Expand description
§Introduction
This tool produces complex dust particle opacities right from the command line. It is derived from Michiel Min’s DHS OpacityTool and also implements Ryo Tazaki’s MMF theory for highly porous aggregates.
For a brief overview behind the details of the implementation from a theoretical perspective, read the book.
§Capabilities
- stand-alone tool, fully command line driven, no input files need to be edited
- full scattering matrix output in several formats, including for RADMC-3D
- combining materials through mixing into a complex grain with porosity
- built-in: a curated collection of materials for applications in astronomy
- external refractive index data can be used just as easily
- computational methods: (i) DHS (Distribution of Hollow Spheres) for irregular grains and low-porosity aggregates. Standard Mie theory for perfect spheres is available as a limiting case. (ii) MMF (Modified Mean Field) theory for high-porosity/fractal aggregates. (iii) CDE approximation in the Rayleigh limit.
- Python interface module for plotting and post-processing
§Physical units used by kappa
Due to conventions in our field, the input and output of kappa uses the following units
- grain sizes and wavelengths are in microns
- mass densities of materials are in g/cm^3
- opacities are in cm^2/g
- scattering matrices are in sr^-1 or cm^-1 g^-1 sr^-1
§Examples
A simple grain made only of the default pyroxene, for the default grain size distribution ($a^{-3.5}$ powerlaw from 0.05 to 3000μm), on the default wavelength grid (0.05μm to 1cm).
§Installation
The easiest way to install kappa is to first get the source code from GitHub:
git clone https://github.com/ProsiaLAB/kappa.gitThen, you can build the executable with cargo:
cd kappa
cargo build --releaseThis will create a binary called kappa in the target/release directory.
§Usage
The command line interface is documented in the help message:
kappa --help§Grain composition
If no composition is specified, the DIANA composition is used by default.
§Core material
Specify a material to include in the grain. MATERIAL can be the key for a builtin material, the path to an lnk file, or colon-separated numbers n:k:rho3. MFRAC is the mass fraction (default 1.0) of the material. You can give up to 20 materials to build up the grain. Mass fractions do not have to add up to one, they will be renormalized. All materials will be mixed together using the Bruggeman rule, and vacuum can be added through the porosity. -c in front of each material is optional.
§Mantle material
Like -c, but place this material into the grain mantle. Multiple mantle materials will be mixed using the Bruggeman rule, and then that mix will be added to the core using the Maxwell-Garnett rule. The -m is not optional, it must be present.
§Porosity
Porosity, the volume fraction of vacuum, a number smaller than 1. The default is 0. A single value will apply to both core and mantle, but a second value will be specific for the mantle (and may be 0).
§Grain geometry and computational method
If no method is explicitly specified, the default is -dhs 0.8, i.e. DHS with fmax=0.8.
§Distribution of Hollow Spheres
Use the Distribution of Hollow Spheres (DHS, Min+ 2005) approach to model deviations from perfect spherical symmetry and low-porosity aggregates. Spheres with inner holes with volume fractions between 0 and fmax (default 0.8) are averaged to mimic irregularities. fmax=0 means to use solid spheres (Mie theory), i.e. perfectly regular grains. For backward compatibility, -fmax can be used instead of -dhs
§Modified Mean Field theory
Use Modified Mean Field theory (MMF, Tazaki & Tanaka 2018) to compute opacities of highly porous or fractal aggregates. -c, -m, and -p determine the composition of monomers with radius A0 (default 0.1μm). Particles will be aggregates with a compact size given by the -a switch, giving rise to N = a3/a30 monomers. DFRAC-OR-FILL specifies either the fractal dimension (if >1) or the volume filling factor (if <1). The default is 0.2. KF may be used to change the default prefactor.
§Mie theory
Do a standard Mie calculation for perfect spheres. This is short for -dhs 0
§Continuum Distribution of Ellipsoids
Compute CDE (continuous distribution of ellipsoids) Rayleigh limit opacities
§Grain size distribution
Grain size distributions can be specified using a powerlaw, a (log-)normal or from a file.
§Powerlaw size distribution
Specify (minimum) grain radius, and optionally maximum grain radius, the size distribution powerlaw and the number of size bins. You may also use options to set individual values with -amin, -amax, -apow, -na. The defaults are 0.05 μm, 3000 μm, 3.5, and 15 per size decade with a fixed minimum of 5, respectively.
§(Log-)normal size distribution
Specify the centroid size and the logarithmic width for a log-normal size distribution. You may also use -amean and -asig options to set these values. If ASIG is negative, create a normal distribution with that width (in μm) around AMEAN.
