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## Using stellar SEDs in C07.02 and later
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### Future changes
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In Cloudy versions up to and including C17, the code was set up in such a way that in order to compile the stellar atmosphere grids they had to reside in the local directory. On the other hand, when you wanted to use the compiled grids, they had to be in the data directory. So either you had to move the compiled files into the data directory, or place the downloaded ascii files in the data directory in the first place. After C17, the rules for searching input files will be the same for all commands, which includes the stellar grids. This means that both during compilation and when using the grids during a run, the files are searched along the entire search path. That implies that during compilation the code will find ascii files in other locations (such as the data directory) as long as they are on the search path. On the other hand, during a run the code will be able to use a compiled atmosphere grid that is stored in the local directory. This gives the user more freedom to organize the files.
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After C17 another important change will take effect. All TABLE STAR commands will work directly on the ascii file and the compiled binary *.mod files will no longer serve any purpose. This implies that the ascii files need to be stored somewhere along the data search path. Compiling ascii files is still supported (albeit optional) and now produces index files with names ending in *.idx. These help speed up reading the ascii files and are strongly recommended for large grids. Note that despite the simple appearance of these files, they are (in principle) still platform dependent. The big advantage of this setup is that there is no longer a dependence on the frequency mesh, so _you do not need to recompile the ascii grids when you change the frequency mesh_. Compiling grids that are not in the standard Cloudy format (e.g. Starburst99 output) is still mandatory.
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The page below describes the situation as it exists for C17. The changes described above will take effect once the next major release is available.
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------
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## Overview of the stellar SEDs
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... | ... | @@ -23,51 +12,51 @@ This page describes how to set up the grids of stellar spectral energy distribut |
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[Peter van Hoof](http://homepage.oma.be/pvh/) wrote this part of Cloudy and is the maintainer. Please post questions, comments, and suggestions for new stellar atmosphere grids on the
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[Cloudy discussion board](https://cloudyastrophysics.groups.io/g/Main).
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This page outlines the general method for setting up individual stellar atmosphere grids. Some of the grids are very large and accessing them as ascii files would be slow. They are "compiled" to create direct access binary files. These files, with names ending in "mod", are the files that Cloudy actually uses. These files are hardware-dependent, so if you plan to use the code on more than one platform you may need to create separate binary files for each platform. An important exception would be 32-bit and 64-bit versions of the same hardware, for those platforms the binary files are compatible. Most importantly for IA32 and AMD64/EM64T platforms, the binary files are compatible.
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The following sections describe how to download the ASCII stellar SED files. Each grid of stellar SEDs, along with a link to the paper or web site describing it, is given below. *If you use one of these grids in a publication it is very important that you properly cite the original paper describing that grid!* It is intellectually lazy, and deprives the original authors of their proper citation, to simply state that you used an SED that was available in Cloudy.
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The following sections describe how to download the original ASCII stellar SED files. These files should be placed in the Cloudy data directory.
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Each grid of stellar SEDs, along with a link to the paper or web site describing it, is given below. *If you use one of these grids in a publication it is very important that you properly cite the original paper describing that grid!* It is intellectually lazy, and deprives the original authors of their proper citation, to simply state that you used an SED that was available in Cloudy.
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### Note for older Cloudy versions
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To avoid needless repetition, we will assume after this section that you are using Cloudy C22 or newer. The main differences between these and older Cloudy versions are briefly described here.
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Some of the grids are very large and accessing them can be slow. They can be "compiled" to speed up the process. How this is done depends on the Cloudy version. In Cloudy versions C17 and older, compiling these grids resulted in files with names ending in ".mod". These binary files were platform-dependent. Compiling the grids was mandatory and the resulting *.mod files were the ones that needed to be placed in the Cloudy data directory. Starting with Cloudy version C22 all this changed. The code now works directly on the ASCII files and compiling them became optional. The latter now results in files with names ending in ".idx". These help speed up reading the ASCII file and are recommended for large ASCII files. Despite their simple appearance, these idx files are still (in principle) platform-dependent. Both the *.ascii files and the *.idx files (if you chose to create them) need to be placed in the Cloudy search path. An added advantage of the new setup is that there is no longer a dependence on the frequency mesh, so _you do not need to recompile the ASCII grids when you change the frequency mesh_ (this was mandatory in Cloudy versions C17 and older). Compiling grids that are not in the standard Cloudy format (e.g. Rauch grids or Starburst99 output) is still mandatory.
