From 1bdc65076bb13ee9279f1c4fdf7b0b34648adcab Mon Sep 17 00:00:00 2001
From: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Tue, 13 Feb 2024 14:44:55 -0800
Subject: [PATCH] Update documentation regarding species sources and
 normalization (#2742)

This PR updates the Hydrodynamics section documentation to highlight that sources for passive variables in the conserved state are off by default. It also removes the reference to castro.normalize_species, which does not appear to be a valid runtime parameter any longer. I am happy to introduce additional documentation regarding the species normalization if that would be helpful -- my understanding is that it is on by default now.
---
 Docs/source/Hydrodynamics.rst | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/Docs/source/Hydrodynamics.rst b/Docs/source/Hydrodynamics.rst
index 8d76bd5fdf..44cdf3e553 100644
--- a/Docs/source/Hydrodynamics.rst
+++ b/Docs/source/Hydrodynamics.rst
@@ -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