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+
+
+
+ 20240713152639-aafa3948a460bcd8ae24813a3f6512c18cf7f53b
+ 20240713152639
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 07
+ 2024
+
+
+ 9
+
+ 99
+
+
+
+ Reggae: A Parametric Tuner for PBJam, and a
+Visualization Tool for Red Giant Oscillation Spectra
+
+
+
+ J. M. Joel
+ Ong
+ https://orcid.org/0000-0001-7664-648X
+
+
+ Martin B.
+ Nielsen
+ https://orcid.org/0000-0001-9169-2599
+
+
+ Emily J.
+ Hatt
+ https://orcid.org/0000-0002-1389-1549
+
+
+ Guy R.
+ Davies
+ https://orcid.org/0000-0002-4290-7351
+
+
+
+ 07
+ 13
+ 2024
+
+
+ 6588
+
+
+ 10.21105/joss.06588
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.12730547
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/6588
+
+
+
+ 10.21105/joss.06588
+ https://joss.theoj.org/papers/10.21105/joss.06588
+
+
+ https://joss.theoj.org/papers/10.21105/joss.06588.pdf
+
+
+
+
+
+ Modal Analysis of Stellar Nonradial
+Oscillations by an Asymptotic Method
+ Shibahashi
+ Publications of the ASJ
+ 31
+ 1979
+ Shibahashi, H. (1979). Modal Analysis
+of Stellar Nonradial Oscillations by an Asymptotic Method. Publications
+of the ASJ, 31, 87–104.
+
+
+ PBjam: A Python Package for Automating
+Asteroseismology of Solar-like Oscillators
+ Nielsen
+ Astronomical Journal
+ 2
+ 161
+ 10.3847/1538-3881/abcd39
+ 2021
+ Nielsen, M. B., Davies, G. R., Ball,
+W. H., Lyttle, A. J., Li, T., Hall, O. J., Chaplin, W. J., Gaulme, P.,
+Carboneau, L., Ong, J. M. J., Garcı́a, R. A., Mosser, B., Roxburgh, I.
+W., Corsaro, E., Benomar, O., Moya, A., & Lund, M. N. (2021). PBjam:
+A Python Package for Automating Asteroseismology of Solar-like
+Oscillators. Astronomical Journal, 161(2), 62.
+https://doi.org/10.3847/1538-3881/abcd39
+
+
+ Simplifying asteroseismic analysis of
+solar-like oscillators. An application of principal component analysis
+for dimensionality reduction
+ Nielsen
+ Astronomy and Astrophysics
+ 676
+ 10.1051/0004-6361/202346086
+ 2023
+ Nielsen, M. B., Davies, G. R.,
+Chaplin, W. J., Ball, W. H., Ong, J. M. J., Hatt, E., Jones, B. P.,
+& Logue, M. (2023). Simplifying asteroseismic analysis of solar-like
+oscillators. An application of principal component analysis for
+dimensionality reduction. Astronomy and Astrophysics, 676, A117.
+https://doi.org/10.1051/0004-6361/202346086
+
+
+ joshspeagle/dynesty: v2.0.1
+ Koposov
+ 10.5281/zenodo.7215695
+ 2022
+ Koposov, S., Speagle, J., Barbary,
+K., Ashton, G., Bennett, E., Buchner, J., Scheffler, C., Cook, B.,
+Talbot, C., Guillochon, J., Cubillos, P., Asensio Ramos, A., Johnson,
+B., Lang, D., Ilya, Dartiailh, M., Nitz, A., McCluskey, A., Archibald,
+A., … Angus, R. (2022). joshspeagle/dynesty: v2.0.1 (Version v2.0.1).
+Zenodo; Zenodo.
+https://doi.org/10.5281/zenodo.7215695
+
+
+ Mode Mixing and Rotational Splittings. I.
+Near-degeneracy Effects Revisited
+ Ong
+ Astrophysical Journal
+ 1
+ 940
+ 10.3847/1538-4357/ac97e7
+ 2022
+ Ong, J. M. J., Bugnet, L., &
+Basu, S. (2022). Mode Mixing and Rotational Splittings. I.
+Near-degeneracy Effects Revisited. Astrophysical Journal, 940(1), 18.
+https://doi.org/10.3847/1538-4357/ac97e7
+
+
+ Mode mixing and rotational splittings. II.
+Reconciling different approaches to mode coupling
+ Ong
+ Astrophysical Journal
+ 1
+ 946
+ 10.3847/1538-4357/acbf2f
+ 2023
+ Ong, J. M. J., & Gehan, C.
