deploy: 5728a64

docs/FlowChart.html

@@ -399,12 +399,8 @@ <h3>Single Step Flowchart<a class="headerlink" href="#single-step-flowchart" tit
 <p>In <code class="docutils literal notranslate"><span class="pre">initialize_do_advance()</span></code>:</p>
 <ol class="upperalpha simple">
 <li><p>Create <code class="docutils literal notranslate"><span class="pre">Sborder</span></code>, initialized from <code class="docutils literal notranslate"><span class="pre">S_old</span></code></p></li>
-<li><p>Call <code class="docutils literal notranslate"><span class="pre">clean_state()</span></code> to make sure the thermodynamics are in</p></li>
-</ol>
-<blockquote>
-<div><p>sync, in particular, compute the temperature.</p>
-</div></blockquote>
-<ol class="upperalpha simple" start="3">
+<li><p>Call <code class="docutils literal notranslate"><span class="pre">clean_state()</span></code> to make sure the thermodynamics are in
+sync, in particular, compute the temperature.</p></li>
 <li><p>[<code class="docutils literal notranslate"><span class="pre">SHOCK_VAR</span></code>] zero out the shock flag.</p></li>
 <li><p>Create the source corrector (if <code class="docutils literal notranslate"><span class="pre">castro.source_term_predictor</span></code> = 1)</p></li>
 </ol>

docs/Hydrodynamics.html

@@ -575,6 +575,14 @@ <h2>Source Terms<a class="headerlink" href="#source-terms" title="Link to this h
 S_{{\rm ext},\rho X_k} \\
 S_{{\rm ext},\rho Y_k}
 \end{array}\right)^n.\end{split}\]</div>
+<div class="admonition note" id="index-0">
+<p class="admonition-title">Note</p>
+<p>To reduce memory usage, we do not include source terms for the
+advected quantities, species, and auxiliary variables in the conserved
+state vector by default. If your application needs external source terms for
+these variables, set <code class="docutils literal notranslate"><span class="pre">USE_SPECIES_SOURCES=TRUE</span></code> when compiling so that space
+will be allocated for them.</p>
+</div>
 </section>
 <section id="primitive-forms">
 <h2>Primitive Forms<a class="headerlink" href="#primitive-forms" title="Link to this heading"></a></h2>
@@ -768,7 +776,7 @@ <h3>Primitive Variable System<a class="headerlink" href="#primitive-variable-sys
 <li><p>Solving the Riemann problem</p></li>
 <li><p>Doing the conservative update</p></li>
 </ol>
-<p id="index-0">Each of these steps has a variety of runtime parameters that
+<p id="index-1">Each of these steps has a variety of runtime parameters that
 affect their behavior. Additionally, there are some general
 runtime parameters for hydrodynamics:</p>
 <ul>
@@ -780,10 +788,8 @@ <h3>Primitive Variable System<a class="headerlink" href="#primitive-variable-sys
 after the solution update (0 or 1; default: 0)</p>
 <p>See <a class="reference internal" href="sponge.html#sponge-section"><span class="std std-ref">Sponge</span></a> for more details on the sponge.</p>
 </li>
-<li><p><code class="docutils literal notranslate"><span class="pre">castro.normalize_species</span></code>: enforce that <span class="math notranslate nohighlight">\(\sum_i X_i = 1\)</span>
-(0 or 1; default: 0)</p></li>
 </ul>
-<p id="index-1">Several floors are imposed on the thermodynamic quantities to prevet unphysical
+<p id="index-2">Several floors are imposed on the thermodynamic quantities to prevet unphysical
 behavior:</p>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">castro.small_dens</span></code>: (Real; default: -1.e20)</p></li>
@@ -1025,7 +1031,7 @@ <h3>Edge State Prediction<a class="headerlink" href="#edge-state-prediction" tit
 framework, the details follow exactly as given in Section 4.2.1 in
 Miller &amp; Colella, except for the details of the Riemann solver,
 which are given below.</p>
-<p id="index-2">For the reconstruction of the interface states, the following apply:</p>
+<p id="index-3">For the reconstruction of the interface states, the following apply:</p>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">castro.ppm_type</span></code> : use piecewise linear vs PPM algorithm (0 or 1;
 default: 1).  A value of 1 is the standard piecewise parabolic
@@ -1066,7 +1072,7 @@ <h3>Riemann Problem<a class="headerlink" href="#riemann-problem" title="Link to
 solver. The first two are both
 two-shock approximate solvers, but differ in how they approximate
 the thermodynamics in the “star” region.</p>
-<div class="admonition note" id="index-3">
+<div class="admonition note" id="index-4">
 <p class="admonition-title">Note</p>
 <p>These Riemann solvers are for Newtonian hydrodynamics, however, we enforce
 that the interface velocity cannot exceed the speed of light in both the
@@ -1211,7 +1217,7 @@ <h3>Compute Fluxes and Update<a class="headerlink" href="#compute-fluxes-and-upd
 </section>
 <section id="temperature-fixes">
 <span id="sec-ppm-temp-fix"></span><h2>Temperature Fixes<a class="headerlink" href="#temperature-fixes" title="Link to this heading"></a></h2>
-<p id="index-4">There are a number of experimental options for improving the behavior
+<p id="index-5">There are a number of experimental options for improving the behavior
 of the temperature in the reconstruction and interface state
 prediction. The options are controlled by <code class="docutils literal notranslate"><span class="pre">castro.ppm_temp_fix</span></code>,
 which takes values:</p>
@@ -1242,7 +1248,7 @@ <h3>Compute Fluxes and Update<a class="headerlink" href="#compute-fluxes-and-upd
 <h2>Resets<a class="headerlink" href="#resets" title="Link to this heading"></a></h2>
 <section id="flux-limiting">
 <span id="app-hydro-flux-limiting"></span><h3>Flux Limiting<a class="headerlink" href="#flux-limiting" title="Link to this heading"></a></h3>
-<p id="index-5">Multi-dimensional hydrodynamic simulations often have numerical
+<p id="index-6">Multi-dimensional hydrodynamic simulations often have numerical
 artifacts that result from the sharp density gradients. A somewhat
 common issue, especially at low resolution, is negative densities that
 occur as a result of a hydro update. Castro contains a prescription

