Molfra Handler Engine Utility
ReaxFF molecular fragment analysis (molfra.out) handler.
This module provides a handler for parsing ReaxFF molfra.out and
molfra_ig.out files, which report molecule/fragment compositions
and their frequencies as a function of simulation iteration.
Typical use cases include:
- tracking molecular species formation and decay
- monitoring reaction pathways and fragment distributions
- computing molecule counts and system-level mass summaries
Usage context
- ReaxFF parsing: Read ReaxFF text outputs into normalized tabular structures.
- Workflow ingestion: Provide canonical handler interfaces used by adapters/workflows.
- Diagnostics/export: Preserve parsed metadata for reporting and downstream conversion.
Class: MolFraHandler
Bases: BaseHandler
Parser for ReaxFF molecular fragment output files
(molfra.out, molfra_ig.out).
This class parses molecular fragment frequency data and exposes both per-molecule and per-iteration summary information as structured tabular datasets.
Parsed Data
Molecule table
One row per (iteration, molecular species), returned by
dataframe(), with columns:
["iter", "molecular_formula", "freq", "molecular_mass"]
Totals table
One row per iteration, accessible via totals(), with columns:
["iter", "total_molecules", "total_atoms", "total_molecular_mass"]
Notes
- Molecular species are identified by their chemical formula strings.
- Frequency values represent counts per iteration.
- Totals are parsed from summary blocks following molecule listings.
- This handler is iteration-based rather than frame-based, but exposes a minimal frame-like API for consistency.