Overview
Compiling
ancillary files with the *.in input files
The *.ini files
Hummer and Storey Case B data
files
Lists of emission lines for
cdGetLineList
FeII
Star files
Other data files
The resolution of the continuum
energy mesh
last reviewed 25-Dec-2005
This documents the data files included in the Cloudy data distribution. It is meant as a reminder of the purpose of the various files and is not intended as instructions for setting up the code. Those instructions are on the web site.
Three types of files are present in this directory. 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 some user-editable files that change how the code operates. These can change the continuum resolution or add new entries into the main emission-line output. Finally, the majority of the files are atomic/molecular data files that are needed for the code to operate.
Certain sets of ancillary files must be generated before the code will fully function. These include the stellar atmospheres, grain data files, and possibly the opacities. A series of simple input scripts are included here to do this. These input scripts should be executed after Cloudy has been compiled and is fully functional. The following gives the script name and says what it does.
These need to be compiled before the Atlas, Costar, Rauch, and Werner options on the table star command will function. This step does not need to be done if these stellar continua are not needed. The Miscellaneous Commands section of Part I of Hazy explains more about this step - see the section on compiling stellar atmospheres.
compilestars.in - will
compile all the stellar atmospheres - this is the only one that need be done if
all atmospheres are to be used
compile1star.in - will compile
only one of the stellar atmospheres (edit the file to determine which one).
compileatlas.in - will compile
only the atlas stellar atmospheres
compilecostar.in - will
compile only the CoStar stellar atmospheres
compilerauch.in - compile only
the Rauch stellar atmospheres
compilewerner.in - compiles
only the Werner stellar atmospheres
Compiled grain opacities must exist before the pgrains command will function. 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.
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_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
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.
to be completed ......
behar_uta.dat - these data files are from Behar, E., Sako, M, Kahn, S.M.,
2001, ApJ, 563, 497-504 and Behar, E., & Netzer, H., 2002, ApJ, 570, 165-170
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