diff --git a/joss.06032/10.21105.joss.06032.crossref.xml b/joss.06032/10.21105.joss.06032.crossref.xml new file mode 100644 index 0000000000..b274bad073 --- /dev/null +++ b/joss.06032/10.21105.joss.06032.crossref.xml @@ -0,0 +1,684 @@ + + + + 20240615124742-adf19d2a3d58af8a9eaa33568f8ac32bb642a285 + 20240615124742 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 06 + 2024 + + + 9 + + 98 + + + + Mayawaves: Python Library for Interacting with the +Einstein Toolkit and the MAYA Catalog + + + + Deborah + Ferguson + https://orcid.org/0000-0002-4406-591X + + + Surendra + Anne + + + Miguel + Gracia-Linares + https://orcid.org/0000-0002-5033-2973 + + + Hector + Iglesias + https://orcid.org/0009-0008-1089-9239 + + + Aasim + Jan + https://orcid.org/0000-0003-2050-7231 + + + Erick + Martinez + + + Lu + Lu + + + Filippo + Meoni + + + Ryan + Nowicki + + + Max L. + Trostel + https://orcid.org/0000-0001-9743-0303 + + + Bing-Jyun + Tsao + https://orcid.org/0000-0003-4614-0378 + + + Finny + Valorz + + + + 06 + 15 + 2024 + + + 6032 + + + 10.21105/joss.06032 + + + 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.11551465 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/6032 + + + + 10.21105/joss.06032 + https://joss.theoj.org/papers/10.21105/joss.06032 + + + https://joss.theoj.org/papers/10.21105/joss.06032.pdf + + + + + + Numerical Relativity Injection +Infrastructure + Schmidt + 10.48550/arXiv.1703.01076 + 2017 + Schmidt, P., Harry, I. W., & +Pfeiffer, H. P. (2017). Numerical Relativity Injection Infrastructure. +https://doi.org/10.48550/arXiv.1703.01076 + + + Advanced LIGO + Aasi + Classical and Quantum Gravity + 7 + 32 + 10.1088/0264-9381/32/7/074001 + 1361-6382 + 2015 + Aasi, J., Abbott, B. P., Abbott, R., +Abbott, T., Abernathy, M. R., Ackley, K., Adams, C., Adams, T., Addesso, +P., Adhikari, R. X., Adya, V., Affeldt, C., Aggarwal, N., Aguiar, O. D., +Ain, A., Ajith, P., Alemic, A., Allen, B., Amariutei, D., … Zweizig, J. +(2015). Advanced LIGO. 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(2023). +Second MAYA catalog of binary black hole numerical relativity waveforms. +https://doi.org/10.48550/arXiv.2309.00262 + + + Accuracy limitations of existing numerical +relativity waveforms on the data analysis of current and future +ground-based detectors + Jan + 10.48550/arXiv.2312.10241 + 2023 + Jan, A., Ferguson, D., Lange, J., +Shoemaker, D., & Zimmerman, A. (2023). Accuracy limitations of +existing numerical relativity waveforms on the data analysis of current +and future ground-based detectors. +https://doi.org/10.48550/arXiv.2312.10241 + + + Black hole - neutron star binary mergers: The +impact of stellar compactness + Tsao + 10.48550/arXiv.2404.09924 + 2024 + Tsao, B.-J., Khamesra, B., +Gracia-Linares, M., & Laguna, P. (2024). Black hole - neutron star +binary mergers: The impact of stellar compactness. +https://doi.org/10.48550/arXiv.2404.09924 + + + + + + diff --git a/joss.06032/10.21105.joss.06032.pdf b/joss.06032/10.21105.joss.06032.pdf new file mode 100644 index 0000000000..d371b6760e Binary files /dev/null and b/joss.06032/10.21105.joss.06032.pdf differ diff --git a/joss.06032/paper.jats/10.21105.joss.06032.jats b/joss.06032/paper.jats/10.21105.joss.06032.jats new file mode 100644 index 0000000000..f04c7131f2 --- /dev/null +++ b/joss.06032/paper.jats/10.21105.joss.06032.jats @@ -0,0 +1,10702 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6032 +10.21105/joss.06032 + +Mayawaves: Python Library for Interacting with the +Einstein Toolkit and the MAYA Catalog + + + +https://orcid.org/0000-0002-4406-591X + +Ferguson +Deborah + + + +* + + + +Anne +Surendra + + + + +https://orcid.org/0000-0002-5033-2973 + +Gracia-Linares +Miguel + + + + +https://orcid.org/0009-0008-1089-9239 + +Iglesias +Hector + + + + +https://orcid.org/0000-0003-2050-7231 + +Jan +Aasim + + + + + +Martinez +Erick + + + + + +Lu +Lu + + + + + +Meoni +Filippo + + + + + +Nowicki +Ryan + + + + +https://orcid.org/0000-0001-9743-0303 + +Trostel +Max L. + + + + +https://orcid.org/0000-0003-4614-0378 + +Tsao +Bing-Jyun + + + + + +Valorz +Finny + + + + + +University of Texas at Austin, Austin TX, USA + + + + +University of Illinois Urbana-Champaign, Urbana IL, +USA + + + + +* E-mail: + + +15 +6 +2024 + +9 +98 +6032 + +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) + + + +Python +Numerical Relativity +Gravitational Waves +Black Holes + + + + + + Summary +

