fix DOIs for the JOSS paper

paper/paper.bib

@@ -6,7 +6,8 @@ @article{br-refine
   number={5},
   pages={1278--1286},
   year={1991},
-  publisher={IEEE}
+  publisher={IEEE},
+  doi={10.1109/21.120081}
 }
 
 @ARTICLE{colglaz,
@@ -27,7 +28,7 @@ @ARTICLE{castro_I
    {Day}, M.~S. and {Howell}, L.~H. and {Joggerst}, C.~C. and {Lijewski}, M.~J. and
    {Nonaka}, A. and {Singer}, M. and {Zingale}, M.},
   title = "{CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-gravity}",
-  journal = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
   year = 2010,
   month = jun,
   volume = 715,
@@ -50,7 +51,7 @@ @ARTICLE{ppm
 @ARTICLE{colgwhite,
    author = {{Colgate}, S.~A. and {White}, R.~H.},
    title = "{The Hydrodynamic Behavior of Supernovae Explosions}",
-   journal = {ApJ},
+   journal = {The Astrophysical Journal},
    year = 1966,
    month = mar,
    volume = 143,
@@ -59,19 +60,11 @@ @ARTICLE{colgwhite
 }
 
 
-@book{quirk1997,
-  title={A contribution to the great Riemann solver debate},
-  author={Quirk, James J},
-  year={1997},
-  publisher={Springer}
-}
-
-
 @ARTICLE{maestro:III,
    author = {{Almgren}, A.~S. and {Bell}, J.~B. and {Nonaka}, A. and {Zingale}, M.
    },
    title = "{Low Mach Number Modeling of Type Ia Supernovae. III. Reactions}",
-   journal = {ApJ},
+   journal = {The Astrophysical Journal},
    keywords = {Convection, Hydrodynamics, Methods: Numerical, Nuclear Reactions, Nucleosynthesis, Abundances, Stars: Supernovae: General, Stars: White Dwarfs},
    year = 2008,
    month = sep,
@@ -84,7 +77,7 @@ @ARTICLE{maestro:III
 @ARTICLE{zingalekatz,
    author = {{Zingale}, M. and {Katz}, M.~P.},
    title = "{On the Piecewise Parabolic Method for Compressible Flow With Stellar Equations of State}",
-   journal = {ApJS},
+   journal = {The Astrophysical JournalS},
    keywords = {hydrodynamics, methods: numerical},
    year = 2015,
    month = feb,
@@ -100,7 +93,7 @@ @ARTICLE{flash
    {Zingale}, M. and {Lamb}, D.~Q. and {MacNeice}, P. and {Rosner}, R. and
    {Truran}, J.~W. and {Tufo}, H.},
   title = "{FLASH: An Adaptive Mesh Hydrodynamics Code for Modeling Astrophysical Thermonuclear Flashes}",
-  journal = {ApJS},
+  journal = {The Astrophysical Journal Supplement},
   year = 2000,
   month = nov,
   volume = 131,
@@ -111,7 +104,7 @@ @ARTICLE{flash
 @ARTICLE{timmes:1999,
    author = {{Timmes}, F.~X. and {Arnett}, D.},
     title = "{The Accuracy, Consistency, and Speed of Five Equations of State for Stellar Hydrodynamics}",
-  journal = {ApJS},
+  journal = {The Astrophysical Journal Supplement},
  keywords = {EQUATION OF STATE, HYDRODYNAMICS, METHODS: NUMERICAL, STARS: GENERAL, STARS: INTERIORS, Equation of State, Hydrodynamics, Methods: Numerical, Stars: General, Stars: Interiors},
      year = 1999,
     month = nov,
@@ -125,7 +118,7 @@ @ARTICLE{timmes:1999
 @ARTICLE{timmes:2000,
    author = {{Timmes}, F.~X. and {Swesty}, F.~D.},
     title = "{The Accuracy, Consistency, and Speed of an Electron-Positron Equation of State Based on Table Interpolation of the Helmholtz Free Energy}",
-  journal = {Astrophysical Journal Supplement},
+  journal = {The Astrophysical Journal Supplement},
  keywords = {EQUATION OF STATE, HYDRODYNAMICS, METHODS: NUMERICAL, STARS: GENERAL, Equation of State, Hydrodynamics, Methods: Numerical, Stars: General},
      year = 2000,
     month = feb,
@@ -183,7 +176,7 @@ @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 = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
 archivePrefix = "arXiv",
    eprint = {0801.1643},
  keywords = {Galaxies: Evolution, Nuclear Reactions, Nucleosynthesis, Abundances, Stars: Supernovae: General, Stars: White Dwarfs},
@@ -200,7 +193,7 @@ @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 = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
 archivePrefix = "arXiv",
    eprint = {0908.2668},
      year = 2009,
@@ -216,7 +209,7 @@ @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 = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
  keywords = {convection, hydrodynamics, methods: numerical, nuclear reactions, nucleosynthesis, abundances, supernovae: general, white dwarfs},
      year = 2011,
     month = oct,
@@ -232,7 +225,7 @@ @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 = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
 archivePrefix = "arXiv",
    eprint = {1009.2507},
  primaryClass = "astro-ph.SR",
@@ -250,7 +243,7 @@ @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 = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
 archivePrefix = "arXiv",
    eprint = {1410.5796},
  primaryClass = "astro-ph.HE",
@@ -269,7 +262,7 @@ @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 = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
 archivePrefix = "arXiv",
    eprint = {1404.6286},
  primaryClass = "astro-ph.HE",
@@ -287,7 +280,7 @@ @ARTICLE{xrb:II
 @ARTICLE{wallacewoosley:1981,
        author = {{Wallace}, R.~K. and {Woosley}, S.~E.},
         title = "{Explosive hydrogen burning}",
-      journal = {Astrophysical Journal Supplement},
+      journal = {The Astrophysical Journal Supplement},
      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,
@@ -306,12 +299,13 @@ @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={Astrophysical Journal Supplement},
+  journal={The Astrophysical Journal Supplement},
   volume={189},
   number={1},
   pages={240},
   url={http://stacks.iop.org/0067-0049/189/i=1/a=240},
-  year={2010}
+  year={2010},
+  doi={10.1088/0067-0049/189/1/240}
 }
 
