Update docs

annotated.html

@@ -332,7 +332,7 @@
 <tr id="row_112_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIdxRangeSlice.html" target="_self">IdxRangeSlice</a></td><td class="desc">A class which describes a collection of equally spaced Idxs which form a index range </td></tr>
 <tr id="row_113_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structIdxRangeSliceIterator.html" target="_self">IdxRangeSliceIterator</a></td><td class="desc">An iterator type for the <a class="el" href="classIdxRangeSlice.html" title="A class which describes a collection of equally spaced Idxs which form a index range.">IdxRangeSlice</a> </td></tr>
 <tr id="row_114_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structIdxRangeToSlice.html" target="_self">IdxRangeToSlice</a></td><td class="desc">A class to create a <a class="el" href="classIdxRangeSlice.html" title="A class which describes a collection of equally spaced Idxs which form a index range.">IdxRangeSlice</a> type from a TypeSeq </td></tr>
-<tr id="row_115_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIEquilibrium.html" target="_self">IEquilibrium</a></td><td class="desc">An abstract class for initializing a distribution function in (species,vpar,mu) </td></tr>
+<tr id="row_115_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIEquilibrium.html" target="_self">IEquilibrium</a></td><td class="desc">An abstract class for initializing a distribution function in (species,vpar,mu,r,theta) </td></tr>
 <tr id="row_116_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIFluidInitialization.html" target="_self">IFluidInitialization</a></td><td class="desc">An abstract class that allows for initializing a fluid species </td></tr>
 <tr id="row_117_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIFluidTransportSolver.html" target="_self">IFluidTransportSolver</a></td><td class="desc">An abstract class for solving the transport of a fluid model </td></tr>
 <tr id="row_118_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIFootFinder.html" target="_self">IFootFinder</a></td><td class="desc">Define a base class for all the time integration methods used for the advection </td></tr>
@@ -381,7 +381,7 @@
 <tr id="row_161_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMatrixBatchCsr.html" target="_self">MatrixBatchCsr</a></td><td class="desc"><a class="el" href="classMatrix.html">Matrix</a> class which is able to manage and solve a batch of sparse linear systems </td></tr>
 <tr id="row_162_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMatrixBatchEll.html" target="_self">MatrixBatchEll</a></td><td class="desc"><a class="el" href="classMatrix.html">Matrix</a> class which is able to manage and solve a batch of sparse linear systems </td></tr>
 <tr id="row_163_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMatrixBatchTridiag.html" target="_self">MatrixBatchTridiag</a></td><td class="desc">A structure for solving a set of independant tridiagonal systems using a direct method </td></tr>
-<tr id="row_164_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMaxwellianEquilibrium.html" target="_self">MaxwellianEquilibrium</a></td><td class="desc">Equilibrium operator as Maxwellian. This initializes all species </td></tr>
+<tr id="row_164_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMaxwellianEquilibrium.html" target="_self">MaxwellianEquilibrium</a></td><td class="desc">Equilibrium operator as normalized Maxwellian. This initializes all species </td></tr>
 <tr id="row_165_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMetricTensor.html" target="_self">MetricTensor</a></td><td class="desc">An operator for calculating the metric tensor </td></tr>
 <tr id="row_166_" class="even"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_166_" class="arrow" onclick="toggleFolder('166_')">&#9658;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMoments.html" target="_self">Moments</a></td><td class="desc"><a class="el" href="classMoments.html" title="Moments discrete dimension to access constant attributes related to fluid moments.">Moments</a> discrete dimension to access constant attributes related to fluid moments </td></tr>
 <tr id="row_166_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMoments_1_1Impl.html" target="_self">Impl</a></td><td class="desc"><a class="el" href="classMoments_1_1Impl.html" title="Impl object storing attributes in MemorySpace.">Impl</a> object storing attributes in <code>MemorySpace</code> </td></tr>

