11},
-	pages = {113017},
-	title = {A new paradigm for {E}x{B} velocity shear suppression of gyro-kinetic turbulence and the momentum pinch},
-	volume = {53},
-	year = 2013
-}
-
-@Article{staebler:2016,
-	author = {Staebler,G. M. and Candy,J. and Howard,N. T. and Holland,C.},
-	doi = {10.1063/1.4954905},
-	journal = pop,
-	number = {6},
-	pages = {062518},
-	title = {The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence},
-	volume = {23},
-	year = {2016}
+  author =	 {G.M. Staebler and J. Candy and R.E. Waltz and
+                  J.E. Kinsey and W.M. Solomon},
+  doi =		 {10.1088/0029-5515/53/11/113017},
+  journal =	 {Nuclear Fusion},
+  number =	 11,
+  pages =	 113017,
+  title =	 {A new paradigm for {E}x{B} velocity shear
+                  suppression of gyro-kinetic turbulence and the
+                  momentum pinch},
+  volume =	 53,
+  year =	 2013
 }
 
-
 @Article{staebler:2020,
 	author = {G M Staebler and J Candy and E A Belli and J E Kinsey and N Bonanomi and B Patel},,
 	doi = {10.1088/1361-6587/abc861},
@@ -1078,17 +1119,31 @@ @Article{staebler:2020
 	year = 2020
 }
 
+@Article{staebler:2016,
+  author =	 {Staebler,G. M. and Candy,J. and Howard,N. T. and
+                  Holland,C.},
+  doi =		 {10.1063/1.4954905},
+  journal =	 pop,
+  number =	 6,
+  pages =	 062518,
+  title =	 {The role of zonal flows in the saturation of
+                  multi-scale gyrokinetic turbulence},
+  volume =	 23,
+  year =	 2016
+}
 
 @Article{staebler:2021,
-	author = {G.M. Staebler and E. A. Belli and J. Candy and J.E. Kinsey and H. Dudding and B. Patel},
-	doi = {10.1088/1741-4326/ac243a},
-	journal = {Nuclear Fusion},
-	number = {11},
-	pages = {116007},
-	publisher = {{IOP} Publishing},
-	title = {Verification of a quasi-linear model for gyrokinetic turbulent transport},
-	volume = {61},
-	year = 2021
+  author =	 {G.M. Staebler and E. A. Belli and J. Candy and
+                  J.E. Kinsey and H. Dudding and B. Patel},
+  doi =		 {10.1088/1741-4326/ac243a},
+  journal =	 {Nuclear Fusion},
+  number =	 11,
+  pages =	 116007,
+  publisher =	 {{IOP} Publishing},
+  title =	 {Verification of a quasi-linear model for gyrokinetic
+                  turbulent transport},
+  volume =	 61,
+  year =	 2021
 }
 
 @Article{	  sugama:1996,
@@ -1172,13 +1227,29 @@ @Article{	  sugama:2011
   year =	 2011
 }
 
+@Article{	  thome:2021,
+  title =	 {{Response of thermal and fast-ion transport to beam
+                  ion population, rotation and Te/Ti in the DIII-D
+                  steady state hybrid scenario}},
+  author =	 {K.E. Thome and X.D. Du and B.A. Grierson and
+                  G.J. Kramer and C.C. Petty and C. Holland and
+                  M. Knolker and G.R. McKee and J. McClenaghan and
+                  D.C. Pace and T.L. Rhodes and S.P. Smith and C. Sung
+                  and F. Turco and M.A. Van Zeeland and L. Zeng and
+                  Y.B. Zhu},
+  journal =	 nf,
+  pages =	 036036,
+  volume =	 61,
+  year =	 2021
+}
+
 @InProceedings{	  vetter:2005,
   author =	 {J.S. Vetter and S. Alam and T.H. Dunigan, Jr. and
                   M.R.  Fahey and P.C. Roth and P. Worley},
   title =	 {Early Evaluation of the Cray XT3 at ORNL},
   booktitle =	 {Proceedings of the 47th Cray User Group Conference,
                   Knoxville, TN, May 16-19},
-		  year = 2005
+  year =	 2005
 }
 
 @Article{	  waltz:1980,
@@ -1202,7 +1273,8 @@ @Article{	  waltz:1989
 }
 
 @Article{	  waltz:1990,
-  title =	 {{Magnetic-field scaling of dimensionally similar tokamak discharges}},
+  title =	 {{Magnetic-field scaling of dimensionally similar
+                  tokamak discharges}},
   author =	 {R.E. Waltz and J.C. DeBoo and M.N. Rosenbluth},
   journal =	 prl,
   pages =	 2390,
@@ -1358,7 +1430,8 @@ @Article{	  waltz:2007
 }
 
 @Article{	  waltz:2007b,
-  author =	 {R.E. Waltz and G.M. Staebler and J. Candy and F.L. Hinton},
+  author =	 {R.E. Waltz and G.M. Staebler and J. Candy and
+                  F.L. Hinton},
   title =	 {Gyrokinetic theory and simulation of angular
                   momentum transport},
   journal =	 pop,
@@ -1379,7 +1452,8 @@ @Article{	  waltz:2008
 
