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Archive data update (#339)

* Added parsing of masses and (partial) charges for MD

* WIP

* Still a WIP

Fixed bugs in MSD calculation

Updated molecular_dynamcis to handle new home of mass and charge

Added partial_charges and effective_masses to class ForceField (#346)

* Added partial_charges and effective_masses to class ForceField

* Update src/nomad_simulations/schema_packages/force_field.py

Co-authored-by: Esma B. Boydas <80156958+EBB2675@users.noreply.github.com>

* Update src/nomad_simulations/schema_packages/force_field.py

Co-authored-by: Esma B. Boydas <80156958+EBB2675@users.noreply.github.com>

* Added effective_masses type to positive_float, enforced len(shape) = n_particles

* Added AtomParameters for force field parameters, following the  architecture.

* Combined corrected species_scope approach with a nomadic structural check.

* Small improvement of AtomsParameterContainer.normalize

* Corrected logger handling in normalizer signature

* Corrected mistake in force_field docstring

* Fixed tests

* Removed unused imports, improved test coverage

* Implemented selection of representative_system, extended tests

* Corrected docstring

* Improved AtomParametersContainer.normalize

* Fixed Ruff violations

* Fixed expeced normalizer sequence, corrected logger message formatting

* Removed f-strings from logger messages

* Generalized function names, changed species_scope to type ParticleState

* Generalized field names from atom to particle

---------

Co-authored-by: Esma B. Boydas <80156958+EBB2675@users.noreply.github.com>

* Updated molecular_dynamics to process archive.data

Fixed failing test

Fixed Ruff violation

More linting errors

MDAnalysis doesn't accept bonds = None anymore

Fixing merge conflict

* fix: make molecular_dynamics access ParticleParameters quantities, pass MolecularDynamicsResults to normalizer

* fix: untyped data structures in archive_to_universe

* updated test_molecular_dynamics to work with ParticlePar... (continued)

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Source Files on job 24124214824.3