 @BOOK{NR,
@@ -328,24 +322,26 @@ @BOOK{NR
 @ARTICLE{vode,
   author={P. N. Brown and G. D. Byrne and A. C. Hindmarsh},
   title={{VODE}: A Variable Coefficient ODE Solver},
-  journal={SIAM J. Sci. Stat. Comput.},
+  journal={SIAM Journal on Scientific and Statistical Computing},
   volume={10},
   pages={1038-1051},
-  year={1989}
+  year={1989},
+  doi={10.1137/0910062}
 }
 
 
 @ARTICLE{ShenBildsten,
    author = {{Shen}, K.~J. and {Bildsten}, L.},
     title = "{Unstable Helium Shell Burning on Accreting White Dwarfs}",
-  journal = {Astrophysical Journal},
+  journal = {The Astrophysical Journal},
 archivePrefix = "arXiv",
    eprint = {0903.0654v2},
  primaryClass = "astro-ph.HE",
      year = 2009,
     month = mar,
    volume = 699,
-    pages = {10}}
+    pages = {10},
+    doi={10.1088/0004-637X/699/2/1365}}
 
 @ARTICLE{castro_sdc,
        author = {{Zingale}, M. and {Katz}, M.~P. and {Bell}, J.~B. and {Minion}, M.~L. and
@@ -361,15 +357,16 @@ @ARTICLE{castro_sdc
        eprint = {1908.03661},
  primaryClass = {physics.comp-ph},
        adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190803661Z},
-      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+       doi = {10.3847/1538-4357/ab4e1d}
 }
 
 
 @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 = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
      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 +385,7 @@ @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 = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
          year = 1973,
         month = apr,
        volume = {181},
@@ -401,7 +398,7 @@ @ARTICLE{graboske:1973
 @ARTICLE{alastuey:1978,
        author = {{Alastuey}, A. and {Jancovici}, B.},
         title = "{Nuclear reaction rate enhancement in dense stellar matter.}",
-      journal = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
      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 +412,7 @@ @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 = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
      keywords = {Nonuniform Plasmas, Reaction Kinetics, Thermonuclear Reactions, Astrophysics, Binary Mixtures, Dense Plasmas, Monte Carlo Method, Astrophysics},
          year = 1979,
         month = dec,
@@ -506,7 +503,7 @@ @article{mott_qss
         pages = {407-428},
         year = {2000},
         issn = {0021-9991},
-        doi = {https://doi.org/10.1006/jcph.2000.6605},
+        doi = {10.1006/jcph.2000.6605},
         author = {David R. Mott and Elaine S. Oran and Bram {van Leer}},
         abstract = {A quasi-steady-state method is presented that integrates stiff differential equations arising from reaction kinetics. This predictor–corrector method is A-stable for linear equations and second-order accurate. The method is used for all species regardless of the time scales of the individual equations, and it works well for problems typical of hydrocarbon combustion. Start-up costs are low, making the method ideal for use in process-split reacting-flow simulations which require the solution of an initial-value problem in every computational cell for every global time step. The algorithm is described, and error analysis and linear stability analysis are included. The algorithm is also applied to several test problems, and the results are compared to those of the stiff integrator CHEMEQ. The method, which we call α-QSS, is more stable, more accurate, and less costly than CHEMEQ.}
 }
@@ -545,7 +542,7 @@ @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 = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
      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,
@@ -585,7 +582,8 @@ @article{Kushnir_2020
  primaryClass = {astro-ph.HE},
        adsurl = {https://ui.adsabs.harvard.edu/abs/2020MNRAS.493.5413K},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System},
-      journal = {Monthly Notices of the Royal Astronomical Society}
+      journal = {Monthly Notices of the Royal Astronomical Society},
+          doi = {10.1093/mnras/staa594}
 }
 
