Use space_t in more places instead of simul_box_t

Description

• Reduced the usage of sb%periodic_dim, sb%dim and der%dim by using the corresponding components of space_t.
• Removed the simul_box_is_periodic and simul_box_has_zero_bc functions.
• Some cleanup and cosmetic changes.

Checklist

• I have checked that my code follows the Octopus coding standards
• I have added tests for all the new features added in this request.