Feature/update-AtomsBase-0.5

[yangmr04]

Update to use AtomsBase 0.5

This pull request includes significant changes to the AbstractWalkers and EnergyEval modules, focusing on updating functions to use new methods for handling atomic systems and periodic boundary conditions. The changes also include improvements to the handling of atomic symbols and positions within various helper functions.

Main changes in AtomsBase:

• Periodic() and DirichletZero() boundary conditions are deprecated. Simple booleans are used now.
• atomic_symbol() and other similar functions now need the atom index in the particles list to work.
• atomic_system() is now the easiest way to construct a flexible system.
• boundary_conditions and bounding_box are no longer fields of a system, they are now periodicity and cell_vectors, respectively.

Now using up-to-date ExtXYZ and AtomsIO packages as well, as they are changed to accommodate AtomsBase 0.5.

No breaking changes in the exported method, although some output now looks different.

Resolves #89.

Key Changes:

AbstractWalkers Module:

• src/AbstractWalkers/AbstractWalkers.jl: Added exports for new helper functions sort_components_by_atomic_number, split_components, split_components_by_chemical_species, and check_num_components.
• src/AbstractWalkers/atomistic_walkers.jl: Updated AtomWalker to use list comprehensions for extracting atomic symbols and positions, improving the handling of frozen species. [1] [2]
• src/AbstractWalkers/helpers.jl: Refactored split_components and split_components_by_chemical_species to use new methods for creating FastSystem objects. [1] [2]
• src/AbstractWalkers/helpers.jl: Updated sort_components_by_atomic_number to use new methods for handling atomic symbols and positions, ensuring proper sorting and merging of species. [1] [2]

EnergyEval Module:

• src/EnergyEval/EnergyEval.jl: Removed exports for sort_components_by_atomic_number and split_components, as these functions are now handled within the AbstractWalkers module.
• src/EnergyEval/atomistic_energies.jl: Refactored pbc_dist to use periodicity and cell_vectors methods for boundary conditions and box dimensions.

FreeBirdIO Module:

• src/FreeBirdIO/FreeBirdIO.jl: Updated set_pbc to use a simplified method for setting periodic boundary conditions.
• src/FreeBirdIO/FreeBirdIO.jl: Refactored append_system and extract_free_par to use new methods for handling atomic systems and periodicity. [1] [2]
• src/FreeBirdIO/FreeBirdIO.jl: Updated generate_random_starting_config and generate_multi_type_random_starting_config to use new methods for setting boundary conditions and creating atomic systems. [1] [2]

Tests:

• test/test-AbstractWalkers.jl: Updated tests to verify the new methods for handling cell vectors and periodicity in atomic systems. [1] [2] [3]
• test/test-EnergyEval.jl: Updated tests for pbc_dist to use the new methods for setting non-periodic boundary conditions.

Documentation preview: https://wexlergroup.github.io/FreeBird.jl/previews/PR90/

[junchichen21]

I saw many changes both in the source codes and test codes due to employing the newer version of package AtomsBase 0.5. From my perspectives, these changes make the code more readable. Good work!