Cloudy & Associates

Commit 1034cc0c authored by Chatzikos, Marios's avatar Chatzikos, Marios
Browse files

Convert all README files in data/ to Markdown

parent 7e38b820
## Notes
This specifies optional SEDs. One of these files will be used if the command
table SED "filename.sed"
appears.
......@@ -18,7 +20,7 @@ appears then the flux can be given in relative nu f_nu units.
Comments begin with "#" and can occur anywhere in the file.
The list of energies and fluxes are concluded with a field of stars,
for example, *****.
for example, \*\*\*\*\*.
Everything after the field of stars is ignored, so can be used to document the
SED.
......@@ -29,7 +31,7 @@ part of the SED to the low-energy limit of the code using a power law.
The following SED files are now included;
AGN_Jin*.sed
AGN_Jin\*.sed
These are the SEDs summarized in 2020MNRAS.494.5917F and derived by
2012MNRAS.420.1825J and 2017MNRAS.471..706J
......
## Notes
Trapezium cluster massive stars
stellar types listed in Table 1 of Ferland+12
http://adsabs.harvard.edu/abs/2012ApJ...757...79F
That paper used TLusty stellar atmospheres.
Trapezium_Tlusty shows this
Wagle+ in preparation claim that WMbasic gives better fit to [Ne III] lines.
Trapezium_WMbasic shows this
Veusz file and pdf compare these two.
* * *
The original form came from Will Henney in email of
2012 Dec 5. His notes follow:
> Stellar parameters for C, A, D are from Simón-Díaz \cite{2006A&A…448..351S}
> I originally had th1B as a B2V star, which should be cooler than what Gary had (28kK and 10**4.4 Lsun), but I can't find the provenance of this
> actually th1B (BM Ori) is a quintuple system: see SIMBAD record
> SIMBAD says primary is B1V citing \cite{Close:2003}, but that paper does not mention spectral types at all. I suspect this is a confusion with B1, B2, etc being the designations of the quintuple components
> \cite{Weigelt:1999} find a B3 spectral type for the primary (B1) with log L = 3.25 and T = 18000
> B2, B3, and B4 are all lower mass, but B5 has mass similar to B1 accoding to \cite{Weigelt:1999}. However, this must be a mistake: according to \cite{Abt:1991}, who detect B1 and B5 as an eclipsing spectroscopic binary, the mass ratio is 0.3, implying that B5 has a mass of only 2 Msun..
> th1C is a triple system \cite{Lehmann:2010a}
> \cite{Schertl:2003} have broad constraints on the parameters of C2 (dark gray line in their Fig 4). If we take the middle of this range, we get a giantish B3IV star: log L = 3.8, T = 17000, M = 9 Msun, age much less than 1 Myr.
> We can work out the surface gravity:
> g = G M / R2 = G M 4 pi sigma T4 / L = 6.673e-8 9 1.989e33 4 pi 5.6703e-5 17000**4 / 10**3.8 3.82e33 = 2950 cm/s2 => log g = 3.5
> [X] We should check these parameters against \cite{Lehmann:2010a}, who say 12 Msun in their abstract. The article itself is not freely available -grab it when I get back to work
> If we use the same evo tracks as in \cite{Schertl:2003}, then this would imply B2IV with log L = 4.0, T = 21000
> So, after checking out the Lehman article, it seems the 12 Msun is robust, since it is based on orbital solution. The translation to luminosity and Teff is rather more speculative.
> In fact, according to \cite{Kraus:2007}, the companion is O9.5V with Teff = 32000, log L = 4.68. This is also consistent with the Schertl tracks, but it is assuming 15.5 Msun.
> If we instead use 12 Msun as the best mass estimate \cite{Lehmann:2010a}, then we would get log L = 4.2, Teff = 25,000
> Recalculate surface gravity for new parameters
> g = G M / R2 = G M 4 pi sigma T4 / L = 6.673e-8 12 1.989e33 4 pi 5.6703e-5 25000**4 / 10**4.2 3.82e33 = 7322 cm/s2 => log g = 3.86
>
> 2014 May 06, changed some tlusty stars to WMBasic - had used tlusty for all stars originally. WMBasic produces better agreement with H II region optical emission, especially [Ne III]
> Using this new solution for th1C2 changes the broadband ratios by about 5%.
