mal — Modern Atomic Linelists

A project to take over, modernize, and extend the production of atomic line lists in the lineage of Robert L. Kurucz's work — the energy levels and oscillator strengths (gf-values) that underpin stellar-atmosphere opacity and spectral synthesis.

Why

Kurucz's line lists are critical infrastructure for stellar spectroscopy, but the gf-generating engine (his private branch of R. D. Cowan's atomic-structure codes) is not publicly available. This project rebuilds the generating capability around the public Cowan code (the exact lineage Kurucz forked from ~1970) and modernizes the one stage Kurucz never updated in ~50 years: the semi-empirical least-squares fit (RCE).

Strategy (two tiers)

• Tier 1 — industrialize + UQ (the spine): apply validated modern fitting methods (regularization; orthogonal operators where they scale) plus per-line uncertainty quantification across all ions → a complete, better, uncertainty-bearing replacement for gfall. The hard/novel part is automating the per-ion "black magic" of the RCE fit.
• Tier 2 — Bayesian + spectral coupling (the research bet): a fully Bayesian fit that folds the solar/stellar spectrum into the likelihood, coupling lines through shared radial parameters → spectrum-informed gf with posteriors. Forward model: the in-house ATLAS12/SYNTHE port (~/kurucz/atlas12). Confirmed novel.

See docs/ and the planning notes for the full rationale and research basis.

Status

• Cowan kernel builds & runs on macOS/arm64 (gfortran 15). All four programs (RCN, RCN2, RCG, RCE) compile; RCG generates the CFP decks and runs to normal exit. See notes/build_notes.md.
• Worked example end to end (Sn^7+). RCN->RCN2->RCG drives the shipped IN36+IN2 deck to a real line list: converged radial wavefunctions (rwfn.dat) and ~1700 E1 transitions with energy levels + log gf (OUTG11). Reproduce with work/run_sn7plus.sh; figures in the explainer.
• Add observed levels and run RCE (the semi-empirical fit) on the example.
• Reproduce a known Kurucz Fe II gf (first deliverable).
• Prototype a modern regularized fit + per-line gf UQ on Fe II.

Layout

build/          editable Cowan source + build scripts
  src/          Fortran (from NIST/Kramida branch; see build_notes.md for edits)
  build.sh      compile all four programs with gfortran -> build/bin/
  make_cfp.sh   generate the binary CFP decks RCG needs (run once)
  cfp/          generated decks + run scratch (gitignored)
cowan_nist/     vendored NIST/Kramida package (zip & Windows .exe/.dll removed)
  extracted/for/    pristine Fortran source (RCN36K.F, RCN2K.F, rcg11k.f, RCE20K.F)
  extracted/code/   perl utilities, .bat reference scripts, ING11.CFP, SENIOR
  extracted/work/   example input decks (IN2, IN36, ...)
  extracted/*_DOC.txt, readme.cowan.htm   the Cowan documentation
tools/          pipeline/orchestration code (to come)
work/           per-ion working calculations (to come)
notes/, docs/   build notes, methodology, references

Building

bash build/build.sh       # -> build/bin/{rcn,rcn2,rcg,rce}
bash build/make_cfp.sh    # -> build/cfp/{FOR072,FOR073,FOR074}

Requires gfortran. Source provenance and the (physics-neutral) modifications vs. the pristine NIST source are documented in notes/build_notes.md.

Provenance & license

Cowan code: A. Kramida (NIST) branch, "A suite of atomic structure codes originally developed by R. D. Cowan adapted for Windows-based personal computers," doi:10.18434/T4/1502500, NIST open license. Original author R. D. Cowan (LANL); spec is Cowan, The Theory of Atomic Structure and Spectra (1981).