bumpontailequilibrium_8hpp_source.html

@@ -164,7 +164,7 @@
 <div class="ttc" id="aclassBumpontailEquilibrium_html_aacc82cfd448632f072b0e536c93ea668"><div class="ttname"><a href="classBumpontailEquilibrium.html#aacc82cfd448632f072b0e536c93ea668">BumpontailEquilibrium::compute_twomaxwellian</a></div><div class="ttdeci">void compute_twomaxwellian(DFieldVx fMaxwellian, double epsilon_bot, double temperature_bot, double mean_velocity_bot) const</div><div class="ttdoc">Compute a distribution function defined as a sum of two Maxwellians.</div></div>
 <div class="ttc" id="aclassBumpontailEquilibrium_html_ade9524f9a546fdcb20c3e60f9d788edd"><div class="ttname"><a href="classBumpontailEquilibrium.html#ade9524f9a546fdcb20c3e60f9d788edd">BumpontailEquilibrium::init_from_input</a></div><div class="ttdeci">static BumpontailEquilibrium init_from_input(IdxRangeSp idx_range_kinsp, PC_tree_t const &amp;yaml_input_file)</div><div class="ttdoc">Read the density, temperature and mean velocity required to initialize the bump-on-tail Maxwellian in...</div></div>
 <div class="ttc" id="aclassBumpontailEquilibrium_html_af3995062c5408eea2ae7761113d30c52"><div class="ttname"><a href="classBumpontailEquilibrium.html#af3995062c5408eea2ae7761113d30c52">BumpontailEquilibrium::BumpontailEquilibrium</a></div><div class="ttdeci">BumpontailEquilibrium(host_t&lt; DFieldMemSp &gt; epsilon_bot, host_t&lt; DFieldMemSp &gt; temperature_bot, host_t&lt; DFieldMemSp &gt; mean_velocity_bot)</div><div class="ttdoc">Creates an instance of the BumpontailEquilibrium class.</div></div>
-<div class="ttc" id="aclassIEquilibrium_html"><div class="ttname"><a href="classIEquilibrium.html">IEquilibrium</a></div><div class="ttdoc">An abstract class for initializing a distribution function in (species,vpar,mu).</div><div class="ttdef"><b>Definition:</b> iequilibrium.hpp:11</div></div>
+<div class="ttc" id="aclassIEquilibrium_html"><div class="ttname"><a href="classIEquilibrium.html">IEquilibrium</a></div><div class="ttdoc">An abstract class for initializing a distribution function in (species,vpar,mu,r,theta).</div><div class="ttdef"><b>Definition:</b> iequilibrium.hpp:11</div></div>
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 </div><!-- doc-content -->
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classBumpontailEquilibrium-members.html

@@ -112,10 +112,12 @@
   <tr><td class="entry"><a class="el" href="classBumpontailEquilibrium.html#ade9524f9a546fdcb20c3e60f9d788edd">init_from_input</a>(IdxRangeSp idx_range_kinsp, PC_tree_t const &amp;yaml_input_file)</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classBumpontailEquilibrium.html#a0288d56e370eca487bc93d038b178114">mean_velocity_bot</a>() const</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr><td class="entry"><a class="el" href="classBumpontailEquilibrium.html#a4c85a379ea216bb7ac95186cf8af8817">operator()</a>(DFieldSpVx allfequilibrium) const override</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#a425f7b104d75900fcc769bdee9c0cdbd">IEquilibrium::operator()</a>(DFieldSpVparMu allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classIEquilibrium.html#ac3766d5ef01c1e949ec3dd6d55892a75">IEquilibrium::operator()</a>(DFieldSpVxVy allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classBumpontailEquilibrium.html#a8e74948ac659299209e1550bab1fe694">temperature_bot</a>() const</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>~BumpontailEquilibrium</b>() override=default (defined in <a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a>)</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#a58d9872d82ccadfbb3f215528463e30d">IEquilibrium::operator()</a>(DFieldSpV2DTor2D allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classIEquilibrium.html#a425f7b104d75900fcc769bdee9c0cdbd">IEquilibrium::operator()</a>(DFieldSpVparMu allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#ac3766d5ef01c1e949ec3dd6d55892a75">IEquilibrium::operator()</a>(DFieldSpVxVy allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classBumpontailEquilibrium.html#a8e74948ac659299209e1550bab1fe694">temperature_bot</a>() const</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~BumpontailEquilibrium</b>() override=default (defined in <a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a>)</td><td class="entry"><a class="el" href="classBumpontailEquilibrium.html">BumpontailEquilibrium</a></td><td class="entry"></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>