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Since Cloudy release C22 the policy for reading data files (including stellar atmosphere grids) has been unified and made more flexible. The concept of the Cloudy data directory has been generalized to the Cloudy search path. See the section titled "The Search Path for Input Files" in Hazy 1 for more details. When the Cloudy search path is mentioned below, it should be implicitly replaced with the Cloudy data directory for Cloudy versions C17 and older.
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For Cloudy versions C17 and older, modify all commands that use explicit file names between double quotes by replacing the .ascii filename extension with .mod (except for the *compile stars* command, which always works on an .ascii file).
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### Procedure for setting up a stellar SED grid
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This describes the general procedure for setting up an individual stellar SED grid. The method is basically the same for all the grids.
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1) Cloudy should already have been set up if you got to this page by following the usual steps. I assume you used the recommended directory structure and that the atomic data files are located in a directory *data* and that Cloudy can be run from any directory.
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2) Download the files from the individual websites listed below. *It is OK to skip the grids you don't need* (or to skip all of them if you are not going to use stellar atmosphere files at all). Cloudy will work just fine without them as long as you are not explicitly requesting a stellar atmosphere from a missing grid. Some grids are on the original author's web site, while other files are located in the "stars" directory below the main Cloudy
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[data site](https://data.nublado.org/).
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Links are given at the top of each of the sections describing the grids below. Most files have names that end in ASCII. An example is *ostar2002_p03.ascii* (a file from the Tlusty web site). The downloaded grid files should be stored directly in the data directory. Most files have been compressed with gzip. Explode the ASCII files using the command `gunzip *.gz`. If you downloaded any of the Rauch grids, explode the tarballs with `tar xfz *.tgz`.
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1) Cloudy should already have been set up by following the usual steps described on the [StepByStep](StepByStep) page.
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3) Execute Cloudy with the single command *compile stars* in the data directory containing the downloaded ASCII files. I would do this by first creating a file *compile.in* containing only this command and then running the code as `cloudy.exe -r compile`, which directs its output to *compile.out*.
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2) Download the SED files from the individual websites listed below. *It is OK to skip the grids you don't need* (or to skip all of them if you are not going to use stellar atmosphere files at all). Cloudy will work just fine without them as long as you are not explicitly requesting a stellar atmosphere from a missing grid. Some grids are on the original author's web site, while other files are located in the "stars" directory below the main Cloudy
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[data site](https://data.nublado.org/). Links are given at the top of each of the sections below describing the grids. Most files have names that end in "ascii". An example is *ostar2002_p03.ascii* (a file from the Tlusty web site). The downloaded grid files should be stored in the Cloudy search path. Most files have been compressed with gzip or xz. Explode the ASCII files using the command `gunzip *.gz` or `xz -d *.xz` as needed. If you downloaded any of the Rauch grids, explode the tarballs with `tar xfz *.tgz`.
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4) One mod file will be created for each of the downloaded ASCII files.
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An example is *ostar2002_p03.mod* which is created from the file *ostar2002_p03.ascii*.
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Keep the original ASCII files as you will need them in the next major Cloudy release. If you decide to change the resolution of the Cloudy frequency grid, you will need to recompile the stellar atmosphere files. Alternatively, you can compress the ASCII files after compilation to save disk space. If you downloaded any of the Rauch grids you will probably want to remove the individual SED files with the command ```rm -f *0.1```.
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There may be a great many of them, and they are still contained in the tarballs you downloaded.
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3) In most cases this step is optional, except when you downloaded files that are not in the native Cloudy format (i.e. files that do not end with the extension ".ascii"). Some of the grids are very large and accessing them can be slow. They can be "compiled" to speed up the process. Execute Cloudy with the single command *compile stars* in the directory where you placed the downloaded files. A convenient way to do this is running the code with the command `cloudy.exe -e compile stars`. One idx file will be created for each of the downloaded files. An example is *ostar2002_p03.idx* which is created from the file *ostar2002_p03.ascii*. Keep the original ASCII files as you will need them too. If you downloaded any of the Rauch grids you will probably want to remove the individual SED files with the command ```rm -f *0.1```. There may be a great many of them, and they are still contained in the tarballs you downloaded. Some grids are not recognized by Cloudy (e.g., the BPASS grids) in which case you need to use an explicit filename on the command (e.g., *compile stars "BPASSv2.3_imf135_300.a-02_burst_binary.ascii"*). Note that Cloudy will find input files on the entire search path, but output files will always be written in the local directory, regardless of where the corresponding input file resided. It is a good idea though to keep the ASCII and idx files together.
