From 4d25d4046c7c9aa74254382fb43942bf5c26f5fa Mon Sep 17 00:00:00 2001
From: MBradley1985 <2496844@student.swin.edu.au>
Date: Wed, 19 Feb 2025 11:50:34 +1100
Subject: [PATCH] Fixing Makefile and ensuring first attempt works

---
 Makefile         | 4 ++--
 src/core_init.c  | 8 ++++++++
 src/model_misc.c | 6 ++++++
 3 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 1d40e487..8bcca884 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-#USE-MPI := yes # set this if you want to run in embarrassingly parallel (automatically set if the compiler (i.e., the CC variable) is set to `mpicc`)
+USE-MPI := yes # set this if you want to run in embarrassingly parallel (automatically set if the compiler (i.e., the CC variable) is set to `mpicc`)
 USE-HDF5 := yes # set this if you want to read in hdf5 trees (requires hdf5 libraries)
 
 #MEM-CHECK = yes # Set this if you want to check sanitize pointers/memory addresses. Slowdown of ~2x is expected.
@@ -28,7 +28,7 @@ LIBSRC :=  sage.c core_read_parameter_file.c core_init.c core_io_tree.c \
            core_tree_utils.c model_infall.c model_cooling_heating.c model_starformation_and_feedback.c \
            model_disk_instability.c model_reincorporation.c model_mergers.c model_misc.c \
            io/read_tree_lhalo_binary.c io/read_tree_consistentrees_ascii.c io/ctrees_utils.c \
-	       io/save_gals_binary.c io/forest_utils.c io/buffered_io.c
+	       io/save_gals_binary.c io/forest_utils.c io/buffered_io.c ./model_h2_formation.c \
 
 LIBINCL := $(LIBSRC:.c=.h)
 LIBINCL += io/parse_ctrees.h
diff --git a/src/core_init.c b/src/core_init.c
index 8c61dd62..52f4980b 100644
--- a/src/core_init.c
+++ b/src/core_init.c
@@ -30,6 +30,14 @@ void init(struct params *run_params)
 #endif
 
     run_params->Age = mymalloc(ABSOLUTEMAXSNAPS*sizeof(run_params->Age[0]));
+    
+    // Initialize H2 fraction parameters with default values if not set
+    if(run_params->H2FractionFactor <= 0.0) {
+        run_params->H2FractionFactor = 1.0;  // Default value from DarkSAGE
+    }
+    if(run_params->H2FractionExponent <= 0.0) {
+        run_params->H2FractionExponent = 0.92;  // Default value from DarkSAGE
+    }
 
     set_units(run_params);
 
diff --git a/src/model_misc.c b/src/model_misc.c
index 7723ad22..dbdab335 100644
--- a/src/model_misc.c
+++ b/src/model_misc.c
@@ -7,6 +7,7 @@
 #include "core_allvars.h"
 
 #include "model_misc.h"
+#include "model_h2_formation.h"    // Add this line
 
 void init_galaxy(const int p, const int halonr, int *galaxycounter, const struct halo_data *halos,
                  struct GALAXY *galaxies, const struct params *run_params)
@@ -44,6 +45,8 @@ void init_galaxy(const int p, const int halonr, int *galaxycounter, const struct
     galaxies[p].deltaMvir = 0.0;
 
     galaxies[p].ColdGas = 0.0;
+    galaxies[p].H2_gas = 0.0;  // Initialize H2 gas
+    galaxies[p].HI_gas = 0.0;  // Initialize HI gas
     galaxies[p].StellarMass = 0.0;
     galaxies[p].BulgeMass = 0.0;
     galaxies[p].HotGas = 0.0;
@@ -51,6 +54,9 @@ void init_galaxy(const int p, const int halonr, int *galaxycounter, const struct
     galaxies[p].BlackHoleMass = 0.0;
     galaxies[p].ICS = 0.0;
 
+    // Initialize H2 fractions
+    init_gas_components(&galaxies[p]);
+
     galaxies[p].MetalsColdGas = 0.0;
     galaxies[p].MetalsStellarMass = 0.0;
     galaxies[p].MetalsBulgeMass = 0.0;