change reference style + add some new references to codes

AMReX-Astro · Jan 12, 2025 · f88d252 · f88d252
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diff --git a/Docs/source/conf.py b/Docs/source/conf.py
@@ -68,6 +68,7 @@ def get_version():
 
 # bibtex
 bibtex_bibfiles = ["refs.bib"]
+bibtex_default_style = "unsrt"
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

diff --git a/Docs/source/getting_started.rst b/Docs/source/getting_started.rst
@@ -27,7 +27,7 @@ to set the ``AMREX_HOME`` environment variable to point to the
 
 .. index:: burn_cell
 
-A good unit test to start with is ``burn_cell`` -- this is simply a
+A good unit test to start with is ``burn_cell`` --- this is simply a
 one-zone burn.  In ``Microphysics/`` do:
 
 .. prompt:: bash

diff --git a/Docs/source/index.rst b/Docs/source/index.rst
@@ -10,10 +10,11 @@ AMReX-Astro Microphysics is a collection of microphysics routines (equations of
 reaction networks, ...) and utilities (ODE integrators, NSE solvers)
 for astrophysical simulation codes.
 
-The original design was to support the `AMReX
-<https://github.com/amrex-codes/amrex>`_ codes `CASTRO
-<https://github.com/amrex-astro/Castro>`_ and MAESTRO (now `MAESTROeX
-<https://github.com/amrex-astro/MAESTROeX>`_). These all have a
+The original design was to support codes based on the `AMReX
+<https://github.com/amrex-codes/amrex>`_ adaptive mesh refinement library :cite:`amrex_joss`,
+including `CASTRO
+<https://github.com/amrex-astro/Castro>`_ :cite:`castro_I`, `MAESTROeX
+<https://github.com/amrex-astro/MAESTROeX>`_ :cite:`maestroex`, and Quokka :cite:`quokka`. These all have a
 consistent interface and the separate Microphysics repository allows
 them to share the same equation of state, reaction networks, and more.
 Later, Microphysics was adopted by the `Quokka <https://github.com/quokka-astro/quokka>`_

diff --git a/Docs/source/refs.bib b/Docs/source/refs.bib
@@ -701,3 +701,56 @@ @ARTICLE{itoh:1996
        adsurl = {https://ui.adsabs.harvard.edu/abs/1996ApJS..102..411I},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
+
+@article{amrex_joss,
+         doi = {10.21105/joss.01370},
+         url = {https://doi.org/10.21105/joss.01370},
+         year = {2019},
+         publisher = {The Open Journal},
+         volume = {4},
+         number = {37},
+         pages = {1370},
+         author = {Weiqun Zhang and Ann Almgren and Vince Beckner and John Bell and Johannes Blaschke and Cy Chan and Marcus Day and Brian Friesen and Kevin Gott and Daniel Graves and Max P. Katz and Andrew Myers and Tan Nguyen and Andrew Nonaka and Michele Rosso and Samuel Williams and Michael Zingale},
+         title = {AMReX: a framework for block-structured adaptive mesh refinement},
+         journal = {Journal of Open Source Software} }
+
+
+@ARTICLE{maestroex,
+       author = {{Fan}, Duoming and {Nonaka}, Andrew and {Almgren}, Ann S. and {Harpole}, Alice and {Zingale}, Michael},
+        title = "{MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver}",
+      journal = {\apj},
+     keywords = {Stellar convective zones, Hydrodynamics, Computational methods, Nuclear astrophysics, Nucleosynthesis, Nuclear abundances, 301, 1963, 1965, 1129, 1131, 1128, Physics - Computational Physics, Astrophysics - Solar and Stellar Astrophysics},
+         year = 2019,
+        month = dec,
+       volume = {887},
+       number = {2},
+          eid = {212},
+        pages = {212},
+          doi = {10.3847/1538-4357/ab4f75},
+archivePrefix = {arXiv},
+       eprint = {1908.03634},
+ primaryClass = {physics.comp-ph},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2019ApJ...887..212F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{quokka,
+       author = {{Wibking}, Benjamin D. and {Krumholz}, Mark R.},
+        title = "{QUOKKA: a code for two-moment AMR radiation hydrodynamics on GPUs}",
+      journal = {\mnras},
+     keywords = {hydrodynamics, methods: numerical, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2022,
+        month = may,
+       volume = {512},
+       number = {1},
+        pages = {1430-1449},
+          doi = {10.1093/mnras/stac439},
+archivePrefix = {arXiv},
+       eprint = {2110.01792},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022MNRAS.512.1430W},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+