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Update documentation regarding species sources and normalization #2742

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merged 4 commits into from
Feb 13, 2024
Merged

Update documentation regarding species sources and normalization #2742

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e613a93
Add documentation for USE_SPECIES_SOURCES flag
KiranEiden Feb 5, 2024
669e57f
Remove documentation on normalize_species parameter
KiranEiden Feb 5, 2024
03daa09
Merge remote-tracking branch 'origin/development' into spec_src_doc_u…
KiranEiden Feb 13, 2024
a944b3e
Incorporate Mike's recommendations
KiranEiden Feb 13, 2024
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11 changes: 8 additions & 3 deletions Docs/source/Hydrodynamics.rst
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Expand Up @@ -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
===============

Expand Down Expand Up @@ -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
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