[md] store additional properties + update tests

[mshuaibii]

• Preserve atomic state in MD trajectories: Extends TrajectoryFrame to capture and serialize tags, fixed (from FixAtoms constraints), charge, and spin — fields critical for reconstructing atoms objects.
• MD runner improvements:
  • Saves initial atoms to init_atoms.extxyz before MD begins, so the starting structure is always available.
  • Renames checkpoint files from checkpoint.xyz to checkpoint.extxyz to match the format actually being written (extxyz).
  • Adds dedicated tests for the slab+adsorbate system builder and a new TestTrajectoryFrame test class that verifies tags, constraints, charge, and spin survive a full MD → parquet round-trip.