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5) You can add grids later (if newer ones become available, or if you change your mind about grids you initially skipped). Download the new files, place them in the data directory and simply go through the same procedure outlined above. Cloudy will skip any grids for which it finds a valid mod file in the data directory (i.e., it will skip any grids that are already compiled).
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4) You can add grids later (if newer ones become available, or if you change your mind about grids you initially skipped). Download the new files, place them in the search path and simply go through the same procedure outlined above. Cloudy will skip any grids for which it finds a valid idx file in the search path (i.e., it will skip any grids that are already compiled).
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### Installing Starburst99 grids
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The Starburst99 web page is [here](http://www.stsci.edu/science/starburst99/). This uses the common code base for stellar atmosphere grids and therefore need to be compiled just like any other grid. The first step is to take the spectrum that was generated by Starburst99 (called *_xxx.spectrum*_) and give it a name that ends in *_.stb99*_. An example of the Starburst99 format that Cloudy expects is given [here](https://data.nublado.org/stars/starburst99.stb99.gz). You can compile the file by giving the single Cloudy command *compile stars "<yourname.stb99>"*. You should replace *<yourname.stb99>* by the name you chose and make sure it is surrounded by double quotes (as is always the case when you include filenames in Cloudy input).
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Cloudy will then create two files: *yourname.ascii* and *yourname.mod*. Keep the ASCII file as you will need it in the next version of Cloudy. To use the Starburst99 grid in a simulation, simply include the command *table star "<yourname.mod>" <age>*.
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The Starburst99 web page is [here](http://www.stsci.edu/science/starburst99/). The Starburst99 output needs to be converted into the standard Cloudy format and therefore needs to be compiled. The first step is to take the spectrum that was generated by Starburst99 (called *_xxx.spectrum*_) and give it a name that ends in *_.stb99*_. An example of the Starburst99 format that Cloudy expects is given [here](https://data.nublado.org/stars/starburst99.stb99.gz). You can compile the file by giving the single Cloudy command *compile stars "<yourname.stb99>"*. You should replace *<yourname.stb99>* by the name you chose and make sure it is surrounded by double quotes (as is always the case when you include filenames in Cloudy input).
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Cloudy will then create two files: *yourname.ascii* and *yourname.idx*. Both files are needed by Cloudy.
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Use the starburst file by specifying the file name and the log of the age.
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An example might be
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*table star "starburst.mod" age 6.7*
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An example might be *table star "starburst.ascii" age 6.7*
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The age will have whatever units are in the original Starburst99 file. The default is years.
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The procedure for using Starburst99 grids was changed in c07.02. It was a special command in previous versions.
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The procedure for using Starburst99 grids was changed in C07.02. It was a special command in previous versions.
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### Installing PopStar grids
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The PopStar models can be obtained [here](http://www.fractal-es.com/PopStar/).
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Click on "Download Models" on the left-hand side, and then you need to download 1 or more of the zip files in the column "Spectra zip file" on the right-hand side. Models are present for different initial mass functions (IMFs) and metallicities (Z).
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You can choose to convert a single combination of IMF and Z into a 1-dimensional grid allowing interpolation in age, or combine several runs with the _same_ IMF but different Z values into a 2-dimensional grid allowing interpolation in age as well as log(Z) (*note*: the latter option is *only* supported from c10 onwards). The first step is to take an empty (temporary) directory and unzip the files you downloaded in that directory. Next, you run the script [convert_popstar.pl](https://data.nublado.org/stars/convert_popstar.pl) (make sure that the file has execute permission) and redirect the output to a file with a name of your choosing ending in *.ascii*.