+(2023). Mode mixing and rotational splittings. II. Reconciling different
+approaches to mode coupling. Astrophysical Journal, 946(1), 92.
+https://doi.org/10.3847/1538-4357/acbf2f
+
+
+ New insights on the interior of solar-like
+pulsators thanks to CoRoT: the case of HD 49385
+ Deheuvels
+ Astrophysics and Space
+Science
+ 1-2
+ 328
+ 10.1007/s10509-009-0216-2
+ 2010
+ Deheuvels, S., & Michel, E.
+(2010). New insights on the interior of solar-like pulsators thanks to
+CoRoT: the case of HD 49385. Astrophysics and Space Science, 328(1-2),
+259–263.
+https://doi.org/10.1007/s10509-009-0216-2
+
+
+ Semianalytic Expressions for the Isolation
+and Coupling of Mixed Modes
+ Ong
+ Astrophysical Journal
+ 2
+ 898
+ 10.3847/1538-4357/ab9ffb
+ 2020
+ Ong, J. M. J., & Basu, S. (2020).
+Semianalytic Expressions for the Isolation and Coupling of Mixed Modes.
+Astrophysical Journal, 898(2), 127.
+https://doi.org/10.3847/1538-4357/ab9ffb
+
+
+ Asteroseismic signatures of core magnetism
+and rotation in hundreds of low-luminosity red giants
+ Hatt
+ Hatt, E., Ong, J. M. J., Nielsen, M.
+B., Chaplin, W. J., Davies, G. R., Deheuvels, S., Ballot, J., Li, G.,
+& Bugnet, L. (submitted to MNRAS). Asteroseismic signatures of core
+magnetism and rotation in hundreds of low-luminosity red
+giants.
+
+
+ Fossil Signatures of Main-sequence Convective
+Core Overshoot Estimated through Asteroseismic Analyses
+ Lindsay
+ Astrophysical Journal
+ 2
+ 965
+ 10.3847/1538-4357/ad2ae5
+ 2024
+ Lindsay, C. J., Ong, J. M. J., &
+Basu, S. (2024). Fossil Signatures of Main-sequence Convective Core
+Overshoot Estimated through Asteroseismic Analyses. Astrophysical
+Journal, 965(2), 171.
+https://doi.org/10.3847/1538-4357/ad2ae5
+
+
+ PBJam 2.0: Mixed modes are everywhere, but
+we’ve got it sorted
+ Nielsen
+ Nielsen, M. B., Ong, J. M. J., Hatt,
+E. J., Davies, G. R., & Chaplin, W. J. (in prep.). PBJam 2.0: Mixed
+modes are everywhere, but we’ve got it sorted.
+
+
+ The PLATO Mission
+ Rauer
+ arXiv e-prints
+ 10.48550/arXiv.2406.05447
+ 2024
+ Rauer, H., Aerts, C., Cabrera, J.,
+Deleuil, M., Erikson, A., Gizon, L., Goupil, M., Heras, A.,
+Lorenzo-Alvarez, J., Marliani, F., Martin-Garcia, C., Mas-Hesse, J. M.,
+O’Rourke, L., Osborn, H., Pagano, I., Piotto, G., Pollacco, D.,
+Ragazzoni, R., Ramsay, G., … Zwintz, K. (2024). The PLATO Mission. arXiv
+e-Prints, arXiv:2406.05447.
+https://doi.org/10.48550/arXiv.2406.05447
+
+
+ Core rotation braking on the red giant branch
+for various mass ranges
+ Gehan
+ Astronomy & Astrophysics
+ 616
+ 10.1051/0004-6361/201832822
+ 2018
+ Gehan, C., Mosser, B., Michel, E.,
+Samadi, R., & Kallinger, T. (2018). Core rotation braking on the red
+giant branch for various mass ranges. Astronomy & Astrophysics, 616,
+A24. https://doi.org/10.1051/0004-6361/201832822
+
+
+ Asteroseismology
+ Aerts
+ 10.1007/978-1-4020-5803-5
+ 2010
+ Aerts, C., Christensen-Dalsgaard, J.,
+& Kurtz, D. W. (2010). Asteroseismology.
+https://doi.org/10.1007/978-1-4020-5803-5
+
+
+ Probing the core structure and evolution of
+red giants using gravity-dominated mixed modes observed with
+Kepler
+ Mosser
+ Astronomy & Astrophysics
+ 540
+ 10.1051/0004-6361/201118519
+ 2012
+ Mosser, B., Goupil, M. J., Belkacem,
+K., Michel, E., Stello, D., Marques, J. P., Elsworth, Y., Barban, C.,
+Beck, P. G., Bedding, T. R., De Ridder, J., Garcı́a, R. A., Hekker, S.,
+Kallinger, T., Samadi, R., Stumpe, M. C., Barclay, T., & Burke, C.
