Updated PX0, removed some depecated files

docs/cgyro.html

@@ -206,8 +206,6 @@ <h2>Normalization<a class="headerlink" href="#normalization" title="Link to this
 <h2>Running Cases<a class="headerlink" href="#running-cases" title="Link to this heading"></a></h2>
 <ul class="simple">
 <li><p><a class="reference internal" href="cgyro/running_cases.html"><span class="doc">running cases</span></a></p></li>
-<li><p><a class="reference internal" href="cgyro/cgyro_cori.html"><span class="doc">cori</span></a></p></li>
-<li><p><a class="reference internal" href="cgyro/cgyro_titan.html"><span class="doc">titan</span></a></p></li>
 </ul>
 </section>
 <section id="frequently-asked-questions">

docs/cgyro/cgyro_list.html

@@ -485,6 +485,8 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 <p>Normalized <span class="math notranslate nohighlight">\(\mathbf{E}\times\mathbf{B}\)</span> shearing rate <span class="math notranslate nohighlight">\(\displaystyle \frac{a}{c_s} \gamma_E\)</span>.</p>
 <p><strong>Comments</strong></p>
 <ul class="simple">
+<li><p>This is the radial electric field shear and is a <strong>global</strong> term (can’t be treated in a local simulation)</p></li>
+<li><p>It it zeroed automatically in a linear simulation</p></li>
 <li><p>DEFAULT = 0.0</p></li>
 <li><p>See discussion on <a class="reference internal" href="../rotation.html"><span class="doc">plasma rotation</span></a></p></li>
 </ul>
@@ -879,6 +881,19 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 </ul>
 <hr class="docutils" />
 </section>
+<section id="px0">
+<span id="cgyro-px0"></span><h2>PX0<a class="headerlink" href="#px0" title="Link to this heading"></a></h2>
+<p><strong>Definition</strong></p>
+<p>The ballooning angle parameter <span class="math notranslate nohighlight">\(\mathrm{PX0} = \theta_0/(2\pi)\)</span>.</p>
+<p><strong>Comments</strong></p>
+<ul class="simple">
+<li><p>DEFAULT = 0.0</p></li>
+<li><p>This is used only for linear simulations.</p></li>
+<li><p>The most unstable linear mode is normally at <span class="math notranslate nohighlight">\(\mathrm{PX0} = 0\)</span>.</p></li>
+<li><p>Choose <span class="math notranslate nohighlight">\(0 \le \mathrm{PX0} &lt; 1\)</span>.</p></li>
+</ul>
+<hr class="docutils" />
+</section>
 <section id="q">
 <span id="cgyro-q"></span><h2>Q<a class="headerlink" href="#q" title="Link to this heading"></a></h2>
 <p><strong>Definition</strong></p>

docs/gyro/gyro_history.html

@@ -236,7 +236,7 @@ <h3>UL3: Eulerian codes have inadequate velocity-space resolution<a class="heade
 </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 <cite>rho_* &lt; 0.01</cite>. Moreover, the parallel nonlinearity has nothing whatsoever to do with the entropy paradox or with producing steady-states of turbulence.  To be clear the parallel nonlinearity (related to the nonlinear Landau damping and to wave-particle trapping) is the physical origin of a small turbulent heating source. GYRO is the first code to diagnostically calculate this heating <span id="id78">[<a class="reference internal" href="../zreferences.html#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#id62" 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>

docs/index.html

@@ -238,6 +238,7 @@ <h2>Equilibrium and Profiles<a class="headerlink" href="#equilibrium-and-profile
 <li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-grid">out.neo.grid</a></li>
 <li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-phi">out.neo.phi</a></li>
 <li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-rotation">out.neo.rotation</a></li>
+<li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-species">out.neo.species</a></li>
 <li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-theory">out.neo.theory</a></li>
 <li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-theory-nclass">out.neo.theory_nclass</a></li>
 <li class="toctree-l5"><a class="reference internal" href="neo/outputs.html#out-neo-transport">out.neo.transport</a></li>

