last reviewed 28-Feb-2007
This documents the data files included in the Cloudy data distribution. Those instructions for setting up the code are on the web site.
Three types of files are present in this directory. The majority of the files are atomic/molecular data files that are needed for the code to operate. There are some input scripts (do an ls on "*.in") that are used to compile various helper files such as stellar atmospheres or types of grains. There are also some user-editable files, with names *.ini, that change how the code operates. These can, for instance, change the continuum resolution or add new entries into the main emission-line output.
The download includes all the files you will need to get Cloudy running. The download does not include the stellar continua file that are needed for the table stars command to work. The web site describes how to set up these continua and this only needs to be done if you want to use the table stars command. Several input files (names like compile*.in) are examples of compiling some of the stellar continua.
It is easy to create new grain tipes. Compiled opacities are already included in the data files (the *.opc files), so nothing need be done if you are happy with the default setup. They would need to be recompiled if you change the energy grid of the code, or wish to use a different grain refractive index or size distribution. Distributed grains are new in C96 and were added in collaboration with Peter van Hoof and Peter G. Martin. These use optical properties for each grain material (the *.rfi files) and size distribution files (the *.szd files) to create grain opacities (the *.opc files) that are a function of grain material and size. The code can then do a more realistic simulation of the grain emission and physics
compilegrains.in - This will compile all the standard grains.
compile1grain.in - example of compiling a single grain type for the pgrains command to use.
vanhoof_grain_model.pdf - is a document written by Peter van Hoof which describes the file formats esed to specify grain properties. You need to study this if you want to create your own grains.
These files specify the size distribution (*.szd) and refractive indices (*.rfi) for the new treatment of grain physics that is used with the pgrains command. The *.opc files give the actual opacities used by the code.
These are a series of files that add commands to the input stream when you run a model. They are added by including an init command that names one of the following files.
c84.ini - makes code behave
more like version 84
fast.ini - this includes several commands that make the code run faster, at the
expense of a less accurate simulation
honly.ini - hydrogen only init
file
hheonly.ini - init file for H,
He only
ism.ini turns off level 2
lines and only includes prominent elements for depleted mixture. NB
This does not
add grains to the mix even though many elements are strongly depleted. This is not consistent, and so grains should be added separately.
pdr_leiden.ini and pdr_leiden_hack.ini are used to compute the PDR models given
in Roellig et al.,
The data file bands_Fe2.dat is used to specify a series of FeII bands that are entered into the main emission line output. These bands are described further in the dat file and in the part of Hazy where FeII is discussed.
The data file bands_continuum.dat is used to define a series of bands. Each band has a lower and upper wavelength range and the code will integrate over these bands and enter a total luminosity into the main emission line output.
These are the default lists of emission lines that can be read into arrays of emission lines by calling cdGetLineList. This is useful when the code is being called as a subroutine of other larger codes, as a way to obtain a list of emission lines whose intensities are to be extracted from the calculation. This process is described in the section of a later part of Hazy on calling Cloudy as a subroutine. These files are meant to be changed by the user.
The files have names LineList*.dat and the end of the filename indicates the purpose. At present the lists are the following:
LineList_BLR.dat - lines seen in the spectra of BLR of AGN
LineList_NLR.dat - lines seen in the spectra of NLR of AGN
LineList_HII.dat - lines for HII Regions
LineList_strong.dat - a minimarl list of emission lines
LineList_PDR.dat - a list of PDR lines
LineList_PDR_H2.dat - a PDR line list with many H2 lines from the large molecule
LineList_HeH.dat - a set of H and He emission lines
LineList_He_like.dat - lines for the He-like iso sequence
Some line wavelengths may change over time as the accuracy of energy levels improve. The "table lines name.dat" command is used to check that that the lines in the file name.dat are still correct. Any line list file that is included here in the data director should also be included in an one of the test cases in the test suite.