> th1A is a double system
>
> stars = dict(
> th1C = dict(T=39000., g=4.1, L=5.31),
> th1A = dict(T=30000., g=4.0, L=4.45),
> th1D = dict(T=32000., g=4.2, L=4.47),
> th1B = dict(T=18000., g=4.1, L=3.25),
> th1C2 = dict(T=25000., g=3.86, L=4.2),
> )
Trapezium cluster massive stars
stellar types listed in Table 1 of Ferland+12
http://adsabs.harvard.edu/abs/2012ApJ...757...79F
That paper used TLusty stellar atmospheres.
Trapezium_Tlusty shows this
Wagle+ in preparation claim that WMbasic gives better fit to [Ne III] lines.
Trapezium_WMbasic shows this
Veusz file and pdf compare these two.
***************************
The original form came from Will Henney in email of
2012 Dec 5. His notes follow:
Stellar parameters for C, A, D are from Simón-Díaz \cite{2006A&A…448..351S}
I originally had th1B as a B2V star, which should be cooler than what Gary had (28kK and 10**4.4 Lsun), but I can't find the provenance of this
actually th1B (BM Ori) is a quintuple system: see SIMBAD record
SIMBAD says primary is B1V citing \cite{Close:2003}, but that paper does not mention spectral types at all. I suspect this is a confusion with B1, B2, etc being the designations of the quintuple components
\cite{Weigelt:1999} find a B3 spectral type for the primary (B1) with log L = 3.25 and T = 18000
B2, B3, and B4 are all lower mass, but B5 has mass similar to B1 accoding to \cite{Weigelt:1999}. However, this must be a mistake: according to \cite{Abt:1991}, who detect B1 and B5 as an eclipsing spectroscopic binary, the mass ratio is 0.3, implying that B5 has a mass of only 2 Msun..
th1C is a triple system \cite{Lehmann:2010a}
\cite{Schertl:2003} have broad constraints on the parameters of C2 (dark gray line in their Fig 4). If we take the middle of this range, we get a giantish B3IV star: log L = 3.8, T = 17000, M = 9 Msun, age much less than 1 Myr.
We can work out the surface gravity:
g = G M / R2 = G M 4 pi sigma T4 / L = 6.673e-8 9 1.989e33 4 pi 5.6703e-5 17000**4 / 10**3.8 3.82e33 = 2950 cm/s2 => log g = 3.5
[X] We should check these parameters against \cite{Lehmann:2010a}, who say 12 Msun in their abstract. The article itself is not freely available -grab it when I get back to work
If we use the same evo tracks as in \cite{Schertl:2003}, then this would imply B2IV with log L = 4.0, T = 21000
So, after checking out the Lehman article, it seems the 12 Msun is robust, since it is based on orbital solution. The translation to luminosity and Teff is rather more speculative.
In fact, according to \cite{Kraus:2007}, the companion is O9.5V with Teff = 32000, log L = 4.68. This is also consistent with the Schertl tracks, but it is assuming 15.5 Msun.
If we instead use 12 Msun as the best mass estimate \cite{Lehmann:2010a}, then we would get log L = 4.2, Teff = 25,000
Recalculate surface gravity for new parameters
g = G M / R2 = G M 4 pi sigma T4 / L = 6.673e-8 12 1.989e33 4 pi 5.6703e-5 25000**4 / 10**4.2 3.82e33 = 7322 cm/s2 => log g = 3.86
2014 May 06, changed some tlusty stars to WMBasic - had used tlusty for all stars originally. WMBasic produces better agreement with H II region optical emission, especially [Ne III]
Using this new solution for th1C2 changes the broadband ratios by about 5%.