§Wavelength grid
Specify the (minimum) wavelength, and optionally the maximum wavelength and the number of wavelengths points for the construction of the wavelength grid. The default values are 0.05 μm, 10000 μm, and 300, respectively. You may also use the options -lmin, -lmax, and -nlam (or -nl) to set individual values.
If only one wavelength is specified with -l, then λmax=λmin and nλ=1 are implied.
Grid can also be read from a file.
§Controlling the output
The standard output is the file dustkappa.dat, with the opacities and the asymmetry parameter g. The following options control and extend the output.
- Put the output files in directory DIR instead of the current working directory. ./output will be used if -o is present but DIR is not specified.
- Include the scattering matrix in the output. NANG may optionally change the number of equally-spaced angular grid points to cover the range of angles between 0 and 180 degrees. The default for NANG is 180 and should normally be just fine.
- Divide the computation up into na parts to produce a file for each grain size. Each size will be an average over a range of NSUB grains around the real size.
- Cap the first NDEG (2 if unspecified) degrees of the forward scattering peak.
- Write dustkappa.fits instead of ASCII output. With -d, write na files.
- RADMC-3D uses a different angular grid and scattering matrix normalization. File names will contain LABEL if specified and have the extension .inp.
- Write to STDOUT instead of files. The default is to write λ, κabs, κsca, κext, and g. Many other outputs are possible, run optool -print ? for a full list. For readability, a header line may be printed to STDERR, but STDOUT gets only numbers which can be used in pipes and for redirection. You can use this to extract a single value, for example the 850μm extinction opacity of grains between 1 and 3mm: optool -a 1000 3000 -l 850 -print kext
- Write the files optool_sd.dat and optool_lam.dat with the grain size distribution and the wavelength grid, respectively. Also, write optool_mix.lnk with the result of mixing refractive index data. Exit without doing a computation.
§Material properties
kappa needs refractive index data to work. For your convenience, a
useful list of materials is compiled into kappa. You can also find
and use other data.
To access one of the built-in materials, specify the corresponding key
string like pyr-mg70. In each material class we have selected a
useful default, accessible with an even simpler generic key (for
example, pyr is an alias for pyr-mg70). Most of the built-in
refractive index datasets have a reasonably wide wavelength coverage -
the few exceptions are highlighted by bold-face numbers. If a
material is being used outside of the measured region, kappa will
still function, using extrapolated optical properties.
Even the limited number of materials we have selected to include with
kappa can be daunting. To get started with some kind of standard
opacity, we recommend to work with pyroxene pyr, carbon
c, and, at low temperatures, water ice h2o (Woitke+
2016). If you need to account for sulfur, you may want to include
troilite tro (Birnstiel+ 2016).
| Key | Material | State | $\rho \mathrm{(g/cm^3)}$ | $\lambda_{min}$ ($\mu{}m$) | $\lambda_{max}$ ($\mu{}m$) | Reference |
|---|---|---|---|---|---|---|
pyr-mg100 | $\mathrm{MgSiO_3}$ | Amorphous | 2.71 | 0.2 | 500 | Dorschner+95 |
pyr-mg95 | $\mathrm{Mg_{0.95}Fe_{0.05}SiO_3}$ | Amorphous | 2.74 | 0.2 | 500 | Dorschner+95 |
pyr-mg80 | $\mathrm{Mg_{0.8}Fe_{0.2}SiO_3}$ | Amorphous | 2.9 | 0.2 | 500 | Dorschner+95 |
pyr-mg70 (pyr) | $\mathrm{Mg_{0.7}Fe_{0.3}SiO_3}$ | Amorphous | 3.01 | 0.2 | 500 | Dorschner+95 |