+J. (2012). Probing the core structure and evolution of red giants using
+gravity-dominated mixed modes observed with Kepler. Astronomy &
+Astrophysics, 540, A143.
+https://doi.org/10.1051/0004-6361/201118519
+
+
+ Asteroseismology of solar-type
+stars
+ Garcı́a
+ Living Reviews in Solar
+Physics
+ 1
+ 16
+ 10.1007/s41116-019-0020-1
+ 2019
+ Garcı́a, R. A., & Ballot, J.
+(2019). Asteroseismology of solar-type stars. Living Reviews in Solar
+Physics, 16(1), 4.
+https://doi.org/10.1007/s41116-019-0020-1
+
+
+
+
+
+
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+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+6588
+10.21105/joss.06588
+
+Reggae: A Parametric Tuner for PBJam, and a Visualization
+Tool for Red Giant Oscillation Spectra
+
+
+
+https://orcid.org/0000-0001-7664-648X
+
+Ong
+J. M. Joel
+
+
+
+*
+
+
+https://orcid.org/0000-0001-9169-2599
+
+Nielsen
+Martin B.
+
+
+
+
+https://orcid.org/0000-0002-1389-1549
+
+Hatt
+Emily J.
+
+
+
+
+https://orcid.org/0000-0002-4290-7351
+
+Davies
+Guy R.
+
+
+
+
+
+NASA Hubble Fellow
+
+
+
+
+Institute for Astronomy, University of Hawai`i, 2680
+Woodlawn Drive, Honolulu, HI 96822, USA
+
+
+
+
+School of Physics and Astronomy, University of Birmingham,
+Birmingham B15 2TT, UK
+
+
+
+
+* E-mail:
+
+9
+99
+6588
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+
+
+
+ Summary
+
PBjam
+ (Nielsen
+ et al., 2021) is a software instrument for fitting normal modes
+ (“peakbagging”) in power spectra from space-based photometry of
+ solar-like oscillators (e.g.
+ Garcı́a
+ & Ballot, 2019). Its upcoming second release
+ (Nielsen
+ et al., in prep.) supplements the simple power-spectrum model
+ used in the first version — which included only radial and quadrupole
+ (
+
+ ℓ=0,2)
+ modes — to additionally constrain other features (e.g.
+ Nielsen
+ et al., 2023). Dipole (
+
+ ℓ=1)
+ modes, which had been specifically excluded in the initial version of
+ the tool owing to their complexity, are now specifically included.
+ Since the primary samples of the PLATO mission consist mainly of
+ main-sequence and subgiant stars
+ (Rauer
+ et al., 2024), PBjam implements a single
+ parameterisation of dipole mixed-mode frequencies — as described by
+ their overtone spacings, boundary conditions, and other stellar
+ properties — that reduces to pure p-modes in the former, and is
+ suitable to the latter, outside the red-giant “asymptotic” regime. In
+ keeping with the overall philosophy of PBjam’s
+ design for
+
+ ℓ=0,2,
+ PBjam 2 will specify prior distributions on
+ these parameters empirically, through predetermined values found for
+ existing samples of solar-like oscillators. While the red-giant
+ asymptotic regime has been extensively characterised observationally,
+ the nonasymptotic construction for subgiants here has not, requiring
+ us to construct this prior sample ourselves. To assist in this task,
+ we built a tool — Reggae— to manually fine-tune
+ and fit the dipole-mode model, and check the quality of both our
+ initial guesses and fitted solutions.
+
+
+ Statement of Need
+
Before mode frequencies may be extracted from the power spectrum,
+ specific peaks in it must be identified as dipole modes. An important
+ part of this identification is visual assessment of how well the
+ predicted mode frequencies correspond to actually observed peaks.
+ Reggae produces these visualisations from
+ user-supplied trial values. This is useful for checking solutions of,
+ e.g., the period spacing
+
+ ΔΠ1
+ — inaccurate values result in slanted ridges on period-echelle
+ diagrams (e.g.
+ Mosser
+ et al., 2012), much like with inaccurate
+
+
+ Δν
+ in traditional frequency-échelle diagrams (e.g.
+ Aerts
+ et al., 2010). Similarly, rotational splittings become easily
+ identifiable (e.g.