th1A is a double system
stars = dict(
th1C = dict(T=39000., g=4.1, L=5.31),
th1A = dict(T=30000., g=4.0, L=4.45),
th1D = dict(T=32000., g=4.2, L=4.47),
th1B = dict(T=18000., g=4.1, L=3.25),
th1C2 = dict(T=25000., g=3.86, L=4.2),
)
UTA data sets from several papers, cited in *.dat files
UTA_Gu06.dat
UTA_Kisielius.dat
## Notes
UTA data sets from several papers, cited in \*.dat files:
* UTA\_Gu06.dat
* UTA\_Kisielius.dat
------------------
NOTATION FOR THE OPACITY PROJECT DATA, nrb00*
These sets of inner shell transitions are from Nigel Badnell's web site
http://amdpp.phys.strath.ac.uk/tamoc/DATA/PE/
### NOTATION FOR THE OPACITY PROJECT DATA, nrb00\*
These sets of inner shell transitions are from Nigel Badnell's
[web site](http://amdpp.phys.strath.ac.uk/tamoc/DATA/PE).
Badnell et al. (2005) describe the methods.
ADS URL : http://adsabs.harvard.edu/abs/2005MNRAS.360..458B
They were generated as part of the Seaton/Opacity Project and follow their convention.
[Badnell et al. (2005)](https://adsabs.harvard.edu/abs/2005MNRAS.360..458B)
describe the methods.
They were generated as part of the Seaton/Opacity Project and follow their
convention.
The names designate the electron target because the R-matrix
radiative data is generated from an electron collision problem,
taken down to bound states.
The names begin with nrb00 then the isoelectronic sequence of the next higher ion,
followed by the element. The number after the element is related to the charge,
but think of the number
The names begin with ```nrb00```, followed by the isoelectronic sequence of
the next higher ion, followed by the element.
The number after the element is related to the charge, but think of the number
as Roman since target electron charge = Roman recombined.
So, in this convention, data for O VI, which is Li-sequence, would be He since
that is the parent ion, followed by o6. So,
O VI == he_o6ic1-2.dat
```O VI == he_o6ic1-2.dat```.
Data within the file:
IRSL are the (non-energy-order) levels in
```
INDX IRSL CODE S L WJ WNR
```
The first column here is lower level, second upper level.
```
IRSL IRSL N L DEL(RYD) B(SEC) R(SEC) A(SEC): 1
```
B is Einstein up, R is down and A is Auger.
see
http://www.adas.ac.uk/man/appxa-38.pdf
see [here](https://www.adas.ac.uk/man/appxa-38.pdf)
for the rest of the file spec.
The full BibTeX record of that paper is:
```
@ARTICLE{2005MNRAS.360..458B,
author = {{Badnell}, N.~R. and {Bautista}, M.~A. and {Butler}, K. and
{Delahaye}, F. and {Mendoza}, C. and {Palmeri}, P. and {Zeippen}, C.~J. and
......@@ -55,4 +62,4 @@ for the rest of the file spec.
adsurl = {http://adsabs.harvard.edu/abs/2005MNRAS.360..458B},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
```
## Notes
The files in this directory specify standard chemical compositions and,
optionally, grains.
One of these files will be used if the command
```
abundances "filename.abn"
```
appears.
These ```.abn``` files may also specify grains, although grains are not
included by default.
```default.abn``` specifies our default composition.
```default-reference.abn``` is a copy of that file.
The ```\*.dpl``` files specify depletion factors that account for the elements
that are used to build grains.
These may be parsed by the
```
metals deplete "filename.dpl"
```
or
```
metals deplete Jenkins 2009 Fstar=0.5 "filename.dpl"
```
commands.
The default file, described below, will be used if no file appears between the quotes.
* * *
### Specifying abundances
The default is the "solar" composition in ```default.abn```.
It is used if no others are specified.
```default-backup.abn``` is a backup of this file, used to reestablish default
if you change it.
This is a fairly old set of "solar" abundances that we maintain for backwards
compatibility.
To change the default abundance set, copy one of the abundance files (e.g.,
```default.abn``` or ```solar84.abn```) in your working directory, preferrably
with a custom name, edit it at will, and use it with the command
```
abundances "mycustom.abn"
```
#### Available files
* solar84.abn - abundances used by "old solar" option, used in versions 84-94
of the code.
