- Convert System and Molecule classes to use @dataclass and field for defaults
- Remove unused imports and legacy code from system.py
- Move print_charges_and_dipole method from System to Player for better separation of concerns
- Minor formatting and import order improvements for consistency
- Replace manual property updates with @cached_property for total_mass, com, and inertia_tensor
- Introduce invalidate_computed_properties decorator to auto-invalidate cached properties on atom changes
- Vectorize distances_between_atoms, sizes_of_molecule, and minimum_distance calculations using numpy
- Unify and clarify center of mass and standard orientation methods (move_center_of_mass_to_origin, rotate_to_standard_orientation)
- Remove redundant or outdated code, improve typing and error handling
- Update dependent files and tests to use new method names and behaviors
- Replace atomsymb and atommass tuples with AtomInfo dataclass and PTable enum for atomic data
- Refactor all usages to access atomic symbol and mass via PTable methods
- Remove nptyping dependency, switch to numpy.typing for type annotations
- Update molecule and atom classes to use new typing and atomic data access
- Bump numpy version to 2.x and remove nptyping from dependencies
This commit separates the Dice class in a Dice.py file stored in DPacks/external, also fixes the continue feature in the Dice class.
Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit temporarily uses Gaussian Heassian for step calculations, fixes fchk file reading, fixes step calculation, fixes log file and geoms formation. Also this commit adds type hinting to improve and facilitate the program development.
This commit adds the methods that were present in the Gaussian.py file into the SetGlobals.py file and packages the program into a diceplayer module so it can be ran using 'python3 -m diceplayer'
Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
