Input files
All variable input parameters are controlled by the input files which are bundled in the input folder. These files are:
input.in dust.in species.in gas.in
line.in dust_grid.in e_scat.in exclude.in
Descriptions of the purpose of each file are given below. Details of all variable parameters and where they can be specified are described here.
This file controls all of the fundamental properties of the model including whether the line to be modelled is a doublet, what physics to turn on/off, the number of packets to run, the resolution of the grid, the names of the other input files, the number of threads to run on etc.
This file controls all properties of the dust distribution such as the velocity of the dust, the inner and outer radius of the dust, the dust mass and any clumping parameters. It does not control the dust species/composition or the grain radius distribution.
If dust and gas are coupled, parameters specified in this file will take precedence over equivalent parameters in the gas.in file.
This file allows the user to specify the composition of the dust. It is laid out as:
2
NOTE THAT RELATIVE SPECIES WEIGHTS ARE FRACTIONAL CROSS_SECTIONAL AREAS - OTHER WEIGHTINGS CALCULATED WITHIN THE CODE
id filename weight amin amax power no of divisions
1 'dustData/amC-zb1.nk' 0.8 0.01 0.5 1.0 100
2 'dustData/sil-dlee.nk' 0.2 0.01 1.0 1.0 100
The first line is a number specifying the number of species to include. Each species should be added as a new line with the path to the optical constants given in the second column. Weights must add to 1 and amin, amax and power define the power-law grain radius distribution with amin and amax specified in microns. The number of divisions controls how many unique grain radii will be sampled from the power-law distribution.
This file controls all properties of the gas distribution such as the wavelength(s) of the line or doublet to be modelled, the velocity of the gas, the inner and outer radius of the gas, and the emissivity as a function of the gas density.
If dust and gas are coupled, parameters specified in this file will be overwritten by equivalent parameters in the dust.in file.
If an observed line is being modelled, then the observed data can be specified in this file. The file should be specified in velocity space such that 0 corresponds to the rest wavelength of the line. The first line should specify the number of lines in the file and the error on the fluxes.
586 10.0
-15374.2 570.973
-15332.5 573.568
... ...
Frequently the user will only be interested in the line scaled to arbitrary fluxes. If this is the case, relative fluxes may be used.
If an arbitrary dust distribution is specified then the dust_grid.in file specifies the dust density distribution to use. It should be of the form:
3250 20.0 1.0 !vmax (km/s), R_max (e15cm), v(r) index
# 50 50 50
-2.2449e+16 -2.2449e+16 -2.2449e+16 0.0000e+0
-2.2449e+16 -2.2449e+16 -2.1551e+16 0.0000e+0
... ... ... ...
The first line species vmax (the maximum velocity) at R_max (the maximum radius) and the index of the power-law velocity distribution (in that order).
The second line lists the number of divisions in each axis of the grid.
The rest of the file lists the divisions in x, y and z respectively with a fourth column specifying the relative density of that cell. Note that cells should be specified in increasing order of z then y then x. This file format is compatible with the grid maker developed by Roger Wesson.
Note that the relative densities specified in this grid are scaled to actual densities in the code such that the total dust mass is equal to the dust mass parameter specified in the dust.in file.
This file is only used if the electron scattering flag is turned on in the input.in file. It specifies the electron temperature and Hα luminosity from which the electron density is calculated.
This file is used in the calculation of χ2 when observed data is being used. Any regions of the line to exclude from the calculation of χ2 can be specified here (for example if a broad line is contaminated by narrow line emission).
Note that the dust optical properties referred to by the species.in file are stored in the dustData directory which is installed in /usr/share (Linux) or /usr/local/share at installation. A set of optical constants for a range of species are provided with details as follows:
| Species | File Name | Reference |
|---|---|---|
| MgSiO3 | MgSiO3_Jager2003.nk | Jager, C. et al. 2003, A&A, 408, 193 |
| Mg2SiO4 | Mg2SiO4_Jager2003.nk | Jager, C. et al. 2003, A&A, 408, 193 |
| MgFeSiO4 | MgFeSiO4_Jager1994.nk | Jager, C. et al. 1994, A&A, 292, 641 |
| Mg0.5Fe0.5Si03 | Mg0_5Fe0_5SiO3_Jager1994.nk | Jaeger, C. et al. 1994, A&A, 292, 641 |
| astronomical silicates | sil-dlee.nk | Draine, B. T., & Lee, H. M. 1984, ApJ, 285, 89 |
| astronomical silicates | sil-dlaor.nk | Draine, B. T., & Lee, H. M. 1984, ApJ, 285, 89 |
| amorphous carbon | amC-hann.nk | Hanner 1988, NASA89-13380, 22 |
| amorphous carbon | amC-zb1.nk | Zubko V. et al. 1996, MNRAS, 282, 1321 (BE sample) |
Some dust optical constant files will have a series of numbers in the third line e.g.
Ssil_dl 1400. 3.6 0.588 20.077
These are properties of the dust grains which are, in general, ignored by Damocles. The only parameter of relevance is the second number which is the bulk dust grain density specified in g/cm2 (3.6 g/cm2 in this example).