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This page describes the procedure for the 2009 grids. The PopStar models can be obtained [here](http://www.fractal-es.com/PopStar/). Next select "PopStar2009" and
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click on "Download Models" on the left-hand side. Then you need to download 1 or more of the zip files in the column "Spectra zip file" on the right-hand side. Models are present for different initial mass functions (IMFs) and metallicities (Z).
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You can choose to convert a single combination of IMF and Z into a 1-dimensional grid allowing interpolation in age, or combine several runs with the _same_ IMF but different Z values into a 2-dimensional grid allowing interpolation in age as well as log(Z) (the latter option is only supported from C10 onwards). The first step is to take an empty (temporary) directory and unzip the files you downloaded in that directory. Next, you run the script [convert_popstar.pl](https://data.nublado.org/stars/convert_popstar.pl) (make sure that the file has execute permission) and redirect the output to a file with a name of your choosing ending in *.ascii*.
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An example for a single zip file would be:
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```
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... | ... | @@ -78,20 +67,20 @@ chmod +x convert_popstar.pl |
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convert_popstar.pl > sp-sal1-z0200.ascii
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```
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Next, you start up the Cloudy executable and type:
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You can optionally compile this grid with:
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```
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compile star "sp-sal1-z0200.ascii"
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```
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This will produce a file "sp-sal1-z0200.mod" which you need to move to your Cloudy data directory. After you have done this, you can delete the temporary directory if you wish. Now the grid can be used as described in the next section. The procedure for a 2-dimensional grid is very similar. You need to download and unzip multiple files, but apart from that, the procedure is exactly the same. The conversion script will automatically detect that multiple metallicities are present and will alter the resulting *.ascii* file accordingly. It is not necessary to download all metallicities belonging to a certain IMF, you can also use a subset if you wish. The script will extract the stellar flux *only*.
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This will produce a file "sp-sal1-z0200.idx". Both the files "sp-sal1-z0200.ascii" and "sp-sal1-z0200.idx" (if it was created) should be in the Cloudy search path. After you have done this, you can delete the temporary directory if you wish. Now the grid can be used as described in the next section. The procedure for a 2-dimensional grid is very similar. You need to download and unzip multiple files, but apart from that, the procedure is exactly the same. The conversion script will automatically detect that multiple metallicities are present and will alter the resulting *.ascii* file accordingly. It is not necessary to download all metallicities belonging to a certain IMF, you can also use a subset if you wish. The script will extract the stellar flux *only*.
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The PopStar grids are described in [Molla et al. (2009)](http://cdsads.u-strasbg.fr/abs/2009MNRAS.398..451M).
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### Installing BPASS grids
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The BPASS (Binary Population and Spectral Synthesis) stellar population synthesis models are available [here](http://bpass.auckland.ac.nz/index.html). We support the v2.0 through v2.3 releases. These have been converted into Cloudy format and can be downloaded [here](http://data.nublado.org/stars/bpass). The grids are available for several different choices of the initial mass function. There are grids for either an instantaneous starburst of 1e6 Msol, or continuous star formation of 1 Msol/yr lasting 1e6 years (the latter only for v2.0). Each of these releases has separate grids for single-star and binary-star evolution. Grids are available for a range of metallicities ranging from Z=0.001 to 0.040 (v2.0) or Z=0.00001 to 0.040 (all later versions). The first step is to download the compressed ASCII file. Below we will use the v2.3 release as an example.
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The BPASS (Binary Population and Spectral Synthesis) stellar population synthesis models are available [here](http://bpass.auckland.ac.nz/index.html). We support the v2.0 through v2.3 releases. These have been converted into Cloudy format and can be downloaded [here](https://data.nublado.org/stars/bpass). The grids are available for several different choices of the initial mass function. There are grids for either an instantaneous starburst of 1e6 Msol, or continuous star formation of 1 Msol/yr lasting 1e6 years (the latter only for v2.0). Each of these releases has separate grids for single-star and binary-star evolution. Grids are available for metallicities ranging from Z=0.001 to 0.040 (v2.0) or Z=0.00001 to 0.040 (all later versions). The first step is to download the compressed ASCII file. Below we will use the v2.3 release as an example.
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```
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<download BPASSv2.3_imf135_300.a+00_burst_single.ascii.xz>
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```
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In the file name "burst" refers to the single starburst models and "cont" to the continuous star formation models. Furthermore, "single" refers to the single-star evolution models and "binary" to the binary-star evolution models.