The file continuum_mesh.dat contains data the defines the continuum mesh used during a calculation. It is possible to make the continuum have any resolution at all by changing this file. The continuum resolution largely sets the execution time so be careful. The file contains documentation of its use.
The file bands_continuum.dat specifies a series of wavelength bands - the code will enter the total line and continuum emission integrated over these bands.
The files HS_e1b.dat through HS_e8b.dat, and HS_e1a.dat through HS_e8a.dat are from Storey P.J., Hummer D.G.
1995, MNRAS 272, 41
http://adc.gsfc.nasa.gov/adc-cgi/cat.pl?/catalogs/6/6064/
The files mewe_fluor.dat and mewe_nelectron.dat are tables 2 and 3 of the atomic data from Kaastra, J.S., & Mewe, R., 1993, A&AS, 97, 443
The file mewe_gbar.dat is the Mewe data files for g-bar collision strengths.
Three files contain the data needed to set up the large FeII model ion, described in Verner et al. (1999, ApJS 120, 101. The data formats are described following the name of the file and the reference for the data it contains.
This file contains Einstein transition probabilities. The original data sources are given in the header of this file.
lower level number
upper level number
lower level statistical weight
upper level statistical weight
Einstein A coefficient, s**(-1)
Energy, cm**(-1)
type of transition (1 - allowed, 2 - semiforbidden, 3 - forbidden)
This file contains collision data. These data are from Zhang & Pradhan (1995; A&A 293, 953), Bautista (private communication), and the g-bar approximation (Mewe 1972; A&AS 20, 215).
lower level number in Zhang and Pradhan notation, from 1 to 141
upper level number in Zhang and Pradhan notation, from 2 to 142
collision strengths at 20 temperatures,
1e3,3e3,5e3,7e3,1e4,12e3,15e3,17e3,2e4,25e3,3e4,35e3,4e4,45e3,5e4,6e4,7e4,8e
4,9e4,1e5
nn(142) - actual level numbers for each of Zhang and Pradhan levels
This gives the spectroscopic levels sorted in increasing order within the model atom.
collision rates for various projectiles striking H2
H2_coll_H.dat
H2_coll_H2ortho.dat
H2_coll_H2para.dat
H2_coll_He.dat
H2_coll_He_Stancil.dat
H2_coll_Hp.dat
dissociation probabilities for various electronic configurations of H2
H2_dissprob_B.dat
H2_dissprob_B_primed.dat
H2_dissprob_C_minus.dat
H2_dissprob_C_plus.dat
H2_dissprob_D_minus.dat
H2_dissprob_D_plus.dat
energies for various electronic configurations of H2
H2_energy_B.dat
H2_energy_B_primed.dat
H2_energy_C_minus.dat
H2_energy_C_plus.dat
H2_energy_D_minus.dat
H2_energy_D_plus.dat
H2_energy_X.dat
distribution functions for populating levels of H2 following
formation from H-
H2_hminus_deposit.dat
transition probabilities between various configurations of H2
H2_transprob_B.dat
H2_transprob_B_primed.dat
H2_transprob_C_minus.dat
H2_transprob_C_plus.dat
H2_transprob_D_minus.dat
H2_transprob_D_plus.dat
H2_transprob_X.dat
There are three, all with names UTA*.dat. These are the following
UTA_Behar.dat - from Behar et al. 2001, ApJ, 563, 497. These had been
the default for Fe0 through Fe+12.
UTA_Gu06.dat - from Gu et al. ApJ, 641, 1227. These are now the default
for Fe0 through Fe+12.
UTA_Kisielius.dat - from Kisielius et al. MNRAS 344, 696, used for Fe+13
- Fe+15.
level1.dat, the main set of level 1 lines, this file is designed to be edited by humans.
level2.dat, the level 2 lines, do not edit this file!
Visit www.nublado.org for more details and the latest updates.
Good luck!
Gary J. Ferland