From cf6280ce10fd9833151b3be2857b2af9e15f3474 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue, 12 Dec 2023 13:40:21 -0500
Subject: [PATCH] add optional species sources for the conserved state

---
 Exec/Make.Castro               | 4 ++++
 Source/driver/_variables       | 6 +++---
 Source/driver/set_variables.py | 3 +++
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/Exec/Make.Castro b/Exec/Make.Castro
index cfd7e187a9..79e747b5c8 100644
--- a/Exec/Make.Castro
+++ b/Exec/Make.Castro
@@ -270,6 +270,10 @@ ifeq ($(USE_ROTATION), TRUE)
   DEFINES += -DROTATION
 endif
 
+ifeq ($(USE_SPECIES_SOURCES), TRUE)
+  DEFINES += -DCONS_SPECIES_HAVE_SOURCES
+endif
+
 ifeq ($(USE_PARTICLES), TRUE)
   Bdirs += Source/particles
 endif
diff --git a/Source/driver/_variables b/Source/driver/_variables
index 36d05dfc06..b6408c82a8 100644
--- a/Source/driver/_variables
+++ b/Source/driver/_variables
@@ -16,9 +16,9 @@
    energy-density         UEDEN     NSRC                                  1                 None
    internal-energy        UEINT     NSRC                                  1                 None
    temperature            UTEMP     NSRC                                  1                 None
-   advected               UFA       None                                  NumAdv            None
-   species                UFS       None                                  NumSpec           None
-   auxiliary              UFX       None                                  NumAux            None
+   advected               UFA       [(NSRC, CONS_SPECIES_HAVE_SOURCES)]   NumAdv            None
+   species                UFS       [(NSRC, CONS_SPECIES_HAVE_SOURCES)]   NumSpec           None
+   auxiliary              UFX       [(NSRC, CONS_SPECIES_HAVE_SOURCES)]   NumAux            None
    shock                  USHK      None                                  1                 SHOCK_VAR
    mu_p                   UMUP      None                                  1                 NSE_NET
    mu_n                   UMUN      None                                  1                 NSE_NET
diff --git a/Source/driver/set_variables.py b/Source/driver/set_variables.py
index a70af00834..12c5cb5743 100755
--- a/Source/driver/set_variables.py
+++ b/Source/driver/set_variables.py
@@ -132,6 +132,7 @@ def doit(variables_file, odir, defines, nadv):
                 count = fields[3]
                 ifdef = fields[4]
 
+                print("here: ", name, var, adds_to_temp, count, ifdef)
                 # we may be fed a pair of the form (SET, DEFINE),
                 # in which case we only add to SET if we define
                 # DEFINE
@@ -153,6 +154,8 @@ def doit(variables_file, odir, defines, nadv):
                     if adds_to_temp == "None":
                         adds_to = None
                     else:
+                        if adds_to_temp.startswith("("):
+                            print("here")
                         adds_to = [adds_to_temp]
 
                 # only recognize the index if we defined any required preprocessor variable