Einstein’s Theory of General Relativity (GR) dictates how matter + responds to the curvature of space-time and how space-time curves due + to matter. From GR came the prediction that orbiting massive objects + would create ripples in space-time called gravitational waves (GW). In + 2015, the Laser Interferometer Gravitational-Wave Observatory (LIGO) + (Aasi + et al., 2015) detected the first such GW signal from merging + binary black holes (BBHs) + (B. + P. Abbott, Abbott, Abbott, Abernathy, Acernese, Ackley, Adams, Adams, + Addesso, Adhikari, Adya, Affeldt, Agathos, Agatsuma, Aggarwal, Aguiar, + Aiello, Ain, Ajith, Allen, Allocca, Altin, Anderson, Anderson, Arai, + Arain, et al., 2016), and in the years since, the LIGO, Virgo, + and KAGRA Collaborations (LVK) have accumulated 90 detections of + merging compact objects + (B. + P. Abbott et al., 2019; + R. + Abbott et al., 2021, + 2023; + Acernese + et al., 2014; + Akutsu + et al., 2020). Extracting these signals from noise and using + them to infer the parameters of coalescing black holes (BHs) relies + upon having vast template banks that accurately predict the expected + GWs + (B. + P. Abbott, Abbott, Abbott, Abernathy, Acernese, Ackley, Adams, Adams, + Addesso, Adhikari, Adya, Affeldt, Agathos, Agatsuma, Aggarwal, Aguiar, + Aiello, Ain, Ajith, Allen, Allocca, Altin, Anderson, Anderson, Arai, + Araya, et al., 2016; + B. + P. Abbott et al., 2017, + 2020; + Blackman + et al., 2017; + Bohé + et al., 2017; + Hannam + et al., 2014; + Husa + et al., 2016; + Khan + et al., 2016; + Lange + et al., 2017; + Schmidt + et al., 2017; + Shibata + et al., 2017).

+

While analytic solutions exist for the simplest cases within GR, + e.g. single BHs, merging BBHs have no analytic solution. Approximate + methods can be used when the BHs are far apart or have highly unequal + masses, but the coalescence of BHs of comparable mass must be solved + computationally. Numerical relativity (NR) simulations accomplish this + by evolving a BBH space-time on supercomputers, enabling us to study + the dynamics of BBH systems as well as predict the GWs they emit. The + Einstein Toolkit (ETK) is a set of tools created to perform these NR + simulations + (Löffler + et al., 2012), and MAYA is a branch of + ETK used by the MAYA collaboration + (Ferguson + et al., 2023; + Healy + et al., 2009; + Herrmann + et al., 2007; + Jani + et al., 2016; + Pekowsky + et al., 2013; + Vaishnav + et al., 2007). The Einstein Toolkit is a finite-differencing + code, evolved using the BSSN formulation + (Baumgarte + & Shapiro, 1998; + Shibata + & Nakamura, 1995). It is built upon the Cactus + infrastructure + (Goodale + et al., 2003) with Carpet mesh refinement + (Schnetter + et al., 2004).

+

These tools allow us to study the coalescence of compact objects, + their evolution, and the gravitational radiation they emit. The + Mayawaves library introduced in this paper is + an analysis pipeline used to process and analyze such NR simulations, + specifically for BBHs.

+ + + Statement of need +

NR simulations are crucial for studying BHs and have been + instrumental in the detection of GWs by the LVK. However, these + simulations produce vast amounts of data that must be processed in + order to perform studies, create models, and use them with GW + detection pipelines. Additionally, given the complexity of these + simulations, they are typically performed for many days or weeks + across many processors, leading to data which is split into several + output directories and files. Sifting through all this data can be + overwhelming for newcomers to the field and is cumbersome for even the + most experienced numerical relativists. While it can be important to + develop an understanding of these files and their complexities, in + many situations, a simpler, more streamlined workflow is + beneficial.

+

Mayawaves is an open-source Python library + for processing, studying, and exporting NR simulations performed using + ETK and MAYA. While other tools exist to + analyze ETK simulations including, but not limited to, Kuibit + (Bozzola, + 2021), POWER + (Johnson + et al., 2017), PyCactus + (Kastaun, + 2021), and SimulationTools + (Hinder + & Wardell, n.d.), Mayawaves is + unique in the way it not only streamlines simulation analysis but also + the production of NR catalogs. Mayawaves builds + upon the existing set of tools, creating a new Python library designed + for convenience and intuition, while still being versatile and + powerful enough to perform more complex analyses. It interacts + effortlessly with the MAYA waveform catalog and + also easily exports ETK simulations to the LVK catalog of NR + waveforms. The architecture of Mayawaves is + easily extensible, designed to naturally grow to encompass more types + of simulation output. One of the ways in which + Mayawaves has uniquely improved the NR analysis + infrastructure is that it stitches together raw NR simulations and + stores them in HDF5 files, a format that handles numerical data more + efficiently than ASCII. This significantly reduces the disc space + taken by simulations while still retaining the precision of the raw + data. By preprocessing the simulations into this format, the library + also reduces computational time for future analysis, as the data only + has to be stitched once. It also keeps all the data organized in one + place, making it easier to share and distribute simulations.