* Other .abn files - see the comments within the file for more details.
The file name gives a good indication of its contents
* * *
### Default depletion files
The command
```
metals deplete
```
by default will read the ISM_CloudyClassic.dpl files.
The format should be clear.
If the element is not specified, then its depletion is set to unity.
The command
```
metals deplete Jankins2009 Fstar
```
reads the ISM_Jenkins09_Tab4.dpl file instead.
If this file is updated or replaced then its current format must be maintained.
Chamani Gunasekera created the spreadsheet from Table 4 of
[Jenkins et al. (2009)](https://ui.adsabs.harvard.edu/abs/2009ApJ...700.1299J).
S does not have data in Table 4, so Chamani used the information provided in
Section 9.
* * *
### Format of the \*.abn files
Comments begin with #.
The file parsing ends with a line containing a field of stars, as
```
***************
```
Everything after the field of stars is ignored, so remaining lines can be used
to document the abundances, in addition to comment lines starting with #.
The grains command can be included.
The abundance files recognize all grain command options.
This makes it possible to include grains in your mix of gas and dust.
Names of elements are followed by the abundance by number relative to hydrogen.
Hydrogen may be in specified, or may not be.
If the abundance of hydrogen is given and is not equal to unity the code will
rescale the abundances by the entered value for hydrogen.
If hydrogen is not specified it is assumed to have an abundance of 1.
All elements heavier than hydrogen are turned off before the ```.abn``` files
are read.
An element is turned on if it appears in the abn file.
If an element is not included in the ```.abn``` file, it will not be included
in the calculation.
* * *
Original coding by Joshua Schlueter, NSF REU 2012 Summer
The files in this directory specify standard chemical compositions and, optionally, grains.
One of these files will be used if the command
abundances "filename.abn"
appears.
These abn files may also specify grains, although grains are not included by default.
default.abn specifies our default composition. default-reference.abn is a copy of that file.
The *.dpl files specify depletion factors that account for the elements that are used to build grains.
These may be parsed by the
metals deplete "filename.dpl"
or
metals deplete Jenkins 2009 Fstar=0.5 "filename.dpl"
commands. The default file, described below, will be used if no file appears between the quotes.
==================================================
default "solar" composition
default.abn gives the default composition used if no others are specified.
default-backup.abn is a backup of this file, use to reestablish default if you change it
This is a fairly old set of "solar" abundances that we maintain for backwards compatibility
To change the default abundance set
replace the default.abn file with your own set of default abundances.
Copy default-backup.abn to default.abn to reestablish our default abundances
Available files
solar84.abn - abundances used by "old solar" option, used in versions 84-94
of the code.
Other .abn files - see the comments within the file for more details.
The file name gives a good indication of its contents
=======================================================
default depletion files
metals deplete
by default will read the ISM_CloudyClassic.dpl files. The format should be clear.
If the element is not specified then its depletion is set to unity.
metals deplete Jankins2009 Fstar
reads the ISM_Jenkins09_Tab4.dpl file. If this file is updated or replaced then
its current format must be maintained.
=======================================================
Format of the *.abn files
comments begin with #
The file parsing ends with a line containing a field of stars, as
****************
Everything after the field of stars is ignored, so remaining lines can be used
to document the abundances, in addition to comment lines starting with #.
The grains command can be included. The abundance files recognize all grain command options.
This makes it possible to include grains in your mix of gas and dust.
Names of elements are followed by the abundance by number relative to hydrogen.
Hydrogen may be in specified, or may not be. If the abundance of hydrogen is
given and is not equal to unity the code will rescale the abundances by the entered value
for hydrogen. If hydrogen is not specified it is assumed to have an abundance
of 1.
All elements heavier than hydrogen are turned off before the abn files are read.
An element is turned on if it appears in the abn file.
If an element is not included in the *.abn file it will not be included in the calculation.
