Topology

PILOTS can optionally read LAMMPS data topology information and inject it into measures via the :c++:type:SystemContext.

Loaded topology sections are audited in results.json.

Inputs

  • topology.format = lammps_data

  • topology.path = system.data

  • topology.load = masses,bonds,angles,... (mask; only parse what is needed)

Sections

The topology container can hold:

  • Masses (by type)

  • Bonds

  • Angles

  • Dihedrals

  • Impropers

Mol-first

Measures that aggregate by molecule should prefer mol from the dump. Optionally, the runner can derive molecule IDs from bond connectivity (disabled by default to avoid implicit semantics).