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For Cloudy versions C17 and older, the ASCII files must be converted into binary files by starting Cloudy and typing:
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The ASCII files can be compiled by starting Cloudy and typing:
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```
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compile stars "BPASSv2_imf135_100_burst_single.ascii"
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```
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and similar for each file that you downloaded. This step is optional for Cloudy versions C22 and later, but still recommended as the ASCII files are large and compiling them will speed up reading them. For Cloudy versions C17 and older, you now need to move the resulting *.mod files into the data directory. For Cloudy versions C22 and later, you need to move the *.ascii and *.idx (if present) files into the data directory. After this, they can then be used in Cloudy.
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This step is optional for Cloudy versions C22 and later, but still recommended as the ASCII files are large and compiling them will speed up reading them. Now you need to move the *.ascii and *.idx (if present) files into the search path. After this, they can then be used in Cloudy.
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These are 2D grids allowing interpolation in age and metallicity. You can produce a mix of single and binary stars using e.g.:
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... | ... | @@ -117,13 +106,11 @@ table star "BPASSv2.3_imf135_300.a+00_burst_binary.ascii" 2e8 -1.8 |
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intensity <yyy>
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```
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For Cloudy versions C17 and older, you need to replace the ".ascii" file name extension with ".mod".
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The BPASS v2.3 release is described in [Byrne et al. (2022)](https://ui.adsabs.harvard.edu/abs/2022MNRAS.512.5329B/abstract) and [Stanway & Eldridge (2018)](https://ui.adsabs.harvard.edu/abs/2018MNRAS.479...75S/abstract). For the older releases, each [subdirectory](http://data.nublado.org/stars/bpass) contains a README file that contains instructions how to cite the release.
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### Installing your own grids
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It is possible to install your own atmosphere grids. For this you need to create your own ASCII file. Instructions for this are included in the file [vanhoof_atmosphere_grids.pdf](../tree/master/trunk/docs/vanhoof_atmosphere_grids.pdf?format=raw) which is also included as Appendix B of Hazy 1 (starting from c10.00). Once you created the ASCII file, compiling it and using it is quite similar to Starburst99 files. To compile, issue the command *compile stars "<yourname.ascii>"*. To use it, issue the command *table star "<yourname.mod>" <par1> <par2> ...* (the number of parameters here should exactly match the number of parameters you defined in the grid).
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It is possible to install your own atmosphere grids. For this you need to create your own ASCII file. Instructions for this are given in Appendix B of Hazy 1 (starting from C10.00). Once you created the ASCII file, compiling it and using it is quite similar to Starburst99 files. To (optionally) compile, issue the command *compile stars "<yourname.ascii>"*. To use it, issue the command *table star "<yourname.ascii>" <par1> <par2> ...* (the number of parameters here should exactly match the number of parameters you defined in the grid).
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### If you don't set up all the stellar SED grids
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... | ... | @@ -139,7 +126,7 @@ If you decide not to download all of the stellar grids then the *stars\** tests |
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Two commands will generate information about available grids. You can use these to document which grids are installed after the code has been set up.
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The command *_table star available*_ will list the available grids with parameters. Some of the lines of the output it generates on my system appear as follows:
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The command *_table star available*_ will list the available grids with parameters. Some of the lines of the output it generates may look as follows:
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```
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... <snip> ...
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... | ... | @@ -177,7 +164,7 @@ Teff\lg g| 3.00 3.25 3.50 3.75 4.00 4.25 4.50 4.75 |
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55000 | -- -- -- -- 66 67 68 69
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```
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Entries with a number indicate models that are present in the grid. The number is the sequence number in the input file. The command will also work for user-defined grids by supplying the name of the mod file between quotes, e.g. *table star "usergrid.mod" list*.
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Entries with a number indicate models that are present in the grid. The number is the sequence number in the input file. The command will also work for user-defined grids by supplying the name of the ASCII file between quotes, e.g. *table star "usergrid.ascii" list*.
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### Using the grids
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... | ... | @@ -189,7 +176,7 @@ The *table star available* command which was explained in the previous section w |
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are both valid and will both produce the exact same model.