==========================================================
Chamani Gunasekera created the spreadsheet from Table 4 of Jenkins 2009,
https://ui.adsabs.harvard.edu/abs/2009ApJ...700.1299J/abstract
S does not have data in Table 4 so Chamani used the information
provided in Section 9
==========================================================
Original coding by Joshua Schlueter, NSF REU 2012 Summer
## Notes
This directory contains a selection of molecular line lists that were
calculated with the CALPGM program suite written by Herbert Pickett and which
are hosted on the Cologne Database for Molecular Spectroscopy (CDMS) and the
......@@ -7,30 +9,34 @@ permission.
Files with names c???0??.cat come from JPL.
Files with names c???5??.cat come from CDMS.
------------------
* * *
Interfaces to the respective databases can be found here:
http://www.astro.uni-koeln.de/cdms/entries
http://spec.jpl.nasa.gov/ftp/pub/catalog/catdir.html
* [CDMS](https://cdms.astro.uni-koeln.de)
* [JPL](http://spec.jpl.nasa.gov/ftp/pub/catalog/catdir.html)
------------------
Pages giving the partition function for each molecule can be found here:
http://www.astro.uni-koeln.de/site/vorhersagen/catalog/partition_function.html
https://cdms.astro.uni-koeln.de/classic/entries/partition_function.html
http://spec.jpl.nasa.gov/ftp/pub/catalog/catdir.cat
<!--
N/A anymore
These are needed to convert the line intensity given in the CALPGM files into
Einstein-A coefficients. The conversion formulas are here:
http://www.astro.uni-koeln.de/cdms/catalog#equations
-->
------------------
The CALPGM program suite written by Herbert Pickett can be found here:
http://www.astro.uni-koeln.de/cdms/pickett
https://cdms.astro.uni-koeln.de/classic/pickett
------------------
......
by default Cloudy uses the Chianti species in CloudyChianti.ini
when Chianti is used. There are other versions of the Chianiti
## Notes
By default Cloudy uses the Chianti species in CloudyChianti.ini
when Chianti is used. There are other versions of the Chianti
list in this directory.
##--Use--##
......@@ -18,21 +20,18 @@ CloudyChinatiFeKurucz.ini lists Fe 3, 4, and 5 data from Kurucz and others (see
Fe 3:
model Blagrave, K.P.M., Martin, P.G. & Baldwin, J.A. 2006, ApJ, 644, 1006B
energies NIST version 3 Atomic Spectra Database
Ein A's Quinet, P., 1996, A&AS, 116, 573
Ein A s Quinet, P., 1996, A&AS, 116, 573
CS Zhang, H. 1996, 119, 523
Fe 4:
energies NIST version 3 Atomic Spectra Database
Ein A's Garstang, R.H., MNRAS 118, 572 (1958)
Ein A s Garstang, R.H., MNRAS 118, 572 (1958)
CS Berrington and Pelan Ast Ap S 114, 367
Fe 5:
energies NIST version 3 Atomic Spectra Database
Ein A's NIST
Ein A s NIST
CS Shields ApJ 219, 559.
CloudyChiantiAllKurucz.ini is CloudyChiantiAll.ini plus Fe 3, 4, and 5 from Kurucz
CloudyChiantiKuruczOnly.ini is only Fe 3, 4, and 5 from Kurucz
master list.* are original files from Chianti distribution
## Notes
The small H2 model computes the H2 line cooling according to the prescription
of Glover & Abel 2008, MNRAS, 388, 1627. The total cooling at intermediate
densities is computed according to their eqn (39), which combines the cooling
......