docs/_sources/FlowChart.rst.txt

@@ -309,7 +309,7 @@ In the code, the objective is to evolve the state from the old time,
    A. Create ``Sborder``, initialized from ``S_old``
 
    B. Call ``clean_state()`` to make sure the thermodynamics are in
-     sync, in particular, compute the temperature.
+      sync, in particular, compute the temperature.
 
    C. [``SHOCK_VAR``] zero out the shock flag.
 

docs/_sources/Hydrodynamics.rst.txt

@@ -342,6 +342,14 @@ accounted for in **Steps 1** and **6**. The source terms are:
    S_{{\rm ext},\rho Y_k}
    \end{array}\right)^n.
 
+.. index:: USE_SPECIES_SOURCES
+
+.. note:: To reduce memory usage, we do not include source terms for the
+   advected quantities, species, and auxiliary variables in the conserved
+   state vector by default. If your application needs external source terms for
+   these variables, set ``USE_SPECIES_SOURCES=TRUE`` when compiling so that space
+   will be allocated for them.
+
 Primitive Forms
 ===============
 
@@ -585,9 +593,6 @@ runtime parameters for hydrodynamics:
 
    See :ref:`sponge_section` for more details on the sponge.
 
--  ``castro.normalize_species``: enforce that :math:`\sum_i X_i = 1`
-   (0 or 1; default: 0)
-
 .. index:: castro.small_dens, castro.small_temp, castro.small_pres
 
 Several floors are imposed on the thermodynamic quantities to prevet unphysical

docs/_sources/faq.rst.txt

@@ -106,10 +106,10 @@ Debugging
 
    ::
 
-           print_state(mf, IntVect(D_DECL(10, 20, 30)));
+           print_state(mf, IntVect(AMREX_D_DECL(10, 20, 30)));
 
    Here, the IntVect has the dimension that we were compiled with
-   (and this is handled through the preprocessor ``D_DECL``). In
+   (and this is handled through the preprocessor ``AMREX_D_DECL``). In
    this case, we are inspecting zone (10, 20, 30), in the global index
    space. Note that since a multifab exists only on a single level, the
    integer indices here refer to the global index space on that level.

docs/_sources/index.rst.txt

@@ -60,7 +60,7 @@ https://github.com/amrex-astro/Castro
 
    filelist
    classlist
-   .. namespacelist
+.. namespacelist
 
 .. toctree::
    :caption: References

docs/_sources/io.rst.txt

@@ -271,8 +271,6 @@ radiation quantities).
 | (where X is any of the species    | :math:`\omegadot_k = DX_k/Dt`                     |                                      |
 | defined in the network)           |                                                   |                                      |
 +-----------------------------------+---------------------------------------------------+--------------------------------------+
-| ``enuc``                          | Nuclear energy generation rate / gram             | :math:`{\rm erg~g^{-1}~s^{-1}}`      |
-+-----------------------------------+---------------------------------------------------+--------------------------------------+
 | ``rho_enuc``                      | Nuclear energy generation rate density            | :math:`{\rm erg~cm^{-3}~s^{-1}}`     |
 +-----------------------------------+---------------------------------------------------+--------------------------------------+
 | ``phiGrav``                       | Gravitational potential                           | :math:`{\rm erg~g^{-1}}`             |
@@ -393,7 +391,8 @@ Derived variables
 | ``y_velocity``,                   | :math:`\ub = (\rho \ub)/\rho`                     |                             |                                         |
 | ``z_velocity``                    |                                                   |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
-
+| ``enuc``                          | Nuclear energy generation rate / gram             | ``derenuc``                 | :math:`{\rm erg~g^{-1}~s^{-1}}`         |
++-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 
 problem-specific plotfile variables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^