pyr-mg60 | $\mathrm{Mg_{0.6}Fe_{0.4}SiO_3}$ | Amorphous | 3.1 | 0.2 | 500 | Dorschner+95 |
pyr-mg50 | $\mathrm{Mg_{0.5}Fe_{0.5}SiO_3}$ | Amorphous | 3.2 | 0.2 | 500 | Dorschner+95 |
pyr-mg40 | $\mathrm{Mg_{0.4}Fe_{0.6}SiO_3}$ | Amorphous | 3.3 | 0.2 | 500 | Dorschner+95 |
pyr-c-mg96 (ens) | $\mathrm{Mg_{0.96}Fe_{0.04}SiO3}$ | Crystalline | 2.8 | 2.0 | 99 | Jäger+98 |
ol-mg50 (ol) | $\mathrm{MgFeSiO_4}$ | Amorphous | 3.71 | 0.2 | 500 | Dorschner+95 |
ol-mg40 | $\mathrm{Mg_{0.8}Fe_{1.2}SiO_4}$ | Amorphous | 3.71 | 0.2 | 500 | Dorschner+95 |
ol-c-mg100 (for) | $\mathrm{Mg_{2}SiO_4}$ | Crystalline | 3.27 | 5.0 | 200 | Suto+06 |
ol-c-mg95 | $\mathrm{Mg_{1.9}Fe_{0.1}SiO_4}$ | Crystalline | 3.33 | 2.0 | 8190 | Fabian+01 |
ol-c-mg00 (fay) | $\mathrm{Fe_{2}SiO_4}$ | Crystalline | 4.39 | 3.0 | 250 | Fabian+01 |
astrosil | $\mathrm{MgFeSiO_4}$ | Mixed | 3.3 | $6\times 10^-5$ | $1 \times 10^5$ | Draine+03 |
c-z (c) | $\mathrm{C}$ | Amorphous? | 1.8 | 0.05 | $1 \times 10^4$ | Zubko+96 |
c-p | $\mathrm{C}$ | Amorphous | 1.8 | 0.11 | 800 | Preibisch+93 |
c-gra (gra) | $\mathrm{C}$ graphite | Crystalline | 2.16? | 0.001 | 1000 | Draine+03 |
c-org (org) | $\mathrm{CHON}$ organics | Amorphous | 1.4 | 0.1 | $1 \times 10^5$ | Henning+96 |
fe-c (iron) | $\mathrm{Fe}$ | Metal | 7.87 | 0.1 | $1 \times 10^5$ | Henning+96 |
c_nano | $\mathrm{C}$ nano-diamond | Crystalline | 2.3 | 0.02 | 110 | Mutschke+04 |
fes (tro) | $\mathrm{FeS}$ | Metal | 4.83 | 0.1 | $1 \times 10^5$ | Henning+96 |
sic | $\mathrm{SiC}$ | Crystalline | 3.22 | 0.001 | 1000 | Laor93 |
sio2 (qua) | $\mathrm{SiO_2}$ | Amorphous | 2.65 | 0.0006 | 500 | Kitamura+07 |
cor-c (cor) | $\mathrm{Al_{2}O_3}$ | Crystalline | 4.0 | 0.5 | 40 | Koike+95 |
h2o-w (h2o) | Water ice | Crystalline | 0.92 | 0.04 | $2 \times 10^6$ | Warren+08 |
h2o-a | Water ice | Amorphous | 0.92 | 0.04 | $2 \times 10^6$ | Hudgins+93 |
co2-w (co2) | $\mathrm{CO_2}$ ice | Crystalline | 1.6 | 0.05 | $2 \times 10^5$ | Warren+86 |
nh3-m (nh3) | $\mathrm{NH_3}$ ice | Crystalline | 0.75 | 0.14 | $2 \times 10^0$ | Martonchik+83 |
co-a (co) | $\mathrm{CO}$ ice | Amorphous | 0.81 | 3.8 | 5.8 | Palumbo+06 |
co2-a / c | $\mathrm{CO_2}$ ice | Amorphous / Crystalline | 1.2 | 2.5 | 20 | Gerakines+20 |
ch4-a / c | $\mathrm{CH_4}$ ice | Amorphous / Crystalline | 0.47 | 2.0 | 20 | Gerakines+20 |
ch3oh-a / c | $\mathrm{CH_{3}OH}$ ice | Amorphous / Crystalline | 0.78/1.02 | 2.0 | 24 | Gerakines+20 |
Modules§
- cli
- Command line interface for the
kappa. - components
- This module defines structs, variables and other statically defined
data structures for built-in materials in
kappa. - config
- dhs
- Distribution of Hollow Spheres (DHS) for irregular grains and
low-porosity aggregates.
In order to simulate irregularities in grains (irregular shapes, or the properties of
low-porosity aggregates),
kappaaverages the opacities of grains with an inner empty region, over a range of volume fractions of this inner region between 0 andfmax. The subroutine used to compute the opacities and scattering matrix elements for these structures istoon_ackerman_1981(Toon & Ackerman 1981). For speed, you can set xlim 1e3 or so to set a limit for the size parameter (x = 2πa/λ) wherekappaswitches from DHS tocrate::mie::de_rooij_1984. - fractal
- Computes light scattering properties of randomly oriented fractal dust aggregates by means of the modified mean field theory developed in Tazaki & Tanaka (2018). This code is also capable of computing the light scattering solution based on the Rayleigh-Gans-Debye theory and the Mean field theory.
- geofractal
- io
- Read the
lnkfiles - mie
- Mie scattering calculation
- opac
- The heart of
kappa. This module contains the main routines to compute opacities and scattering matrices. - types
- utils