Logger add periodicity

Implement #726 (closed) @nnrw56 you might be interested.

Here I am doing a few different things in order to add the periodicity:

• Finally starting to implement the yaml file.
• Adding a structure that stores the required parameters
• Adding some checks in src/logger.c
• Fixing a small issue in logger/logger_index.c
• Improving the script tools/read_index_file.py in order to be able to read a bit the logfile.
• Adding a python function that provides the box size.

logger/chemistry/GEAR/logger_chemistry.h

@@ -25,6 +25,7 @@
 #include "chemistry_logger.h"
 #include "logger_interpolation.h"
 #include "logger_loader_io.h"
+#include "logger_parameters.h"
 #include "logger_python_tools.h"
 
 /* Index of the mask in the header mask array */
@@ -70,12 +71,14 @@ chemistry_logger_reader_link_derivatives_spart(struct header *head) {}
  * @param t Requested time.
  * @param field The field to reconstruct (follows the order of
  * #chemistry_logger_fields).
+ * @param params The simulation's #logger_parameters.
  */
 __attribute__((always_inline)) INLINE static void
 chemistry_logger_interpolate_field_part(
     const double t_before, const struct logger_field *restrict before,
     const double t_after, const struct logger_field *restrict after,
-    void *restrict output, const double t, const int field) {
+    void *restrict output, const double t, const int field,
+    const struct logger_parameters *params) {
 #ifdef SWIFT_DEBUG_CHECKS
   /* Check the times */
   if (t_before > t || t_after < t) {
@@ -112,12 +115,14 @@ chemistry_logger_interpolate_field_part(
  * @param t Requested time.
  * @param field The field to reconstruct (follows the order of
  * #chemistry_logger_fields).
+ * @param params The simulation's #logger_parameters.
  */
 __attribute__((always_inline)) INLINE static void
 chemistry_logger_interpolate_field_spart(
     const double t_before, const struct logger_field *restrict before,
     const double t_after, const struct logger_field *restrict after,
-    void *restrict output, const double t, const int field) {
+    void *restrict output, const double t, const int field,
+    const struct logger_parameters *params) {
 
 #ifdef SWIFT_DEBUG_CHECKS
   /* Check the times */
@@ -132,7 +137,8 @@ chemistry_logger_interpolate_field_spart(
   switch (field) {
     case chemistry_logger_field_spart_metal_mass_fractions:
       interpolate_linear_double_ND(t_before, before, t_after, after, output, t,
-                                   GEAR_CHEMISTRY_ELEMENT_COUNT);
+                                   GEAR_CHEMISTRY_ELEMENT_COUNT,
+                                   /* periodic= */ 0, params);
       break;
 
     default: