AstroChemistry

AstroChemistry.jl is a package that solves a user-defined chemistry network for astrophysical applications (in particular for the interstellar medium). It can be used to post-process snapshots of hydrodynamical simulations with a built-in Octree that calculates the column densities for shielding against the FUV radiation. The chemistry coefficients are based on the UMIST database and the CO shielding is based on Visser et al. 2009. The code is multithreading parallel using Julia's built-in functionality.

Dependencies

AstroChemistry.jl makes use of the following Julia packages:

Installation

Open the REPL (type julia in the terminal) and install the relevant packages:

import Pkg
Pkg.add("StaticArrays")
Pkg.add("Parameters")
Pkg.add("DifferentialEquations")
Pkg.add("Healpix")
Pkg.add("AstroChemistry")

Quick Start

using AstroChemistry

#specify the chemical species in the network
all_species = ["H", "H-", "H2", "H+", "H2+", "e-"]

#initialize the network
net, dict = initialize_chemistry_network(all_species, grRec=false)

#initialize the total (gas-phase) elemental abundance
abtot = AbundTotal()

#specify the physical parameters
nH, temp, ξ, IUV, Zp = 100., 20., 1e-16, 0., 1.
par = Par{1,0,Float64}(nH=nH, temp=temp, ξ=ξ, IUV=IUV, Zp=Zp)

#initialize the chemical abundance array
N_spec = length(all_species)
abund = zeros(N_spec)
init_abund(abund, Zp, [], abtot, net)

#solve the network
dt = 1e10 #yr
retcode, rr = solve_equilibrium_abundances(abund, dt, par, abtot, net)

#print the final abundances of H+, H and H2
@show retcode, abund[dict["H+"]], abund[dict["H"]], abund[dict["H2"]]

Examples

1D PDR calculation: see examples/PDRtest.jl for reproducing the "F1" test problem described in the PDR code comparison project Röllig et al. 2017.
post-processing: see examples/chem_octree.jl for how to read a Gadget snapshot (format 3) and calculate the chemical abundances in post-processing.

Gallery

The output image of examples/PDRtest.jl.
Post-processing results from a hydrodynamical simulation of the interstellar medium in the solar-neighborhood (Hu et al. 2021).

Author

Chia-Yu Hu @ Max Planck Institute for Extraterrestrial Physics (cyhu.astro@gmail.com)