Various memory related issued fixed.

- Fixes a memory leak
- Avoids some warnings when debugging python code with valgrind
- Fixes an issue with IAS15 array sizes (closes #805)

rebound/simulation.py

@@ -8,6 +8,11 @@
 import sys
 import warnings
 
+# Avoid unboxing strings. See
+# https://sourceforge.net/p/ctypes/mailman/message/8469497/
+class allocated_c_char_p(c_char_p):
+    pass
+
 import types
 
 ### The following enum and class definitions need to
@@ -281,9 +286,10 @@ def __eq__(self, other):
     def diff(self, other):
         if not isinstance(other,Simulation):
             return NotImplemented
-        clibrebound.reb_simulation_diff_char.restype = c_char_p
+        clibrebound.reb_simulation_diff_char.restype = allocated_c_char_p
         output = clibrebound.reb_simulation_diff_char(byref(other), byref(self))
-        print(output.decode("utf-8"))
+        print(output.value.decode("utf-8"))
+        clibrebound.reb_free(output)
 
     def __add__(self, other):
         if not isinstance(other,Simulation):

src/input.c

@@ -229,11 +229,12 @@ void reb_input_fields(struct reb_simulation* r, FILE* inf, enum reb_simulation_b
             reb_tree_add_particle_to_tree(r, l);
         }
     }
-    if (r->ri_ias15.at){ 
-        // Assume that all arrays were saved whenever ri_ias15.at was saved.
-        // Only 3*N entries got saved. 
-        r->ri_ias15.N_allocated = 3*r->N;
-    }
+    // Commented out on Nov 26 2024. Not sure why this was added. Might be for an older SA version.
+    // if (r->ri_ias15.at){ 
+    //     // Assume that all arrays were saved whenever ri_ias15.at was saved.
+    //     // Only 3*N entries got saved. 
+    //     r->ri_ias15.N_allocated = 3*r->N;
+    // }
     r->ri_whfast512.recalculate_constants = 1;
 }
 

src/particle.c

@@ -25,6 +25,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <stdint.h>
+#include <string.h>
 #include "rebound.h"
 #include "tree.h"
 #include "boundary.h"
@@ -52,8 +53,10 @@ static void reb_simulation_add_local(struct reb_simulation* const r, struct reb_
 		return;
 	}
 	while (r->N_allocated<=r->N){
+		unsigned int old_N_allocated = r->N_allocated;
 		r->N_allocated = r->N_allocated ? r->N_allocated * 2 : 128;
 		r->particles = realloc(r->particles,sizeof(struct reb_particle)*r->N_allocated);
+		memset(r->particles + old_N_allocated, 0, (r->N_allocated - old_N_allocated) * sizeof(struct reb_particle));
 	}
 
 	r->particles[r->N] = pt;

src/rebound.c

@@ -485,6 +485,7 @@ void reb_clear_pre_post_pointers(struct reb_simulation* const r){
 }
 
 void reb_simulation_init(struct reb_simulation* r){
+    memset(r, 0, sizeof(struct reb_simulation));
     r->rand_seed = reb_tools_get_rand_seed();
     reb_simulation_reset_function_pointers(r);
     r->t        = 0; 
@@ -950,6 +951,11 @@ int reb_check_fp_contract(){
     return r1 != r2;
 }
 
+// Wrapper to free pointers from python.
+void reb_free(void* p){
+    free(p);
+}
+
 #ifdef _WIN32
 
 void PyInit_librebound() {};

src/rebound.h

@@ -1374,6 +1374,8 @@ DLLEXPORT void reb_particles_transform_jacobi_to_inertial_posvel(struct reb_part
 DLLEXPORT void reb_particles_transform_jacobi_to_inertial_pos(struct reb_particle* const particles, const struct reb_particle* const p_j, const struct reb_particle* const p_mass, const unsigned int N, const unsigned int N_active);
 DLLEXPORT void reb_particles_transform_jacobi_to_inertial_acc(struct reb_particle* const particles, const struct reb_particle* const p_j, const struct reb_particle* const p_mass, const unsigned int N, const unsigned int N_active);
 
+DLLEXPORT void reb_free(void* p);
+
 // Democratic heliocentric coordinates
 DLLEXPORT void reb_particles_transform_inertial_to_democraticheliocentric_posvel(const struct reb_particle* const particles, struct reb_particle* const p_h, const unsigned int N, const unsigned int N_active);
 DLLEXPORT void reb_particles_transform_democraticheliocentric_to_inertial_pos(struct reb_particle* const particles, const struct reb_particle* const p_h, const unsigned int N, const unsigned int N_active);