Merge branch 'development' into add_zoom_plots

Author: zingale

Docs/source/eos_implementations.rst

@@ -71,7 +71,7 @@ formulation here is only correct for a :math:`\gamma = 5/3` gas.
 ``helmholtz`` contains a general, publicly available stellar
 equation of state based on the Helmholtz free energy, with
 contributions from ions, radiation, and electron degeneracy, as
-described in :cite:`timmes:1999`, :cite:`timmes:2000`, :cite:`flash`.
+described in :cite:`timmes:1999, timmes:2000, flash`.
 
 .. note::
 

Docs/source/networks.rst

@@ -22,7 +22,7 @@ Microphysics knows the properties of the fluid.
 .. note::
 
    Many of the networks here are generated using `pynucastro
-   <https://pynucastro.github.io/>`_ using the ``AmrexAstroCxxNetwork``
+   <https://pynucastro.github.io/>`_ :cite:`pynucastro, pynucastro2` using the ``AmrexAstroCxxNetwork``
    class.
 
 ``general_null``
@@ -494,7 +494,7 @@ triple-\ :math:`\alpha`, and rp-breakout burning up through :math:`^{56}\mathrm{
 using the ideas from :cite:`wallacewoosley:1981`, but with modern
 reaction rates from ReacLib :cite:`ReacLib` where available.
 This network was used for the X-ray burst studies in
-:cite:`xrb:II`, :cite:`xrb:III`, and more details are contained in those papers.
+:cite:`xrb:II, xrb:III`, and more details are contained in those papers.
 
 ``triple_alpha_plus_cago``
 ==========================

Docs/source/nse_tabular.rst

@@ -34,14 +34,19 @@ Composition and EOS
 ===================
 
 The NSE table was generated using `pynucastro
-<https://pynucastro.github.io/pynucastro/>` using 96 nuclei and
-electron/positron capture/decay rates from :cite:`langanke:2001`.  The
-table takes $Y_e$ as the primary composition variable and provides a
-set of mass fractions that is mapped into those used by ``aprox19``.
-Using the value allows us to attain a lower :math:`Y_e` than
-``aprox19`` can represent.
-
-For this reason, when we are using the NSE network, we always take the
+<https://pynucastro.github.io/pynucastro/>`_ :cite:`pynucastro,
+pynucastro2`, using 96 nuclei and electron/positron capture/decay
+rates from :cite:`langanke:2001`.  The table takes $Y_e$ as the
+primary composition variable and provides a set of mass fractions that
+is mapped into those used by ``aprox19``.  Using the value allows us
+to attain a lower :math:`Y_e` than ``aprox19`` can represent.
+
+.. note::
+
+   The full details of the NSE table are provided in :cite:`sdc-nse`.
+   The table can be regenerated using the script ``nse_tabular/make_nse_table.py``.
+
+When we are using the NSE network, we always take the
 composition quantities in the EOS directly from ``eos_state.aux[]``
 instead of from ``eos_state.xn[]``.  The ``AUX_THERMO`` preprocessor
 variable is enabled in this case, and the equations of state interpret

