Merge branch 'development' into doc_build

Author: aisclark91

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

@@ -474,7 +474,7 @@ 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/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,

Docs/source/screening.rst

@@ -62,7 +62,7 @@ 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`.