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#### User-defined grids (including Starburst99 and PopStar grids)
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#### User-defined grids (including Starburst99, PopStar, and BPASS grids)
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For user-defined grids a slightly different syntax is used to include them in a simulation: *table star "<yourname.mod>" <par1> <par2> ...*
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The number of parameters supplied must exactly match the number of parameters in the grid.
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... | ... | @@ -296,7 +283,7 @@ The [Tlusty](http://tlusty.oca.eu/) code is maintained by Ivan Hubeny & Thierry |
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There are 11 sets of O star SEDs compiled from the [OSTAR2002 grid](http://tlusty.oca.eu/Tlusty2002/tlusty-frames-OS02.html) with names "ostar2002_*.ascii.gz". They are described in the reference [Lanz, T., & Hubeny, I. 2003, ApJS, 146, 417](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?2003ApJS..146..417L&db_key=AST). These SEDs are used by the *stars_ostar2002\*.in* simulations in the test suite.
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At the time of this writing, the B star grid is still under construction. There are currently 7 sets of B star SEDs compiled from the [BSTAR2006 grid](http://tlusty.oca.eu/Tlusty2002/tlusty-frames-BS06.html) with names *bstar2006\*.ascii.gz*. They are described in the reference [Lanz, T., & Hubeny, I. 2007, ApJS, 169, 83](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2007ApJS..169...83L&db_key=AST&data_type=HTML&format=&high=45d30ec84024291). These SEDs are used by the *stars_bstar2006\*.in* simulations in the test suite.
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There are 7 sets of B star SEDs compiled from the [BSTAR2006 grid](http://tlusty.oca.eu/Tlusty2002/tlusty-frames-BS06.html) with names *bstar2006\*.ascii.gz*. They are described in the reference [Lanz, T., & Hubeny, I. 2007, ApJS, 169, 83](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2007ApJS..169...83L&db_key=AST&data_type=HTML&format=&high=45d30ec84024291). These SEDs are used by the *stars_bstar2006\*.in* simulations in the test suite.
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Starting with the C10 release of Cloudy, we have added support for merged OSTAR2002/BSTAR2006 grids. The resulting grids have a temperature coverage from 15 to 55 kK. In the overlap region between 27.5 and 30 kK, the BSTAR2006 models have been adopted. The merged grids have been produced for all metallicities supported by the BSTAR2006 grid. They have names *obstar\_merged\*.ascii.gz*. When you use one of these grids, you should cite both [Lanz, T., & Hubeny, I. 2003, ApJS, 146, 417](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?2003ApJS..146..417L&db_key=AST) and [Lanz, T., & Hubeny, I. 2007, ApJS, 169, 83](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2007ApJS..169...83L&db_key=AST&data_type=HTML&format=&high=45d30ec84024291).
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These SEDs are used by the *stars\_obstar\_merged\*.in* simulations in the test suite.
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... | ... | @@ -309,7 +296,7 @@ In general, you will not need all the files listed on the Tlusty website (unless |
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[wmbasic.ascii.gz](https://data.nublado.org/stars/wmbasic.ascii.gz).
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The WMbasic code is maintained by [Adi Pauldrach](http://www.usm.uni-muenchen.de/people/adi/Programs/Contact.html) who has a home page [here](http://www.usm.uni-muenchen.de/people/adi/adi.html). He computed a small grid of non-LTE, line-blanketed, and wind-blanketed hot stars with metallicities log Z = 0.0 and -0.3. The original grid of models is [here](http://www.usm.uni-muenchen.de/people/adi/Models/Model.html) and is described in
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The WMbasic code was maintained by [Adi Pauldrach](http://www.usm.uni-muenchen.de/people/adi/Programs/Contact.html) who still has a home page [here](http://www.usm.uni-muenchen.de/people/adi/adi.html). He computed a small grid of non-LTE, line-blanketed, and wind-blanketed hot stars with metallicities log Z = 0.0 and -0.3. The original grid of models is [here](http://www.usm.uni-muenchen.de/people/adi/Models/Model.html) and is described in
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[Pauldrach et al., 2001](http://www.usm.uni-muenchen.de/people/adi/Programs/Summary.html#History). The grid has been rebinned to create the file that is available above.
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This is a three-dimensional grid so you must specify temperature, log g, and log Z, in that order.
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