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Refactoring model system (#170)

* work with basesections.v2

* remove the redundant child model_system subsection

* move positions Quantity to ModelSystem

* AtomsState(Element), remove helper functions, modify normalize() to check consistency between chemical_symbol and atomic_number

* remove positions and velocities from Cell

* move ASE Atoms object creation to ModelSystem

* add sub_systems to ModelSystem

* add total_charge and total_spin to ModelSystem

* add ModelSystem.sub_systems instead of ModelSystem.model_system

* move comparison functions from AtomicCell to ModelSystem

* add ParticleState and CoarseGrainedState

* Refactor symmetry resolution: use dict mapping for cell types

* remove atom_types and related tests

* remove too many warnings in get_chemical_symbols

* ModelSystem.particle_states instead of atom_states

* remove redundant positions length checks

* n_particles and particle_indices (instead of n_atoms and atom_indices)

* add a note in GeometricSpace.get_geometric_space_for_atomic_cell

* modify to_ase_atoms, test_numerical_settings.py 

* modify conftest so that model_system.positions are populated

* import the v2 Entity in physical_property.py

* Fix DOSProfile normalization factor resolution to use model_system.particle_states

* Remove unused variable from SlaterKosterBond normalization test

* fix APW-refs fixture in conftest.py

* fix spectral profile tests

* Remove redundant try/except around get_geometric_space_for_atomic_cell

* add a test for composition formula

1899 of 2804 relevant lines covered (67.72%)

0.68 hits per line

Source Files on job 14861134994.1