Commits

Shea Garrison-Kimmel committed f35b438

Finished updating the documentation on command line scripts.

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 .. program:: ahf2irate
 
 The ``ahf2irate`` script converts files in the AHF ASCII format to IRATE.
-Use it as ``gb2irate input-file output-file [options]``. 
+Use it as ``ahf2irate input-file-base [output-file] [options]``.  The input
+file base should be provided as *.AHF_; i.e. everything up to the "halos" or
+"particles" or "profiles" part of the filename.  If `output-file` isn't given,
+it defaults to the input file base with "irate.hdf5" added.
 
 Options:
 
-*add options*
+.. cmdoption:: --particles
+
+    Include particle data from input-file-base + 'particles'.  If given, the
+    data will be saved in a second HDF5 file that will be linked to the
+    main IRATE catalog file.
+    
+.. cmdoption:: --profiles
+
+    Include radial profiles from input-file-base + 'profiles'.  Data will be
+    saved under /Catalog/RadialProfiles/
+    
+.. cmdoption:: -p
+
+    Include both particles and profiles data; i.e. enables both --particles
+    and --particles.
+    
+.. cmdoption:: --nogas
+
+    Enable if AHF was not compiled with -DGAS_PARTICLES or code will fail in
+    trying to combine spatial datasets related to gas and star particles.
+    
+.. cmdoption:: --paramfile=<parameter file>
+
+    Specify an AHF parameter file to be saved as attributes to 
+    /CatalogHeader/AHF.
+    
+.. cmdoption:: -o, --overwrite
+
+    Overwrite the existing output file, if it exists.
+    
+.. cmdoption:: -s, --size
+
+    Maximum size that particle data will be in memory before writing to a file,
+    in GB.  Note that this only has an effect if using HDF5 1.8; otherwise,
+    all the particles will be read before anything is written.
+    
+.. cmdoption:: --hdf5-16
+
+    Force the usage of HDF5 1.6 API, even if 1.8 is found.  At present, the
+    benefits that 1.8 provides aren't working, so this is always enabled.
 
 
 AHF Particles -> IRATE
 
 .. program:: ahfparticles2irate
 
-The ``gb2irate`` script converts files in the tipsy binary format to IRATE.
-Use it as ``gb2irate input-file output-file [options]``. 
+The ``ahfparticles2irate`` script reads an AHF _particles file, saves it to
+an HDF5 file, then links the resulting datasets to an existing IRATE catalog
+file. Use it as 
+``ahfparticles2irate particle-file irate-file [output-file] [options]``.  If
+`output-file` isn't specified, it defaults to irate-file + '-particles.hdf5'.
 
 Options:
 
-*add options*
+.. cmdoption:: -o, --overwrite
+
+    Overwrite the existing output file, if it exists.
+    
+.. cmdoption:: -s, --size
+
+    Maximum size that particle data will be in memory before writing to a file,
+    in GB.  Note that this only has an effect if using HDF5 1.8; otherwise,
+    all the particles will be read before anything is written.
+    
+.. cmdoption:: --hdf5-16
+
+    Force the usage of HDF5 1.6 API, even if 1.8 is found.  At present, the
+    benefits that 1.8 provides aren't working, so this is always enabled.
 
 
 Rockstar -> IRATE
 
 .. program:: rockstar2irate
 
-The ``gb2irate`` script converts files in the tipsy binary format to IRATE.
-Use it as ``gb2irate input-file output-file [options]``. 
+The ``rockstar2irate`` script converts Rockstar halo catalogs to IRATE catalog
+files.  Use it as 
+``rockstar2irate input-file [output-file] [format] [options]``. If
+`output-file` isn't specified, it defaults to input-file with '-irate.hdf5'
+added.
 
 Options:
 
-*add options*
+.. cmdoption::  -b
+
+    Specifies that the input file is a Rockstar binary file.
+    
+.. cmdoption::  -a
+
+    Specifies that the input file is a Rockstar ASCII file.
+    
+.. cmdoption::  -o
+
+    Overwrite the existing IRATE catalog file, if one exists.
+    
+.. cmdoption::  -q
+
+    Run in quiet mode, with minimal output to the screen.