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.