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
<meta name="GENERATOR" content="Microsoft FrontPage 6.0">
<meta name="ProgId" content="FrontPage.Editor.Document">
<title>Read me for Cloudy data files</title>
</head>
<body background="clouds.jpg">
<h1>Read me for Cloudy data files</h1>
<p><font size="1">last reviewed
<!--webbot bot="Timestamp" S-Type="EDITED" S-Format="%d-%b-%Y" startspan -->
<!-- #BeginDate format:Am1 -->October 9, 2008<!-- #EndDate -->
<!--webbot bot="Timestamp" endspan i-checksum="15298" --> </font></p>
<hr>
<h2><a name="Overview">Overview</a></h2>
<p>This documents the data files included in the Cloudy data distribution.&nbsp;
Those instructions for setting up the code are on the
<a href="http://www.nublado.org">web site</a>.</p>
<p>Three types of files are present in this directory.&nbsp; </p>
<p><strong><em>*.ini</em></strong> These are files that are used to set up Cloudy. You can change these files to alter the code's default behavior. These can, for instance, change the continuum resolution or add
new entries into the main emission-line output.</p>
<p><strong><em>*.da</em></strong>t These are the foundation atomic/molecular data files that are needed for the code to operate.&nbsp; Do not change these files.</p>
<p><strong><em>*.in</em></strong> These are input scripts that are used to compile various
helper files such as stellar atmospheres or types of grains.&nbsp;</p>
<hr>
<h2><a name="Compiling ancillary files with the *.in input files">Compiling
ancillary files with the *.in input files</a></h2>
<p>The download includes all the files you will need to get Cloudy running.&nbsp;
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.&nbsp;
Several input files (names like compile*.in) are examples of compiling some of
the stellar continua.</p>
<h3>(Possibly) compiling the size-distributed grains</h3>
<p>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.&nbsp; 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.&nbsp; Distributed grains are new in C96 and were added in collaboration
with Peter van Hoof and Peter G. Martin.&nbsp; 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.&nbsp; The code can then do a more realistic simulation of the grain
emission and physics&nbsp;</p>
<p><font size="3"><kbd><strong>compilegrains.in</strong></kbd></font> - This will
compile all the standard grains.</p>
<p><font size="3"><kbd><strong>compile1grain.in</strong></kbd></font> - example
of compiling a single grain type for the <font size="3"><kbd><strong>pgrain</strong></kbd></font>s
command to use.</p>
<p><font size="3"><kbd><strong>vanhoof_grain_model.pdf</strong></kbd></font> -
is a document written by Peter van Hoof which describes the file formats esed to
specify grain
properties.&nbsp; You need to study this if you want to create your own grains.</p>
<h3>The <a name="grain properties">grain properties</a> files, * szd, *.rfi, *.opc</h3>
<p>These files specify the size distribution (*.szd) and refractive indices (*.rfi)
for the new treatment of grain physics that is used with the <font size="3"><kbd><strong> pgrains</strong></kbd></font>
command.&nbsp; The *.opc files give the actual opacities used by the code.</p>
<hr>
<h2>User-defined files that change the code's behavior</h2>
<h3><a name="The *.ini files">The *.ini files</a></h3>
<p>These are a series of files that add commands to the input stream when you
run a model.&nbsp; They
are added by including an <font size="3"><kbd><strong>init</strong></kbd></font>
command that names one of the following files.&nbsp;&nbsp;</p>
<p><font size="3"><kbd><strong>c84.ini</strong></kbd></font> - makes code behave
more like version 84<br>
fast.ini - this includes several commands that make the code run faster, at the
expense of a less accurate simulation<br>
<font size="3"><kbd><strong>honly.ini</strong></kbd></font> - hydrogen only init
file<br>
<font size="3"><kbd><strong>hheonly.ini</strong></kbd></font> - init file for H,
He only<br>
<font size="3"><kbd><strong>ism.ini</strong></kbd></font> turns off level 2
lines and only includes prominent elements for depleted mixture.&nbsp; <i><b>NB</b></i>
This does not
add grains to the mix even though many elements are strongly depleted.&nbsp; This is not consistent, and so grains should be added separately.<br>
