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Closes #198

-- Rename to `sub_system_indices`
-- Update definition to reflect that they are defined wrt top-level system
-- Update description of the particle states
-- Add a mapping definition similar to `sub_system_indices`
   Note: feel free to rename to `particle_indices`. Changed the naming here to avoid confusion with the legacy.
@ndaelman-hu ndaelman-hu added the improvement/fix Improvement or fix of a previous feature label Jul 9, 2025
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@EBB2675 this was my first attempt, before posting the issue. We may use it as a jumping-off board.

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Clarification on SubSystem specification

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