+ Gehan
+ et al., 2018), as are any perturbations due to magnetic fields
+ (Hatt
+ et al., submitted to MNRAS).
+
Since these global parameters must be supplied for dipole-mode
+ identification, we have constrained them for a preliminary sample of
+ subgiants
+ (Nielsen
+ et al., in prep.), and also for a large sample of
+ low-luminosity red giants
+ (Hatt
+ et al., submitted to MNRAS). We found
+ Reggae very helpful both for these tuning and
+ visualisation tasks, and also as a didactic aid to understanding the
+ dipole mixed-mode parameters. Moreover, no other tools currently exist
+ for performing these tasks in the nonasymptotic parameterisation that
+ PBjam will use. As such, we release
+ Reggae publicly in advance of the second
+ PBjam version, as we believe the community will
+ benefit from access to such a visualisation tool. This will also
+ assist future users of PBjam in devising ad-hoc
+ prior constraints on the mixed-mode parameters, should they wish to
+ perform mode identification for anomalous stars.
+
+
+ Modeling the Oscillation Spectrum
+
Reggae uses individually-fitted modes from
+ PBjam to construct a model of the
+
+
+ ℓ=2,0
+ modes, which is then divided out of the signal-to-noise spectrum; this
+ allows the optimization and visualization of the
+
+
+ ℓ=1
+ mode identification to be performed independently, and far more
+ simply. The dipole p-mode frequencies are parameterised identically to
+ PBjam, with a small frequency offset
+
+
+ d01×Δν
+ to account for imperfections in this idealised asymptotic
+ description.
+
To produce mixed modes, we must specify both pure g-mode
+ frequencies — which we describe using a period spacing
+
+
+ ΔΠ1,
+ a g-mode phase offset
+
+ ϵg,
+ and an analogous curvature parameter
+
+ αg
+ to that used in the p-mode parameterisation — as well as coupling
+ between the p- and g-modes. For this PBJam will
+ adopt the matrix-eigenvalue parameterisation of Deheuvels & Michel
+ (2010),
+ supplemented with a secondary inner-product matrix as described in Ong
+ & Basu
+ (2020)
+ to account for the nonorthogonality of the notional pure p- and g-mode
+ eigenfunctions. This parameterisation is used instead of the classical
+ asymptotic description (e.g.
+ Shibahashi,
+ 1979) in light of its intended application to subgiants
+ specifically. Numerically, these matrices are scaled from values
+ supplied by a reference MESA model (from the grid of
+ Lindsay
+ et al., 2024) using parameters
+
+ pL
+ and
+
+ pD.
+ The correspondence between these matrices and the classical coupling
+ strength
+
+ q
+ is described in Ong & Gehan
+ (2023).
+ Rotation in the p- and g-mode cavities are separately parameterised
+ with
+
+ logΩp
+ and
+
+ logΩg,
+ and a shared inclination parameter
+
+ i,
+ with rotating mixed modes computed fully accounting for
+ near-degeneracy effects (e.g.
+ Ong
+ et al., 2022).
+
Reggae fine-tunes these parameters by
+ numerical optimization, which requires a model of the power spectral
+ density (PSD) that can be compared to the observed residual spectrum.
+ This model is a sum of Lorentzian profiles, one for each of the
+ predicted dipole modes. Their linewidths are artificially broadened to
+ a fraction of
+
+ Δν,
+ smoothing over local minima in the likelihood function. Their heights
+ follow the same Gaussian envelope as PBjam’s
+ model for the
+
+ ℓ=2,0
+ pairs, with additional modulation by mixing fractions
+
+
+ ζ
+ from mode coupling.
+
+
Screenshot of the GUI showing visualisation panel and
+ manual
+ inputs.
+
+
+
These visualization and tuning features are operated through a
+ graphical user interface (GUI), illustrated in
+ [fig:screenshot].
+ The visualisation tools are provided on the left of the interface.
+ Manual guesses and parameter bounds provide initial guesses for
+ simplex or genetic-algorithm optimization. Alternatively all
+ parameters can be sampled at once using the Dynesty nested sampling
+ package
+ (Koposov
+ et al., 2022).
+
+
+ Acknowledgments
+
JMJO acknowledges support from NASA through the NASA Hubble
+ Fellowship grants HST-HF2-51517.001-A, awarded by STScI, which is
+ operated by the Association of Universities for Research in Astronomy,
+ Incorporated, under NASA contract NAS5-26555. MBN acknowledges support
+ from the UK Space Agency.