Proposed updates to fix the outdated parts in the code

[ydanuiuc]

This proposed update tries to fix the follow two issues:

1. Failure to read charge density files formatted according to the CHGCAR format in VASP 5 or newer, which adds a new line to the header specifying the ion species. The updated file chgcar.H will check if such line exists and will skip it if necessary, adapting the Bader Integration code to work with both old and new CHGCAR formats.
2. Warnings raised by the current GCC compilers. Minor updates are done to address these warnings, which mainly involve ignored return values, unmatched data types, or concerns over array sizes, etc. The updates are done and tested using GCC 13.