 
@@ -630,7 +628,7 @@ @misc{autodiff
 @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 = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
      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,
@@ -698,7 +696,7 @@ @ARTICLE{maestro
    author = {{Nonaka}, A. and {Almgren}, A.~S. and {Bell}, J.~B. and {Lijewski}, M.~J. and
    {Malone}, C.~M. and {Zingale}, M.},
     title = "{MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows}",
-  journal = {ApJS},
+  journal = {The Astrophysical Journal Supplement},
 archivePrefix = "arXiv",
    eprint = {1005.0112},
  primaryClass = "astro-ph.IM",
@@ -801,7 +799,7 @@ @ARTICLE{chugunov:2009
 @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 = {The Astrophysical Journal},
          year = 1973,
         month = apr,
        volume = {181},
@@ -814,7 +812,7 @@ @ARTICLE{graboske:1973
 @ARTICLE{alastuey:1978,
        author = {{Alastuey}, A. and {Jancovici}, B.},
         title = "{Nuclear reaction rate enhancement in dense stellar matter.}",
-      journal = {ApJ},
+      journal = {The Astrophysical Journal},
      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,
@@ -880,7 +878,7 @@ @article{Zingale_2024
 @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 = {The Astrophysical Journal Supplement},
      keywords = {DENSE MATTER, ELEMENTARY PARTICLES, RADIATION MECHANISMS: NONTHERMAL, STARS: INTERIORS, METHODS: NUMERICAL},
          year = 1996,
         month = feb,
@@ -894,7 +892,7 @@ @ARTICLE{itoh:1996
 @ARTICLE{timmes:2000b,
        author = {{Timmes}, F.~X.},
         title = "{Physical Properties of Laminar Helium Deflagrations}",
-      journal = {APJ},
+      journal = {The Astrophysical Journal},
      keywords = {HYDRODYNAMICS, METHODS: NUMERICAL, NUCLEAR REACTIONS, NUCLEOSYNTHESIS, ABUNDANCES, STARS: INTERIORS, Hydrodynamics, Methods: Numerical, nuclear reactions, nucleosynthesis; abundances, Stars: Interiors},
          year = 2000,
         month = jan,
@@ -1000,7 +998,7 @@ @article{Guichandut_2024
 @ARTICLE{Harpole_2021,
        author = {{Harpole}, A. and {Ford}, N.~M. and {Eiden}, K. and {Zingale}, M. and {Willcox}, D.~E. and {Cavecchi}, Y. and {Katz}, M.~P.},
         title = "{Dynamics of Laterally Propagating Flames in X-Ray Bursts. II. Realistic Burning and Rotation}",
-      journal = {Astrophysical Journal},
+      journal = {The Astrophysical Journal},
      keywords = {X-ray bursts, Nucleosynthesis, Open source software, Hydrodynamics, Hydrodynamical simulations, Neutron stars, Computational methods, 1814, 1131, 1866, 1963, 767, 1108, 1965, Astrophysics - High Energy Astrophysical Phenomena},
          year = 2021,
         month = may,
@@ -1028,7 +1026,7 @@ @article{Zingale_2024_dd
 pages = {150},
 author = {{Zingale}, M. and {Chen}, Z. and {Rasmussen}, M. and {Polin}, A. and {Katz}, M. and {Smith Clark}, A. and {Johnson}, E. T.},
 title = {Sensitivity of Simulations of Double-detonation Type Ia Supernovae to Integration Methodology},
-journal = {Astrophysical Journal},
+journal = {The Astrophysical Journal},
 abstract = {We study the coupling of hydrodynamics and reactions in
                   simulations of the double-detonation model for Type
                   Ia supernovae. When assessing the convergence of