arepoICgen 0.2.4

Package for generating initial conditions for AREPO

arepoICgen

Package for creating Initial Conditions for the AMR code AREPO¹ for simulations of molecular clouds intended for scientific research. Many parts of this code are adapted from a FORTRAN code developed by Paul Clark called setpartarepo.

This code is available via a direct clone of this repository, or through pip: pip install arepoICgen

Usage Guide

arepoICgen takes in two python dictionaries as inputs, config and params. Config provides the code information about the geometry and metadata of the cloud, while params supplies the physical parameters of the cloud. Some config and param flags are required, and others are optional. Required flags will be marked with a "*". The default option assumed if not specified is marked in bold. Some parameters have default assumed values if not specified, marked in bold brackets ().

Config

Flag	Options	Description	Associated Params
verbose	True, False	Whether to print extended feedback as the code runs (does not affect the ICs)
grid*	boxGrid, boxRan, sphereGrid, sphereRan, ellipseRan, cylinderRan	The geometry and particle distribution (gridded or random).	lengths, radii (for sphere types)
turbulence	static, turbFile	Whether to apply to turbulent velocity field from a file	virialParam
turbFile	path_to_file	The path to a turbulent velocity grid file, needed only for turbFile
turbSize	128, integer	The size of the velocity grid (assumed equal length cubic), needed only for turbFile
rotation	none, rotation	Whether to add rotation to the cloud	beta, rotationRadius
extras	none, bossBodenheimer, densityGradient, bonnorEbert	What density perturbation to add to the cloud, either Boss Bodenheimer2, a linear density gradient3 or a Bonnor-Ebert4 density profile (note this setting automatically outputs density as mass)
padBox	False, True	Whether to pad the cloud with low density particles	tempFactor, boxDims, paddingDensity, paddingPercent
bField	False, True	Whether we need to give the particles an inital magnetic field value (note this does not do anything besides gives particles an initial B field of 0)
outValue	masses, density	Option to output the mass field as density (note this needs AREPO to be compiled with the right config flag for this)	density
filename*	"..."	Name of the IC file (note that the file extension is not needed)

Params

Note that lengths and radii are both marked as required, but only one may be needed in some cases.

Flag	Format/Units	Description	Associated Config
ngas*		Number of particles to populate the cloud with
lengths*	[xLength, yLength, zLength] $\rm [cm]$	The length of the box or ellipse in each direction (for the cylinder, xLength is taken as the length of the cylinder)	grid
radii*	Radius $\rm [cm]$	The radius of a spherical cloud, or the radius of the face of a cylinder (not needed by box or elliptical setups)	grid
mass*	$\rm [M_\odot]$	The total mass of the cloud
temp*	$\rm [K]$, (20)	The inital temperature of the gas inside the cloud
mu*	$\mu$, (1.4)	The mean molecular weight of the gas in the cloud, typically 1.4 for atomic and 2.4 for molecular
virialParam	$\alpha = \rm\frac{E_{Kin}}{E_{Grav}}$, (2)	The virial parameter of the cloud, used for scaling turbulent velocities	turbulence
beta	$\beta = \rm \frac{E_{Rot}}{E_{Grav}}$, (0.01)	The ratio between rotational and gravitational energy	rotation
rotationRadius	AU (0)	The radius outside of which to add rotation. Allows no angular momentum in the centre of the cloud so that numerical rings do not form	rotation
boxSize	[x, y, z], ([2,2,2])	The factor by which the box should be larger than the cloud in each dimension (i.e 2x, 3x, 4x the size)	padBox
tempFactor	(2)	How much hotter to make the padding particles compared to the cloud particles	padBox
paddingDensity	(0.01)	What fraction of the cloud's density should the padding region be (ignored for Bonnor-Ebert profile, padding density set to match outer BE sphere density)	padBox
paddingPercent	(0.02)	Number of cells to pad the box with, as a percent of ngas.	padBox
uMass	$1.991\times10^{33} , \rm g$	Mass code unit	*
uDist	$1\times10^{17} , \rm cm$	Distance code unit	*
uVelo	$36447.2682 , \rm cm , s^{-1}$	Velocity code unit	*
uEner	$1.328\times10^{9} , \rm erg$	Energy code unit	*

Calling generateICs

arepoICgen is called using code similar to the following, where it is wrapped in the generateICs function:

from arepoICgen import arepoICgen

config = {}
params = {}

arepoICgen(config, params)

Examples

See examples.txt for some example setups of the config and params dictionaries.

1. AREPO is publicly available, see here ↩

2. See Boss & Bodenheimer (1979) ↩

3. See Bonnell et al. (2008) ↩

4. See Bonnor (1956) and Ebert (1955) ↩