Fixing Makefile and ensuring first attempt works

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

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);
 

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)
@@ -44,13 +45,18 @@ 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;
     galaxies[p].EjectedMass = 0.0;
     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;