StellarAtmospheres.markdown

@@ -32,10 +32,9 @@ This describes the general procedure for setting up an individual stellar SED gr
 
 1) Cloudy should already have been set up by following the usual steps described on the [StepByStep](StepByStep) page.
 
-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 
-[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`.
+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 [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`.
 
-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.
+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.   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.  For Cloudy versions prior to C25.00 RC2, 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"*). Later Cloudy versions will find any file with the extension ".ascii" on the search path. 
 
 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).
 
@@ -126,19 +125,22 @@ If you decide not to download all of the stellar grids then the *stars\** tests
 
 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.
 
-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:
-
+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 (the example below shows the output produced by Cloudy versions C25.00 RC2 and later):
 ```
    ... <snip> ...
-table star tlusty Ostar 3-dim <Teff> <log(g)> <log(Z)>
-table star werner <Teff> [ <log(g)> ]
-table star wmbasic <Teff> <log(g)> <log(Z)>
+File name: obstar_merged_3d.ascii: valid,  index file: present.
+Grid parameters: ndim: 3  npar: 3  nmods 1082
+Cloudy command: table star "obstar_merged_3d.ascii" <Teff> <log(g)> <log(Z)>
+   ... <snip> ...
+File name: rauch_h-ni_solar.ascii: valid,  index file: present.
+Grid parameters: ndim: 2  npar: 2  nmods 51
+Cloudy command: table star "rauch_h-ni_solar.ascii"  <Teff> [ <log(g)> ]
    ... <snip> ...
 ```
 
-This shows that the _Tlusty_ O star 3-dimensional grid has three parameters, temperature, gravity, and metallicity.  The *Werner* star grid has two parameters (the square brackets indicate that the second parameter is optional), and the *WMbasic* grid again has three parameters.  This output lists all the grids installed on your computer, excluding any grids that you defined yourself (since Cloudy doesn't know the names you gave to those files).
+This shows that the merged *Tlusty* O- and B-star 3-dimensional grid has three parameters, temperature, gravity, and metallicity.  The *Rauch* grid on the other hand has two parameters (the square brackets indicate that the second parameter is optional).  This output lists all the grids that can be found on the search path (Cloudy versions before C25.00 RC2 would exclude any grids that you defined yourself since Cloudy didn't know the names you gave to those files).
 
-Starting with Cloudy C17 the output of the *table star available* command will also list several forms of the *table star hm05* and *table hm12* commands. 
+Starting with Cloudy C17 the output of the *table star available* command will also list several forms of the *table hm05*, *table hm12*, and *table ks19* commands. 
 These grids differ in certain aspects from the standard stellar atmosphere grids (e.g., they implicitly set the intensity). But they use the same underlying code infrastructure and the data files are fully compatible with standard stellar atmosphere grids. This is why they are included in the output.
 
 The command *table star <grid> list* will list the models contained in that grid. 
@@ -172,23 +174,15 @@ Entries with a number indicate models that are present in the grid. The number i
 
 #### Standard grids in Cloudy
 
-The *table star available* command which was explained in the previous section will not only list the available grids on your computer, it will also show the correct syntax to include a stellar atmosphere in your simulation. Parameters between pointed brackets must be replaced by actual numbers. A valid example would be *table star tlusty Ostar 3-dim 42300 4.22 -0.73* to get a Tlusty O-star model with Teff = 42,300 K, log g = 4.22, and log Z = -0.73. Parameters between square brackets may be omitted. This is only the case for the log g parameter in 2-dimensional grids. If it is omitted, it will default to the highest log g available in the grid. Hence the commands *table star tlusty Ostar Z+0.3 42300 4.75* and *table star tlusty Ostar Z+0.3 42300* 
-are both valid and will both produce the exact same model.
-
+The *table star available* command which was explained in the previous section will not only list the available grids on your computer, it will also show the correct syntax to include a stellar atmosphere in your simulation. Parameters between pointed brackets must be replaced by actual numbers. A valid example would be *table star "obstar_merged_3d.ascii" 42300 4.22 -0.73* to get a Tlusty model with Teff = 42,300 K, log g = 4.22, and log Z = -0.73. For certain standard grids, the filename between double quotes may be replaced by keywords. For instance, the command *table star tlusty OBStar 3-dim 42300 4.22 -0.73* would produce the exact same model as the command shown above. Parameters between square brackets may be omitted. This is only the case for the log g parameter in 2-dimensional grids. If it is omitted, it will default to the highest log g available in the grid. Hence the commands *table star tlusty Ostar Z+0.3 42300 4.75* and *table star tlusty Ostar Z+0.3 42300* are both valid and will both produce the exact same model.
 
 #### User-defined grids (including Starburst99, PopStar, and BPASS grids)
 
-For user-defined grids a slightly different syntax is used to include them in a simulation: *table star "<yourname.mod>" <par1> <par2> ...* 
+For user-defined grids only the syntax with the filename between double quotes is accepted:
+*table star "<yourname.ascii>" <par1> <par2> ...* 
 The number of parameters supplied must exactly match the number of parameters in the grid. 
 For grids that were generated from Starburst99 output, there is only a single parameter: 
-the age. For other grids, there may be more, depending on how the grid was defined by the user.
-
-
-### Using ASCII files directly
-
-We are in the process of removing the need for compiled binary files and allow the code to work directly on the ASCII files. This work is still in progress, but some of the new functionality is already available. Starting with Cloudy version C17 you can use the command *table star "<yourname.ascii>" <par1> <par2> ...* to interpolate directly on the data in the ASCII file and skip the compilation stage. This works well for small grids (roughly 1 to 10 MB in size, depending on the speed of the computer). For large grids, we will likely introduce a new (and optional) form of compilation that is independent of the frequency mesh in Cloudy to help speed up the reading process.
-
-Starting with Cloudy C17 we also support the command *table star "<yourname.ascii>" list* to list the contents of an ASCII file. All other *table star* commands still require the use of compiled binary files.
+the age. For other grids, there may be more, depending on how the grid was defined.
 
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