Extracted a subroutine in AO tool and made some name tweaks

What has been done:

• Extracted a method from a conditional that was difficult to read
• Changed a few names to be less misleading (initialize_centers did initialize_centers + export + initialize shells)
• Moved related routines to same position in the file for easier reference

Should there be updates to the changelog?

• No

Should the patch number in parameters.F90 be updated?

• No

Should there be updates to the website?

• No

Compilation and testing:

• Tested with -rcheck? no
• Tested with -fbatch? no
• Tested with intel? GCC10
• Tested with PCM? no
• Tested with int32 and int64? int32