Docs/source/refs.bib

@@ -160,8 +160,7 @@ @ARTICLE{colellasekora
 
 @ARTICLE{millercolella:2002,
    author = {{Miller}, G.~H. and {Colella}, P.},
-       title = "{A Conservative Three-Dimensional Eulerian Method for Coupled Solid-Fluid Shock \
-Capturing}",
+       title = "{A Conservative Three-Dimensional Eulerian Method for Coupled Solid-Fluid Shock Capturing}",
   journal = {Journal of Computational Physics},
   year = 2002,
   month = nov,
@@ -183,7 +182,7 @@ @ARTICLE{chamulak:2008
    author = {{Chamulak}, D.~A. and {Brown}, E.~F. and {Timmes}, F.~X. and
 {Dupczak}, K.},
     title = "{The Reduction of the Electron Abundance during the Pre-explosion Simmering in White Dwarf Supernovae}",
-  journal = {\apj},
+  journal = {ApJ},
 archivePrefix = "arXiv",
    eprint = {0801.1643},
  keywords = {Galaxies: Evolution, Nuclear Reactions, Nucleosynthesis, Abundances, Stars: Supernovae: General, Stars: White Dwarfs},
@@ -200,7 +199,7 @@ @ARTICLE{lowMach4
    author = {{Zingale}, M. and {Almgren}, A.~S. and {Bell}, J.~B. and {Nonaka}, A. and
              {Woosley}, S.~E.},
     title = "{Low Mach Number Modeling of Type IA Supernovae. IV. White Dwarf Convection}",
-  journal = {\apj},
+  journal = {ApJ},
 archivePrefix = "arXiv",
    eprint = {0908.2668},
      year = 2009,
@@ -216,7 +215,7 @@ @ARTICLE{wdconvect
    author = {{Zingale}, M. and {Nonaka}, A. and {Almgren}, A.~S. and {Bell}, J.~B. and
 {Malone}, C.~M. and {Woosley}, S.~E.},
     title = "{The Convective Phase Preceding Type Ia Supernovae}",
-  journal = {\apj},
+  journal = {ApJ},
  keywords = {convection, hydrodynamics, methods: numerical, nuclear reactions, nucleosynthesis, abundances, supernovae: general, white dwarfs},
      year = 2011,
     month = oct,
@@ -232,7 +231,7 @@ @ARTICLE{raskin:2010
    author = {{Raskin}, C. and {Scannapieco}, E. and {Rockefeller}, G. and
 	{Fryer}, C. and {Diehl}, S. and {Timmes}, F.~X.},
     title = "{$^{56}$Ni Production in Double-degenerate White Dwarf Collisions}",
-  journal = {\apj},
+  journal = {ApJ},
 archivePrefix = "arXiv",
    eprint = {1009.2507},
  primaryClass = "astro-ph.SR",
@@ -250,7 +249,7 @@ @ARTICLE{xrb:III
    author = {{Zingale}, M. and {Malone}, C.~M. and {Nonaka}, A. and {Almgren}, A.~S. and
 	{Bell}, J.~B.},
     title = "{Comparisons of Two- and Three-Dimensional Convection in Type I X-Ray Bursts}",
-  journal = {\apj},
+  journal = {ApJ},
 archivePrefix = "arXiv",
    eprint = {1410.5796},
  primaryClass = "astro-ph.HE",
@@ -269,7 +268,7 @@ @ARTICLE{xrb:II
    author = {{Malone}, C.~M. and {Zingale}, M. and {Nonaka}, A. and {Almgren}, A.~S. and
 	{Bell}, J.~B.},
     title = "{Multidimensional Modeling of Type I X-Ray Bursts. II. Two-dimensional Convection in a Mixed H/He Accretor}",
-  journal = {\apj},
+  journal = {ApJ},
 archivePrefix = "arXiv",
    eprint = {1404.6286},
  primaryClass = "astro-ph.HE",
@@ -287,7 +286,7 @@ @ARTICLE{xrb:II
 @ARTICLE{wallacewoosley:1981,
        author = {{Wallace}, R.~K. and {Woosley}, S.~E.},
         title = "{Explosive hydrogen burning}",
-      journal = {\apjs},
+      journal = {ApJS},
      keywords = {Abundance, Astrophysics, Hydrogen, Metallic Stars, Nuclear Fusion, Reaction Kinetics, Stellar Evolution, Gamma Rays, High Temperature, Isotopes, Neutron Stars, Novae, Resonance, Supermassive Stars, X Ray Sources, Astrophysics},
          year = 1981,
         month = feb,
@@ -306,7 +305,7 @@ @article{ReacLib
                   and F. K. Thielemann and Michael Wiescher},
   title={The JINA REACLIB Database: Its Recent Updates and Impact on
                   Type-I X-ray Bursts},
-  journal={\apjs},
+  journal={ApJS},
   volume={189},
   number={1},
   pages={240},
@@ -338,7 +337,7 @@ @ARTICLE{vode
 @ARTICLE{ShenBildsten,
    author = {{Shen}, K.~J. and {Bildsten}, L.},
     title = "{Unstable Helium Shell Burning on Accreting White Dwarfs}",
-  journal = {\apj},
+  journal = {ApJ},
 archivePrefix = "arXiv",
    eprint = {0903.0654v2},
  primaryClass = "astro-ph.HE",
@@ -369,7 +368,7 @@ @ARTICLE{ma:2013
        author = {{Ma}, H. and {Woosley}, S.~E. and {Malone}, C.~M. and {Almgren}, A. and
          {Bell}, J.},
         title = "{Carbon Deflagration in Type Ia Supernova. I. Centrally Ignited Models}",