pdr_leiden.ini and pdr_leiden_hack.ini are used to compute the PDR models given
in Roellig et al., </p>
<h3>FeII bands in the output</h3>
<p>The data file <i>FeII_bands.ini</i> is used to specify a series of FeII bands that are
entered into the main emission line output.&nbsp; These bands&nbsp; are
described further in the dat file and in the part of Hazy where FeII is
discussed. </p>
<h3>Continuum bands in the output</h3>
<p>The data file <i>continuum_bands.ini</i> is used to define a series of wavelength bands.&nbsp;
Each band has a lower and upper wavelength and the code will integrate
all emission over these bands. The total luminosity or intensity is entered into the main emission line
output.</p>
<h3><a name="Lists of emission lines for cdGetLineList">Emission line lists
for cdGetLineList</a></h3>
<p>These are the default lists of emission lines that can be read into arrays of
emission lines by calling cdGetLineList.&nbsp; 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.&nbsp;
This process is described in the section of a later part of Hazy on calling
Cloudy as a subroutine.&nbsp; These files are meant to be changed by the user.&nbsp; </p>
<p>The files have names LineList*.dat and the end of the filename indicates the
purpose.&nbsp; At present the lists are the following:</p>
<p>LineList_BLR.dat - lines seen in the spectra of BLR of AGN<br>
LineList_NLR.dat - lines seen in the spectra of NLR of AGN<br>
LineList_HII.dat - lines for HII Regions<br>
LineList_strong.dat - a minimarl list of emission lines<br>
LineList_PDR.dat - a list of PDR lines<br>
LineList_PDR_H2.dat - a PDR line list with many H<sub>2</sub> lines from the large molecule<br>
LineList_HeH.dat - a set of H and He emission lines<br>
LineList_He_like.dat - lines for the He-like iso sequence</p>
<p>Some line wavelengths may change over time as the accuracy of energy levels
improve.&nbsp; The &quot;table lines name.dat&quot; command is used to check that that the
lines in the file name.dat are still correct.&nbsp; 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.</p>
<h3><a name="The resolution of the continuum mesh">The resolution of the
continuum mesh</a></h3>
<p>The file <em>continuum_mesh.ini</em> contains data the defines the continuum mesh used
during a calculation.&nbsp; It is possible to make the continuum have any
resolution at all by changing this file.&nbsp; The continuum resolution largely
sets the execution time so be careful.&nbsp; The file contains documentation of
its use.</p>
<hr>
<h2><a name="Hummer and Storey Case B data files">Hummer and Storey Case B data
files</a></h2>
<p>The files HS_e1b.dat through HS_e8b.dat, and HS_e1a.dat through HS_e8a.dat&nbsp; are from Storey P.J., Hummer D.G.
1995, MNRAS 272, 41 <br>
<a href="http://adc.gsfc.nasa.gov/adc-cgi/cat.pl?/catalogs/6/6064/">http://adc.gsfc.nasa.gov/adc-cgi/cat.pl?/catalogs/6/6064/</a></p>
<hr>
<h2>Mewe files</h2>
<p>The files mewe_fluor.dat and mewe_nelectron.dat are tables 2 and 3 of the atomic data from Kaastra, J.S., &amp; Mewe, R., 1993, A&amp;AS, 97, 443</p>
<p>The file mewe_gbar.dat&nbsp; is the Mewe data files for g-bar collision
strengths.</p>
<hr>
<h2><a name="FeII">FeII</a></h2>
<h3>Data files</h3>
<p>Three files contain the data needed to set up the large FeII model ion,
described in Verner et al. (1999, ApJS 120, 101.&nbsp; The data formats are
described following the name of the file and the reference for the data it
contains.</p>
<h3>fe2rad.dat:&nbsp;</h3>
<p>This file contains Einstein transition probabilities.&nbsp; The original
data sources are given in the header of this file.</p>
<p>lower level number<br>
upper level number<br>
lower level statistical weight<br>
upper level statistical weight<br>
Einstein A coefficient, s**(-1)<br>
Energy, cm**(-1)<br>
type of transition (1 - allowed, 2 - semiforbidden, 3 - forbidden)</p>
<h3>fe2col.dat :&nbsp;</h3>
<p>This file contains collision data.&nbsp; These data are from Zhang &amp;
Pradhan (1995; A&amp;A 293, 953), Bautista (private communication), and the
g-bar approximation (Mewe 1972; A&amp;AS 20, 215).</p>
<p>lower level number in Zhang and Pradhan notation, from 1 to 141<br>
upper level number in Zhang and Pradhan notation, from 2 to 142<br>