Mapping

Mapping converts atom-level trajectories into bead-level trajectories for AA/UA/complex CG workflows.

The mapping subsystem is part of the reusable algorithm layer (K6) and is audited and checkpointed via a stable spec hash.

Model scale

In the INI file:

[model]
scale = aa    ; aa|ua|cg|auto

Mapping modes

[mapping]
mode = identity   ; none|identity|by_mol|file
position = com_mass  ; com_mass|com_geom|representative_atom

The meaning of each mode:

identity

Beads == atoms.

by_mol

One bead per molecule id (requires mol in dump).

file

External mapping file defines atom_id -> bead_id (and optional weights).

Backmapping

Backmapping is provided as a utility to scatter bead-level results back to per-atom arrays for output or visualization.