 @Article{	  waltz:2008b,
   author =	 {R.E. Waltz and C. Holland},
-  title =	 {Numerical Experiments on the Drift Wave-Zonal Flow Paradigm for Nonlinear Saturation},
+  title =	 {Numerical Experiments on the Drift Wave-Zonal Flow
+                  Paradigm for Nonlinear Saturation},
   journal =	 pop,
   volume =	 15,
   pages =	 122503,
@@ -1421,9 +1495,10 @@ @Article{	  white:2008
   title =	 {{Measurements of core electron temperature and
                   density fluctuations in DIII-D and comparison to
                   nonlinear gyrokinetic simulations}},
-  author =	 {A.E. White and L. Schmitz and G.R. McKee and C. Holland and W.A. Peebles
-                 and T.A. Carter and M.W. Shafer and M.E. Austin and K.H. Burrell and J. Candy
-		 and others},
+  author =	 {A.E. White and L. Schmitz and G.R. McKee and
+                  C. Holland and W.A. Peebles and T.A. Carter and
+                  M.W. Shafer and M.E. Austin and K.H. Burrell and
+                  J. Candy and others},
   journal =	 pop,
   number =	 5,
   pages =	 056116,
@@ -1440,7 +1515,7 @@ @InProceedings{	  worley:2005
   title =	 {Performance Analysis of GYRO: A Tool Evaluation},
   booktitle =	 {Proceedings of the 2005 SciDAC Conference, San
                   Francisco, CA, June 26-30},
-		  year = 2005
+  year =	 2005
 }
 
 @InProceedings{	  worley:2005b,
@@ -1450,23 +1525,5 @@ @InProceedings{	  worley:2005b
                   on the X1, XD1, and XT3},
   booktitle =	 {Proceedings of the 47th Cray User Group Conference,
                   Knoxville, TN, May 16-19},
-		  year = 2005
-}
-
-@Article{	  thome:2021,
-  title =	 {{Response of thermal and fast-ion transport to beam ion population, rotation and Te/Ti in the DIII-D steady state hybrid scenario}},
-  author =	 {K.E. Thome and X.D. Du and B.A. Grierson and G.J. Kramer and C.C. Petty and C. Holland and M. Knolker  and G.R. McKee and J. McClenaghan and D.C. Pace and T.L. Rhodes and S.P. Smith and C. Sung and F. Turco and M.A. Van Zeeland and L. Zeng and Y.B. Zhu},
-  journal =	 nf,
-  pages =	 036036,
-  volume =	 61,
-  year =	 2021
-}
-
-@Article{	 kaye:2019,
-  title =	 {{NSTX/NSTX-U theory, modeling and analysis results}},
-  author =	 {S.M. Kaye and others},
-  journal =	 nf,
-  pages =	 112007,
-  volume =	 59,
-  year =	 2019
+  year =	 2005
 }
diff --git a/html/src/rotation.rst b/html/src/rotation.rst
index a63f23a..d75c0ae 100644
--- a/html/src/rotation.rst
+++ b/html/src/rotation.rst
@@ -17,7 +17,7 @@ The rigorous derivation of the gyrokinetic equations for sonic rotation was carr
 
    \mathbf{U}_0 = \omega_0(\psi) R^2 \nabla \varphi \; .
 
-It is this scalar flux-function, :math:`\omega_0`, that is the true free (input) function in both neoclassical and gyrokinetic theory.  Here, :math:`\psi` is the poloidal flux.
+It is this scalar flux-function, :math:`\omega_0`, that is the true free (input) function in both neoclassical and gyrokinetic theory.  Here, :math:`\psi` is the poloidal flux divided by :math:`2\pi`.
 
 The rotation profile
 --------------------
@@ -90,14 +90,13 @@ where :math:`U_\varphi \doteq \mathbf{e}_\varphi \cdot \mathbf{U}` is the *toroi
    \mathbf{U}_0 = \omega_0(\psi) R \mathbf{e}_{\varphi} \quad \text{where} \quad
    \omega_{0}(\psi) \doteq -c \frac{d \Phi_{-1}}{d \psi} \; .
 
-It is important to note that :math:`\Phi_{-1}` is a **flux function**, whereas higher orders are not constant on a flux surface.
+It is important to note that :math:`\Phi_{-1}` is a **flux function**, whereas higher orders are **not** constant on a flux surface.
 
 Connection to experimental data
 -------------------------------
 
 We remark that :math:`\omega_{0}` is a **theoretical quantity** that cannot be measured in the experiment.  This is similar
-to the observation that the experimentally-measured temperature :math:`T_i` is really the sum of an *equilibrium temperature* and a small *fluctuating temperature* driven by turbulence: :math:`T_i = T_{i0} + T_{i1}`.  If the drift ordering is valid, then we are justified in approximating the equilibrium temperature :math:`T_{i0}` by the measured temperature :math:`T_i`.
-For the rotation frequency, similar considerations hold.  We note that the theory shows that the potential always appears in the combination
+to the observation that the experimentally-measured temperature :math:`T_i` is really the sum of an *equilibrium temperature* and a small *fluctuating temperature* driven by turbulence: :math:`T_i = T_{i0} + T_{i1}`.  If the drift ordering is valid, then we are justified in approximating the equilibrium temperature :math:`T_{i0}` by the measured temperature :math:`T_i`. For the rotation frequency, similar considerations hold.  We note that the theory shows that the potential always appears in the combination
 
 .. math::