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#2538: Inclusion of kuibit
by Gabriele Bozzola 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Gabriele Bozzola): You can use this citation key: ```tex @article{Bozzola:2021hus, requested-for = {kuibit}, author = "Bozzola, Gabriele", title = "{kuibit: Analyzing Einstein Toolkit simulations with Python}", eprint = "2104.06376", archivePrefix = "arXiv", primaryClass = "gr-qc", doi = "10.21105/joss.03099", journal = "J. Open Source Softw.", volume = "6", number = "60", pages = "3099", year = "2021" } ``` `kuibit` relies upon `numpy`, `scipy`, and `h5py` ``` @article{Harris:2020xlr, suggested-for = {kuibit}, author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. van der Walt and Ralf Gommers and Pauli Virtanen and David Cournapeau and Eric Wieser and Julian Taylor and Sebastian Berg and Nathaniel J. Smith and Robert Kern and Matti Picus and Stephan Hoyer and Marten H. van Kerkwijk and Matthew Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and Warren Weckesser and Hameer Abbasi and Christoph Gohlke and Travis E. Oliphant}, title = "{Array programming with NumPy}", eprint = "2006.10256", archivePrefix = "arXiv", primaryClass = "cs.MS", doi = "10.1038/s41586-020-2649-2", journal = "Nature", volume = "585", number = "7825", pages = "357--362", year = "2020" } @article{Virtanen:2019joe, suggested-for = {kuibit}, author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and {van Mulbregt}, Paul and {SciPy 1.0 Contributors}}, title = "{SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python}", eprint = "1907.10121", archivePrefix = "arXiv", primaryClass = "cs.MS", doi = "10.1038/s41592-019-0686-2", journal = "Nature Meth.", volume = "17", pages = "261", year = "2020" } ``` Unfortunately, h5py does not have a recommended citation. ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2538: Inclusion of kuibit
by Roland Haas 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): You can request up to one \(not a hard rule but strongly encouraged\) citations that people should use when using RePrimAnd, as well as multiple \(any number, but you may provide indication under which circumstances which ones are suggested\) suggested citations. Those will be listed on: [https://www.einsteintoolkit.org/citation.html](https://www.einsteintoolkit.… To provide the citation please provide bibtex entries to be included in einsteintoolkit.bib \(in the manifest repo\) that should look something like this: ```perl @Misc{Kranc:web, suggested-for ="McLachlan/ML_BSSN", key = {Kranc}, title = {{Kranc}: {Kranc} Assembles Numerical Code}, url = {http://kranccode.org/}, } @Misc{EinsteinToolkit:2021_05, requested-for ={EinsteinToolkit}, author = {Zachariah Etienne and Steven R. Brandt and Peter Diener and William E. Gabella and Miguel Gracia-Linares and Roland Haas and Atul Kedia and Miguel Alcubierre and Daniela Alic and Gabrielle Allen and Marcus Ansorg and Maria Babiuc-Hamilton and Luca Baiotti and Werner Benger and Eloisa Bentivegna and Sebastiano Bernuzzi and Tanja Bode and Gabriele Bozzola and Brockton Brendal and Bernd Bruegmann and Manuela Campanelli and Federico Cipolletta and Giovanni Corvino and Samuel Cupp and Roberto De Pietri and Harry Dimmelmeier and Rion Dooley and Nils Dorband and Matthew Elley and Yaakoub El Khamra and Joshua Faber and Toni Font and Joachim Frieben and Bruno Giacomazzo and Tom Goodale and Carsten Gundlach and Ian Hawke and Scott Hawley and Ian Hinder and E. A. Huerta and Sascha Husa and Sai Iyer and Daniel Johnson and Thorsten Kellermann and Andrew Knapp and Michael Koppitz and Pablo Laguna and Gerd Lanferman and Frank L{\"o}ffler and Joan Masso and Lars Menger and Andre Merzky and Jonah Maxwell Miller and Mark Miller and Philipp Moesta and Pedro Montero and Bruno Mundim and Andrea Nerozzi and Scott C. Noble and Christian Ott and Ravi Paruchuri and Denis Pollney and David Radice and Thomas Radke and Christian Reisswig and Luciano Rezzolla and David Rideout and Matei Ripeanu and Lorenzo Sala and Jascha A Schewtschenko and Erik Schnetter and Bernard Schutz and Ed Seidel and Eric Seidel and John Shalf and Ken Sible and Ulrich Sperhake and Nikolaos Stergioulas and Wai-Mo Suen and Bela Szilagyi and Ryoji Takahashi and Michael Thomas and Jonathan Thornburg and Malcolm Tobias and Aaryn Tonita and Paul Walker and Mew-Bing Wan and Barry Wardell and Leonardo Werneck and Helvi Witek and Miguel Zilh{\~a}o and Burkhard Zink and Yosef Zlochower}, title = {The Einstein Toolkit}, month = may, year = 2021, note = {To find out more, visit http://einsteintoolkit.org}, publisher = {Zenodo}, version = {The "Lorentz" release, ET\_2021\_05}, doi = {10.5281/zenodo.4884780}, url = {https://doi.org/10.5281/zenodo.4884780} } @article{Noble:2005gf, requested-for = {WVUThorns/IllinoisGRMHD}, author = "Noble, Scott C. and Gammie, Charles F. and McKinney, Jonathan C. and Del Zanna, Luca", title = "{Primitive variable solvers for conservative general relativistic magnetohydrodynamics}", journal = "Astrophys. J.", volume = "641", pages = "626-637", doi = "10.1086/500349", year = "2006", eprint = "arXiv:astro-ph/0512420", SLACcitation = "%%CITATION = ASTRO-PH/0512420;%%", } ``` the preferred entry format is SPIRES-like, in that SPIRES keys are strongly recommended but we list all authors. The top of [einsteintoolkit.th](http://einsteintoolkit.th) explains the convention: [https://bitbucket.org/einsteintoolkit/manifest/raw/master/einsteintoolkit.b… -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2538: Inclusion of kuibit
by Roland Haas 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Changes (by Roland Haas): assignee: Yosef Zlochower (was ) responsible: [] (was ) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2551: include RePriMand in the ET
by Roland Haas 19 Nov '21