docs/neo/outputs.html

@@ -148,22 +148,25 @@ <h2>Standard output files<a class="headerlink" href="#standard-output-files" tit
 <tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-theory"><span class="std std-ref">out.neo.theory</span></a></p></td>
 <td><p>Neoclassical transport coefficients from analytic theory</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-theory-nclass"><span class="std std-ref">out.neo.theory_nclass</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-species"><span class="std std-ref">out.neo.species</span></a></p></td>
+<td><p>Mass and charge of all species</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-theory-nclass"><span class="std std-ref">out.neo.theory_nclass</span></a></p></td>
 <td><p>Neoclassical transport coefficients from the NCLASS code</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-transport"><span class="std std-ref">out.neo.transport</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-transport"><span class="std std-ref">out.neo.transport</span></a></p></td>
 <td><p>Neoclassical transport coefficients from DKE solve</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-transport-flux"><span class="std std-ref">out.neo.transport_flux</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-transport-flux"><span class="std std-ref">out.neo.transport_flux</span></a></p></td>
 <td><p>Neoclassical fluxes in GB units from DKE solve</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-transport-gv"><span class="std std-ref">out.neo.transport_gv</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-transport-gv"><span class="std std-ref">out.neo.transport_gv</span></a></p></td>
 <td><p>Neoclassical fluxes from gyroviscosity</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-vel"><span class="std std-ref">out.neo.vel</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-vel"><span class="std std-ref">out.neo.vel</span></a></p></td>
 <td><p>Poloidal variation of first-order flows</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#neo-out-neo-vel-fourier"><span class="std std-ref">out.neo.vel_fourier</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#neo-out-neo-vel-fourier"><span class="std std-ref">out.neo.vel_fourier</span></a></p></td>
 <td><p>Poloidal variation of first-order flows (Fourier components)</p></td>
 </tr>
 </tbody>
@@ -473,6 +476,27 @@ <h2>Detailed description of NEO output files<a class="headerlink" href="#detaile
 </ol>
 <hr class="docutils" />
 </section>
+<section id="out-neo-species">
+<span id="neo-out-neo-species"></span><h3>out.neo.species<a class="headerlink" href="#out-neo-species" title="Link to this heading"></a></h3>
+<p><strong>Description</strong></p>
+<p>Mass and charge of all species</p>
+<p><strong>Format</strong></p>
+<p>Rectangular array of ASCII data:</p>
+<ul class="simple">
+<li><p>cols: <span class="math notranslate nohighlight">\(2 \times \mathtt{N\_SPECIES}\)</span></p></li>
+</ul>
+<ol class="arabic">
+<li><p>For each species <span class="math notranslate nohighlight">\(\sigma\)</span>:</p>
+<blockquote>
+<div><ul class="simple">
+<li><p><span class="math notranslate nohighlight">\(m_\sigma/m_\mathrm{norm}\)</span>: species mass (we suggest always taking deuterium as the normalizing mass)</p></li>
+<li><p><span class="math notranslate nohighlight">\(z_\sigma\)</span>: species charge</p></li>
+</ul>
+</div></blockquote>
+</li>
+</ol>
+<hr class="docutils" />
+</section>
 <section id="out-neo-theory">
 <span id="neo-out-neo-theory"></span><h3>out.neo.theory<a class="headerlink" href="#out-neo-theory" title="Link to this heading"></a></h3>
 <p><strong>Description</strong></p>

html/src/cgyro.rst

@@ -85,8 +85,6 @@ Running Cases
 -------------
 
 * :doc:`running cases <cgyro/running_cases>`
-* :doc:`cori <cgyro/cgyro_cori>`
-* :doc:`titan <cgyro/cgyro_titan>`
 
 Frequently Asked Questions
 --------------------------

html/src/cgyro/cgyro_list.rst

@@ -541,10 +541,12 @@ GAMMA_E
 
 **Definition**
 
-Normalized :math:`\exb` shearing rate :math:`\displaystyle \frac{a}{c_s} \gamma_E`.
+Normalized :math:`\exb` shearing rate :math:`\displaystyle \frac{a}{c_s} \gamma_E`. 
 
 **Comments**
 
+- This is the radial electric field shear and is a **global** term (can't be treated in a local simulation)
+- It it zeroed automatically in a linear simulation
 - DEFAULT = 0.0
 - See discussion on :doc:`plasma rotation <../rotation>`
 
@@ -1108,6 +1110,24 @@ Selector for profile data input.
 
 ----
 
+.. _cgyro_px0:
+
+PX0
+---
+
+**Definition**
+
+The ballooning angle parameter :math:`\mathrm{PX0} = \theta_0/(2\pi)`.
+
+**Comments**
+
+- DEFAULT = 0.0
+- This is used only for linear simulations.
+- The most unstable linear mode is normally at :math:`\mathrm{PX0} = 0`.
+- Choose :math:`0 \le \mathrm{PX0} < 1`.
+
+----
+
 .. _cgyro_q:
 
 Q
@@ -1122,7 +1142,7 @@ Safety factor, :math:`q`, of the flux surface.
 - DEFAULT = 2.0
 - This is only active with :ref:`cgyro_equilibrium_model` = 2 (the Miller equilibrium model).
 - When experimental profiles are used (:ref:`cgyro_profile_model` = 2), the safety factor as a function of radius is read from :ref:`input.gacode` and the safety factor gradient is computed internally.
-  
+
 ----
 
 .. _cgyro_quasineutral_flag:

html/src/cgyro/running_cases.rst

@@ -4,7 +4,6 @@ Running Cases
 Quick-start example
 -------------------
 
-
 ::
 
    $ cgyro -g reg08