+

When using the library to interact with a simulation, the user does + not need to be familiar with all the types of output files generated + by the simulation, but rather, can think in terms of physical concepts + such as coalescences and compact + objects. This dramatically reduces the barrier to entry for + the field of NR. Some of the key functionalities of this library are + as follows:

+ + +

read and stitch raw NR data

+ + +

store NR data in a more efficient format

+ + +

track properties of the BHs (trajectories, spins, masses, + horizon information, etc.)

+ + +

compute information about the binary orbit (eccentricity, + separation, orbital frequency, kick, etc.)

+ + +

compute quantities pertaining to the gravitational radiation + ( + + Ψ4, + strain, extrapolated strain, energy radiated, etc.)

+ + +

export NR data to the format required for LIGO analyses

+ + +

analyze the MAYA waveform catalog

+ + +

The Coalescence class is the fundamental + basis for Mayawaves. It represents the entirety + of the BBH coalescence and serves as the interface between the user + and the simulation data. The main data format used with + mayawaves is an HDF5 file constructed from the + raw simulation data. With this HDF5 file in hand, the user need only + create a Coalescence object and then proceed + with analyzing the data.

+

Each Coalescence object contains + CompactObjects associated with each of the + merging bodies as well as any remnant object. Through these + CompactObjects, the user can track the objects’ + positions, spins, masses, etc. All radiative information is stored + within the RadiationBundle class. Each + Coalescence object contains a + RadiationBundle and uses it to compute GW + strain, energy radiated, etc.

+

A number of utility modules are included to create effortless + workflows that can move from raw simulations to community standard + formats. A typical workflow would be to use the + PostProcessingUtils functions to create the + HDF5 file from the raw simulation data, use the + Coalescence class to read that HDF5 file and + analyze the simulation, and finally export the + Coalescence object to another format such as + that required by the LVK catalog + (Schmidt + et al., 2017).

+

Mayawaves is also the primary way to + interact with the MAYA Public Catalog of NR waveforms + (Ferguson + et al., 2023) hosted at https://cgp.ph.utexas.edu/waveform. The + simulations are stored in the Mayawaves HDF5 + file format, and can be read using the + Coalescence class. + Mayawaves has a + CatalogUtils module for interacting with the + MAYA waveform catalog. This module includes functions for accessing + and plotting the metadata for the entire catalog as well as functions + to download simulations from the catalog.

+

Several papers have already been released using the + Mayawaves library for their analysis including + the Second MAYA Catalog of NR Waveforms + (Ferguson + et al., 2023), a study of the impact of NR errors on GW + parameter estimation + (Jan + et al., 2023), and a study of the impact of neutron star + compactness when a neutron star merges with a BH + (Tsao + et al., 2024).

+

Mayawaves is open source and is designed to + be easily extensible, and we look forward to additional contributions + from the ETK community.

+ + + Acknowledgements +

The authors thank Deirdre Shoemaker, Pablo Laguna, and Helvi Witek + for their support throughout the duration of this code development. + The work presented in this paper was possible due to grants NASA + 80NSSC21K0900, NSF 2207780 and NSF 2114582. This work was done by + members of the Weinberg Institute and has an identifier of + UTW1-33-2023.

+ + + + + + + + + SchmidtPatricia + HarryIan W. + PfeifferHarald P. + + Numerical Relativity Injection Infrastructure + 201703 + https://arxiv.org/abs/1703.01076 + 10.48550/arXiv.1703.01076 + + + + + + AasiJ + AbbottB P + AbbottR + AbbottT + AbernathyM R + AckleyK + AdamsC + AdamsT + AddessoP + AdhikariR X + AdyaV + AffeldtC + AggarwalN + AguiarO D + AinA + AjithP + AlemicA + AllenB + AmariuteiD + AndersonS B + AndersonW G + AraiK + ArayaM C + ArceneauxC + AreedaJ S + AshtonG + AstS + AstonS M + AufmuthP + AulbertC + AylottB E + BabakS + BakerP T + BallmerS W + BarayogaJ C + BarbetM + BarclayS + BarishB C + BarkerD + BarrB + BarsottiL + BartlettJ + BartonM A + BartosI + BassiriR + BatchJ C + BauneC + BehnkeB + BellA S + BellC + BenacquistaM + BergmanJ + BergmannG + BerryC P L + BetzwieserJ + BhagwatS + BhandareR + BilenkoI A + BillingsleyG + BirchJ + BiscansS + BiwerC + BlackburnJ K + BlackburnL + BlairC D + BlairD + BockO + BodiyaT P + BojtosP + BondC + BorkR + BornM + BoseSukanta + 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