19 Nov '21

#2551: include RePriMand in the ET Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): You also can request up to one \(not a hard rule but strongly encouraged\) citations that people should use when using RePrimAnd, as well as multiple \(any number, but you may provide indication under which circumstances which ones are suggested\) suggested citations. Those will be listed on: [https://www.einsteintoolkit.org/citation.html](https://www.einsteintoolkit.… To provide the citation please provide bibtex entries to be included in einsteintoolkit.bib \(in the manifest repo\) that should look something like this: ```perl @Misc{Kranc:web, suggested-for ="McLachlan/ML_BSSN", key = {Kranc}, title = {{Kranc}: {Kranc} Assembles Numerical Code}, url = {http://kranccode.org/}, } @article{Noble:2005gf, requested-for = {WVUThorns/IllinoisGRMHD}, author = "Noble, Scott C. and Gammie, Charles F. and McKinney, Jonathan C. and Del Zanna, Luca", title = "{Primitive variable solvers for conservative general relativistic magnetohydrodynamics}", journal = "Astrophys. J.", volume = "641", pages = "626-637", doi = "10.1086/500349", year = "2006", eprint = "arXiv:astro-ph/0512420", SLACcitation = "%%CITATION = ASTRO-PH/0512420;%%", } ``` the preferred entry format is SPIRES-like, in that SPIRES keys are strongly recommended but we list all authors. The top of [einsteintoolkit.th](http://einsteintoolkit.th) explains the convention: [https://bitbucket.org/einsteintoolkit/manifest/raw/master/einsteintoolkit.b… -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2551/include-reprimand…

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#2551: include RePriMand in the ET
by Wolfgang Kastaun 19 Nov '21