classBumpontailEquilibrium.html

@@ -116,7 +116,7 @@
  <div class="center">
   <img src="classBumpontailEquilibrium.png" usemap="#BumpontailEquilibrium_map" alt=""/>
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-<area href="classIEquilibrium.html" title="An abstract class for initializing a distribution function in (species,vpar,mu)." alt="IEquilibrium" shape="rect" coords="0,0,134,24"/>
+<area href="classIEquilibrium.html" title="An abstract class for initializing a distribution function in (species,vpar,mu,r,theta)." alt="IEquilibrium" shape="rect" coords="0,0,134,24"/>
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@@ -141,6 +141,9 @@
 <tr class="memdesc:a0288d56e370eca487bc93d038b178114"><td class="mdescLeft">&#160;</td><td class="mdescRight">A method for accessing the m_mean_velocity_bot member variable of the class.  <a href="classBumpontailEquilibrium.html#a0288d56e370eca487bc93d038b178114">More...</a><br /></td></tr>
 <tr class="separator:a0288d56e370eca487bc93d038b178114"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="inherit_header pub_methods_classIEquilibrium"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classIEquilibrium')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classIEquilibrium.html">IEquilibrium</a></td></tr>
+<tr class="memitem:a58d9872d82ccadfbb3f215528463e30d inherit pub_methods_classIEquilibrium"><td class="memItemLeft" align="right" valign="top">virtual DFieldSpV2DTor2D&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classIEquilibrium.html#a58d9872d82ccadfbb3f215528463e30d">operator()</a> (DFieldSpV2DTor2D allfequilibrium) const =0</td></tr>
+<tr class="memdesc:a58d9872d82ccadfbb3f215528463e30d inherit pub_methods_classIEquilibrium"><td class="mdescLeft">&#160;</td><td class="mdescRight">Operator for initializing an equilibrium distribution function.  <a href="classIEquilibrium.html#a58d9872d82ccadfbb3f215528463e30d">More...</a><br /></td></tr>
+<tr class="separator:a58d9872d82ccadfbb3f215528463e30d inherit pub_methods_classIEquilibrium"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a425f7b104d75900fcc769bdee9c0cdbd inherit pub_methods_classIEquilibrium"><td class="memItemLeft" align="right" valign="top">virtual DFieldSpVparMu&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classIEquilibrium.html#a425f7b104d75900fcc769bdee9c0cdbd">operator()</a> (DFieldSpVparMu allfequilibrium) const =0</td></tr>
 <tr class="memdesc:a425f7b104d75900fcc769bdee9c0cdbd inherit pub_methods_classIEquilibrium"><td class="mdescLeft">&#160;</td><td class="mdescRight">Operator for initializing an equilibrium distribution function.  <a href="classIEquilibrium.html#a425f7b104d75900fcc769bdee9c0cdbd">More...</a><br /></td></tr>
 <tr class="separator:a425f7b104d75900fcc769bdee9c0cdbd inherit pub_methods_classIEquilibrium"><td class="memSeparator" colspan="2">&#160;</td></tr>

classIEquilibrium-members.html

@@ -106,9 +106,11 @@
 
 <p>This is the complete list of members for <a class="el" href="classIEquilibrium.html">IEquilibrium</a>, including all inherited members.</p>
 <table class="directory">
-  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#a425f7b104d75900fcc769bdee9c0cdbd">operator()</a>(DFieldSpVparMu allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classIEquilibrium.html#a3ea3adf00a9a416a8e3fe54caba902a4">operator()</a>(DFieldSpVx allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#ac3766d5ef01c1e949ec3dd6d55892a75">operator()</a>(DFieldSpVxVy allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#a58d9872d82ccadfbb3f215528463e30d">operator()</a>(DFieldSpV2DTor2D allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classIEquilibrium.html#a425f7b104d75900fcc769bdee9c0cdbd">operator()</a>(DFieldSpVparMu allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classIEquilibrium.html#a3ea3adf00a9a416a8e3fe54caba902a4">operator()</a>(DFieldSpVx allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classIEquilibrium.html#ac3766d5ef01c1e949ec3dd6d55892a75">operator()</a>(DFieldSpVxVy allfequilibrium) const =0</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>~IEquilibrium</b>()=default (defined in <a class="el" href="classIEquilibrium.html">IEquilibrium</a>)</td><td class="entry"><a class="el" href="classIEquilibrium.html">IEquilibrium</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>