-      journal = {\apj},
+      journal = {ApJ},
      keywords = {hydrodynamics, instabilities, nuclear reactions, nucleosynthesis, abundances, supernovae: general, turbulence, white dwarfs, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics},
          year = 2013,
         month = "jul",
@@ -388,7 +387,7 @@ @ARTICLE{ma:2013
 @ARTICLE{graboske:1973,
        author = {{Graboske}, H.~C. and {Dewitt}, H.~E. and {Grossman}, A.~S. and {Cooper}, M.~S.},
         title = "{Screening Factors for Nuclear Reactions. II. Intermediate Screen-Ing and Astrophysical Applications}",
-      journal = {\apj},
+      journal = {ApJ},
          year = 1973,
         month = apr,
        volume = {181},
@@ -401,7 +400,7 @@ @ARTICLE{graboske:1973
 @ARTICLE{alastuey:1978,
        author = {{Alastuey}, A. and {Jancovici}, B.},
         title = "{Nuclear reaction rate enhancement in dense stellar matter.}",
-      journal = {\apj},
+      journal = {ApJ},
      keywords = {Astrophysics, Magnetohydrodynamics, Nuclear Astrophysics, Reaction Kinetics, Thermonuclear Reactions, Correlation, Nuclei (Nuclear Physics), Perturbation Theory, Potential Theory, Quantum Mechanics, Astrophysics, Nuclear Reactions:Stellar Interiors},
          year = 1978,
         month = dec,
@@ -415,7 +414,7 @@ @ARTICLE{alastuey:1978
 @ARTICLE{itoh:1979,
        author = {{Itoh}, N. and {Totsuji}, H. and {Ichimaru}, S. and {Dewitt}, H.~E.},
         title = "{Enhancement of thermonuclear reaction rate due to strong screening. II - Ionic mixtures}",
-      journal = {\apj},
+      journal = {ApJ},
      keywords = {Nonuniform Plasmas, Reaction Kinetics, Thermonuclear Reactions, Astrophysics, Binary Mixtures, Dense Plasmas, Monte Carlo Method, Astrophysics},
          year = 1979,
         month = dec,
@@ -429,7 +428,7 @@ @ARTICLE{itoh:1979
 @ARTICLE{chugunov:2007,
        author = {{Chugunov}, A.~I. and {Dewitt}, H.~E. and {Yakovlev}, D.~G.},
         title = "{Coulomb tunneling for fusion reactions in dense matter: Path integral MonteCarlo versus mean field}",
-      journal = {\prd},
+      journal = {PRD},
      keywords = {26.30.+k, Nucleosynthesis in novae supernovae and other explosive environments, Astrophysics, Nuclear Theory},
          year = 2007,
         month = jul,
@@ -448,7 +447,7 @@ @ARTICLE{chugunov:2007
 @ARTICLE{yakovlev:2006,
        author = {{Yakovlev}, D.~G. and {Gasques}, L.~R. and {Afanasjev}, A.~V. and {Beard}, M. and {Wiescher}, M.},
         title = "{Fusion reactions in multicomponent dense matter}",
-      journal = {\prc},
+      journal = {PRC},
      keywords = {25.60.Pj, 26.50.+x, 97.10.Cv, Fusion reactions, Nuclear physics aspects of novae supernovae and other explosive environments, Stellar structure interiors evolution nucleosynthesis ages, Astrophysics, Nuclear Theory},
          year = 2006,
         month = sep,
@@ -467,7 +466,7 @@ @ARTICLE{yakovlev:2006
 @ARTICLE{chugunov:2009,
        author = {{Chugunov}, A.~I. and {Dewitt}, H.~E.},
         title = "{Nuclear fusion reaction rates for strongly coupled ionic mixtures}",
-      journal = {\prc},
+      journal = {PRC},
      keywords = {26.30.-k, Nucleosynthesis in novae supernovae and other explosive environments, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - High Energy Astrophysical Phenomena},
          year = 2009,
         month = jul,
@@ -545,7 +544,7 @@ @ARTICLE{jancovici:1977
 @ARTICLE{Wallace:1982,
        author = {{Wallace}, R.~K. and {Woosley}, S.~E. and {Weaver}, T.~A.},
         title = "{The thermonuclear model for X-ray transients}",
-      journal = {\apj},
+      journal = {ApJ},
      keywords = {Binary Stars, Neutron Stars, Red Giant Stars, Stellar Mass Accretion, Stellar Models, Thermonuclear Reactions, X Ray Sources, Eddington Approximation, Stellar Envelopes, Stellar Evolution, Stellar Luminosity, Stellar Mass Ejection, Stellar Temperature, Astrophysics},
          year = 1982,
         month = jul,
@@ -622,7 +621,6 @@ @misc{autodiff
     author = {Leal, Allan M. M.},
     title = {autodiff, a modern, fast and expressive {C++} library for automatic differentiation},
     url = {https://autodiff.github.io},
-    howpublished = {\texttt{https://autodiff.github.io}},
     year = {2018}
 }
 