19 Nov '21

#2551: include RePriMand in the ET Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Wolfgang Kastaun): I have just pushed recent changed to the public repository. Those include: * minor changes triggered by code review * updated natural constants and option to use own * tex documentation, now pointing to new online location on github pages * minor changes to Roland’s thorn building \(no library version in archive name, .tar instead .tar.xz\) * Placed copy of EOS file creation Python module in src/utils * fixing build problems of standalone library \(not relevant for ET thorn\) The online documentation is now on [https://wokast.github.io/RePrimAnd/index.html](https://wokast.github.io/ReP… I have checked that ET builds from scratch with a fresh clone of the public repo on my system. Once we decide to include a given commit \(hopefully this one\) I will tag it as a release so it gets archived on Zenodo as well, with corresponding DOI. The DOI could then be mentioned in the ET release notes. ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2551/include-reprimand…

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#2175: Test "Single, stable neutron star" example
by Gabriele Bozzola 18 Nov '21

18 Nov '21

#2175: Test "Single, stable neutron star" example Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: task Priority: major Component: EinsteinToolkit website Comment (by Gabriele Bozzola): The kuibit code to reproduce the plot should be something like \(not tested\): ```python from kuibit.simdir import SimDir import matplotlib.pyplot as plt PATH = .... rho = SimDir(PATH).timeseries.maximum['rho'] plt.plot(rho / rho(0)) plt.savefig("density.pdf") ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2175/test-single-stabl…

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#2043: new thorn for initial data (Hydro_RNS)
by Roland Haas 18 Nov '21

18 Nov '21

#2043: new thorn for initial data (Hydro_RNS) Reporter: Roberto De Pietri Status: resolved Milestone: Version: development version Type: enhancement Priority: minor Component: Other Changes (by Roland Haas): status: resolved (was new) The LSU and Parma groups used for publications and contributed to the development of the thorn the generate initial data for Rotating-Neutron-Star RNS based on Nik Stergioulas code (http://www.gravity.phys.uwm.edu/rns/) which constructs models of rapidly rotating, relativistic, compact stars using tabulated equations of state which are supplied by the user or polytqopic EOS. The code was widely used in conjunction with the Whisky code and more recently with GRHydro. The relevant code can be found here: [https://bitbucket.org/GravityPR/prthorns/src] I'd like another developer to have a look and give input. Once/If this is deemed ok to be included on technical grounds, we will add the necessary documentation. Test suites and example are already present. **Keyword:** parma -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2043/new-thorn-for-ini…

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#2043: new thorn for initial data (Hydro_RNS)
by Roland Haas 18 Nov '21

18 Nov '21

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#2043: new thorn for initial data (Hydro_RNS)
by Roland Haas 18 Nov '21

18 Nov '21

#2043: new thorn for initial data (Hydro_RNS) Reporter: Roberto De Pietri Status: new Milestone: Version: development version Type: enhancement Priority: minor Component: Other Comment (by Roland Haas): Compared to what is in the ET as of git hash [dfd2be34](https://bitbucket.org/einsteintoolkit/einsteininitialdata/commits… "ReadInterpolate: documnetation fixes" of [einsteininitialdata](https://bitbucket.org/einsteintoolkit/einsteininitiald… the differences in Hydro\_RNS \(git hash [cef42e5](https://bitbucket.org/GravityPR/prthorns/src/master/Hydro_RNSID//c… "Capitalisation Error" of \[\]\([https://bitbucket.org/GravityPR/prthorns/src/master/Hydro\_RNSID/](https://bitbucket.org/GravityPR/prthorns/src/master/Hydro_RNSID/)) \) seem to be that the latter supports a perturbation. Using instead git hash [f788d35](https://bitbucket.org/GravityPR/prthorns/src/master/Hydro_RNSID//c… "Allign to ET version" of \[\]\([https://bitbucket.org/GravityPR/prthorns/src/master/Hydro\_RNSID/\)](https://bitbucket.org/GravityPR/prthorns/src/master/Hydro_RNSID/)) they are identical up to some text formatting and GRHydro support. This ticket should be closed. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2043/new-thorn-for-ini…

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#2469: None of the thorns in WVUThorns_Diagnostics have documentation
by Roland Haas 18 Nov '21

18 Nov '21

#2469: None of the thorns in WVUThorns_Diagnostics have documentation Reporter: Roland Haas Status: new Milestone: ET_2021_05 Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Is there progress on documentation for the remaining 3 thorns: * particle\_tracerET * Seed\_Magnetic\_Fields\_BNS ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2469/none-of-the-thorn…

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