Outputs
A run writes a handful of files; only some of them are results. This page separates the raw outputs of a run from the curated final results that the documentation uses, and says how to regenerate the latter.
Raw outputs of a run
Written to the default results/ and figures/ folders by xi_protocol1b_bao_run.py:
results/
├── summary_protocol1b_combined.txt text summary (medians, χ², acceptance, τ, AIC/BIC, ε/σ)
├── model_comparison_combined.csv χ², k, AIC, BIC, ΔAIC
└── chains_<MODEL>_combined.npy flattened chains (LCDM, CPL, Xi_osc)
figures/
├── corner_<MODEL>_combined.png
├── w_of_z_combined.png
└── bao_residuals_combined.png
A quick smoke test replaces them with a 500-step result. Never cite a file from this level unless you know which run produced it: check Quick mode: in the summary.
Curated final results
The final run's outputs are copied by hand into dedicated sub-folders and these are the reference:
results/protocol1b_pantheon_desi/
├── final_parameter_estimates.csv median, +, − per parameter
├── final_model_comparison.csv χ², k, AIC, BIC, ΔAIC
├── final_model_comparison.md the same as a Markdown table, plus ε/σ
├── summary_protocol1b_combined.txt raw text summary of the final run
└── chains/chains_<MODEL>_combined.npy git-ignored
figures/protocol1b_pantheon_desi/ final corner plots, w(z), BAO residuals
figures/diagnostics/ marginals and running medians (Ξosc)
The two tables are written by scripts/export_final_tables.py (make tables) from values stored in xi_cosmo.results. Those values are typed into the module, not read from the chains, so they must be updated by hand after a new run.
Chain files
Chains are float64 arrays of shape (retained samples, parameters) and are excluded from Git because of their size:
| Model | File | Size in the final run |
|---|---|---|
| ΛCDM | chains_LCDM_combined.npy | 122.9 MB |
| CPL | chains_CPL_combined.npy | 245.8 MB |
| Ξosc | chains_Xi_osc_combined.npy | 368.6 MB |
Keep them locally or attach them to a release. The console log (*.log) is also git-ignored.
Regenerate derived products
python scripts/export_final_tables.py # result tables
python scripts/make_chain_diagnostics.py --model Xi_osc # marginals + running median
The second command expects the chain at results/protocol1b_pantheon_desi/chains/chains_Xi_osc_combined.npy (override with --chains-dir).