@@ -691,7 +689,7 @@ @article{langanke:2001
 @ARTICLE{itoh:1996,
        author = {{Itoh}, Naoki and {Hayashi}, Hiroshi and {Nishikawa}, Akinori and {Kohyama}, Yasuharu},
         title = "{Neutrino Energy Loss in Stellar Interiors. VII. Pair, Photo-, Plasma, Bremsstrahlung, and Recombination Neutrino Processes}",
-      journal = {\apjs},
+      journal = {ApJS},
      keywords = {DENSE MATTER, ELEMENTARY PARTICLES, RADIATION MECHANISMS: NONTHERMAL, STARS: INTERIORS, METHODS: NUMERICAL},
          year = 1996,
         month = feb,
@@ -705,7 +703,7 @@ @ARTICLE{itoh:1996
 @ARTICLE{iso7,
        author = {{Timmes}, F.~X. and {Hoffman}, R.~D. and {Woosley}, S.~E.},
         title = "{An Inexpensive Nuclear Energy Generation Network for Stellar Hydrodynamics}",
-      journal = {\apjs},
+      journal = {ApJS},
      keywords = {Hydrodynamics, Methods: Numerical, Nuclear Reactions, Nucleosynthesis, Abundances, Stars: General},
          year = 2000,
         month = jul,
@@ -733,7 +731,7 @@ @article{amrex_joss
 @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},
+      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,
@@ -753,7 +751,7 @@ @ARTICLE{maestroex
 @ARTICLE{quokka,
        author = {{Wibking}, Benjamin D. and {Krumholz}, Mark R.},
         title = "{QUOKKA: a code for two-moment AMR radiation hydrodynamics on GPUs}",
-      journal = {\mnras},
+      journal = {MNRAS},
      keywords = {hydrodynamics, methods: numerical, Astrophysics - Instrumentation and Methods for Astrophysics},
          year = 2022,
         month = may,
@@ -782,4 +780,33 @@ @article{lsode
         author = {{Radhakrishnan}, Krishnan and {Hindmarsh}, Alan C.},
         journal = {Lawrence Livermore National Laboratory Report UCRL-ID-113855},
         pages = {124}
-}
+}
+
+@article{pynucastro,
+author = {{Willcox}, D.~E. and {Zingale}, M.},
+    title = "{pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations}",
+  journal = {Journal of Open Source Software},
+     year = 2018,
+   volume = 3,
+   number = 23,
+   pages = 588,
+    url = {https://doi.org/10.21105/joss.00588},
+   doi = {10.21105/joss.00588},
+  subject = {nuclear astrophysics}
+}
+
+@article{pynucastro2,
+doi = {10.3847/1538-4357/acbaff},
+url = {https://dx.doi.org/10.3847/1538-4357/acbaff},
+year = {2023},
+month = {apr},
+publisher = {The American Astronomical Society},
+volume = {947},
+number = {2},
+pages = {65},
+author = {Alexander I. Smith and Eric T. Johnson and Zhi Chen and Kiran Eiden and Donald E. Willcox and Brendan Boyd and Lyra Cao and Christopher J. DeGrendele and Michael Zingale},
+title = {pynucastro: A Python Library for Nuclear Astrophysics},
+journal = {The Astrophysical Journal},
+abstract = {We describe pynucastro 2.0, an open-source library for interactively creating and exploring astrophysical nuclear reaction networks. We demonstrate new methods for approximating rates and use detailed balance to create reverse rates, show how to build networks and determine whether they are appropriate for a particular science application, and discuss the changes made to the library over the past few years. Finally, we demonstrate the validity of the networks produced and share how we use pynucastro networks in simulation codes.},
+     subject = {nuclear astrophysics}
+}

Docs/source/screening.rst

@@ -60,7 +60,7 @@ The options are:
   :math:`\Gamma < 0.3`, it uses screening described in
   :cite:`graboske:1973`. In the strong screening regime,
   :math:`\Gamma > 0.8`, it uses screening described in
-  :cite:`jancovici:1977`, :cite:`alastuey:1978`, :cite:`itoh:1979`.
+  :cite:`jancovici:1977, alastuey:1978, itoh:1979`.
   For the intermediate screening regime, :math:`0.3 < \Gamma < 0.8`,
   a weighted blending between the weak and strong screening are used.
   The overall procedure is described in :cite:`Wallace:1982`.