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Title: Implementation of Chemistry in the Athena++ Code

Journal Article · · The Astrophysical Journal. Supplement Series

Chemistry plays a key role in many aspects of astrophysical fluids. Atoms and molecules are agents for heating and cooling, determine the ionization fraction, serve as observational tracers, and build the molecular foundation of life. We present the implementation of a chemistry module in the publicly available magnetohydrodynamic code Athena++. We implement several chemical networks and heating and cooling processes suitable for simulating the interstellar medium (ISM). A general chemical network framework in the KIDA format is also included, allowing users to easily implement their own chemistry. Radiation transfer and cosmic-ray ionization are coupled with chemistry and solved with the simple six-ray approximation. The chemical and thermal processes are evolved as a system of coupled ordinary differential equations with an implicit solver from the CVODE library. We perform and present a series of tests to ensure the numerical accuracy and convergence of the code. Many tests combine chemistry with gas dynamics, including comparisons with analytic solutions, 1D problems of the photodissociation regions and shocks, and realistic 3D simulations of the turbulent ISM. We release the code with the new public version of Athena++, aiming to provide a robust and flexible code for the astrochemical simulation community.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA); National Aeronautics and Space Administration (NASA); Simons Foundation
Grant/Contract Number:
89233218CNA000001; AC02-05CH11231
OSTI ID:
2007373
Report Number(s):
LA-UR--23-26937
Journal Information:
The Astrophysical Journal. Supplement Series, Journal Name: The Astrophysical Journal. Supplement Series Journal Issue: 2 Vol. 268; ISSN 0067-0049
Publisher:
IOP PublishingCopyright Statement
Country of Publication:
United States
Language:
English

References (52)

How the existence of unstable neutral media restricts the aspect ratio of cold neutral media? journal February 2023
The photodissociation and chemistry of CO isotopologues: applications to interstellar clouds and circumstellar disks journal June 2009
Synthetic CO emission and the XCO factor of young molecular clouds: a convergence study journal November 2021
The Dynamics of Low‐Mass Molecular Clouds in External Radiation Fields journal June 1997
A New Numerical Scheme for Cosmic-Ray Transport journal February 2018
On the low ortho-to-para H2 ratio in star-forming filaments journal October 2021
Three-phase Interstellar Medium in Galaxies Resolving Evolution with Star Formation and Supernova Feedback (TIGRESS): Algorithms, Fiducial Model, and Convergence journal September 2017
The X CO Conversion Factor from Galactic Multiphase ISM Simulations journal April 2018
grackle: a chemistry and cooling library for astrophysics journal December 2016
The SILCC (SImulating the LifeCycle of molecular Clouds) project – I. Chemical evolution of the supernova-driven ISM journal September 2015
An Extension of the Athena++ Framework for General Equations of State journal April 2020
KROME - a package to embed chemistry in astrophysical simulations journal February 2014
Simulating Radiating and Magnetized Flows in Multiple Dimensions with ZEUS‐MP
  • Hayes, John C.; Norman, Michael L.; Fiedler, Robert A.
  • The Astrophysical Journal Supplement Series, Vol. 165, Issue 1 https://doi.org/10.1086/504594
journal July 2006
The UMIST database for astrochemistry 2012 journal January 2013
Global Simulations of Protoplanetary Disk Outflows with Coupled Non-ideal Magnetohydrodynamics and Consistent Thermochemistry journal March 2019
Modeling UV Radiation Feedback from Massive Stars. I. Implementation of Adaptive Ray-tracing Method and Tests journal December 2017
Dissociative recombination of rotationally coldH3+ journal November 2004
Enzo: an Adaptive mesh Refinement code for Astrophysics journal March 2014
Simulating the formation of massive seed black holes in the early Universe – I. An improved chemical model journal June 2015
Simulating the Formation of Molecular Clouds. I. Slow Formation by Gravitational Collapse from Static Initial Conditions journal April 2007
Chemistry and radiative shielding in star-forming galactic discs journal October 2016
Cosmic-Ray Transport in Simulations of Star-forming Galactic Disks journal November 2021
The Millennium Arecibo 21 Centimeter Absorption‐Line Survey. II. Properties of the Warm and Cold Neutral Media journal April 2003
Modelling CO formation in the turbulent interstellar medium journal April 2010
Athena: A New Code for Astrophysical MHD journal September 2008
On the Stability and Evolution of Isolated Bok Globules journal October 1999
Uncertainties in H 2 and HD chemistry and cooling and their role in early structure formation journal August 2008
The Athena++ Adaptive Mesh Refinement Framework: Design and Magnetohydrodynamic Solvers journal June 2020
Diffuse Ionized Gas in Simulations of Multiphase, Star-forming Galactic Disks journal July 2020
Cosmological hydrodynamics with adaptive mesh refinement: A new high resolution code called RAMSES journal April 2002
Numerical simulations of compressively driven interstellar turbulence: I. Isothermal gas journal November 2008
The neutral atomic phases of the interstellar medium journal April 1995
FLASH: An Adaptive Mesh Hydrodynamics Code for Modeling Astrophysical Thermonuclear Flashes journal November 2000
Photochemistry and Heating/Cooling of the Multiphase Interstellar Medium with UV Radiative Transfer for Magnetohydrodynamic Simulations journal December 2022
Structure of Stationary Photodissociation Fronts journal September 1996
TIGRESS simulation data dataset January 2022
Photodissociation regions. I - Basic model. II - A model for the Orion photodissociation region journal April 1985
Photoelectric heating of interstellar gas journal April 1978
The Internal Energy for Molecular Hydrogen in Gravitationally Unstable Protoplanetary Disks journal January 2007
Physics of the Interstellar and Intergalactic Medium book December 2011
\documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $\mathrm{H}\,^{+}_{3}$ \end{document} in Diffuse Interstellar Clouds: A Tracer for the Cosmic‐Ray Ionization Rate journal December 2007
Metallicity Dependence of the H/H2 and C+/C/CO Distributions in a Resolved Self-regulating Interstellar Medium journal October 2021
CVODE, A Stiff/Nonstiff ODE Solver in C journal January 1996
Evaporation of Low-mass Planet Atmospheres: Multidimensional Hydrodynamics with Consistent Thermochemistry journal June 2018
A new class of accurate, mesh-free hydrodynamic simulation methods journal April 2015
Introducing TIGRESS-NCR. I. Coregulation of the Multiphase Interstellar Medium and Star Formation Rates journal March 2023
Reaction Networks for Interstellar Chemical Modelling: Improvements and Challenges journal October 2010
Molecular Depletion and Thermal Balance in Dark Cloud Cores journal August 2001
A chemical reaction network solver for the astrophysics code NIRVANA journal January 2016
A Simple and Accurate Network for Hydrogen and Carbon Chemistry in the Interstellar Medium journal June 2017
Cosmic-Ray Transport in Varying Galactic Environments journal April 2022
The Environmental Dependence of the X CO Conversion Factor journal November 2020