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Shea Garrison-Kimmel committed a69a8ca

Some changes to documentation, and fixed a typo in an option in gb2irate

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 .. program:: gb2irate
 
+The ``gb2irate`` script converts files in the Gadget binary format to IRATE.
+Use it as ``gb2irate input-file [output-file] [options]``. If `outfile` is not
+specified, it will be the same as infile with '-irate.hdf5' added.
+
+Options:
+
+.. cmdoption:: -2, --type2
+
+    Specifies that the input file was produced with output format set to 2;
+    i.e. that there are labels indicating what each block type is.
+    
+.. cmdoption:: -d
+
+    Interprets the output-file as a directory, and saves the resulting IRATE
+    file in that directory with the default name.
+    
+.. cmdoption:: -i, --inits
+
+    Specifies that the input file is an initial conditions file, in which case
+    gas densities and smoothing lengths are skipped.
+    
+.. cmdoption:: -p, --potential
+
+    Specifies that the gravitational potential is contained in the GADGET file,
+    which is controlled via the Makefile of GADGET2.  Has no effect if --type2
+    is enabled.
+    
+.. cmdoption:: -a, --acceleration
+
+    Specifies that the acceleration is contained in the GADGET file, which is
+    controlled via the Makefile of GADGET2.  No effect if --type2 is enabled.
+
+.. cmdoption:: -s, --entropy
+    
+    Specifies that the rate of change of entropy of gas particles is included
+    in the GADGET file, which is controlled via the Makefile of GADGET2.  Has
+    no effect if --type2 is enabled.
+    
+.. cmdoption:: -t, --timestep
+
+    Specifies that the timestep of each particle is contained in the GADGET
+    file, which is controlled via the Makefile of GADGET2.  Has no effect if
+    --type2 is enabled.
+    
+.. cmdoption:: --t0tree, --gastree
+
+    Tree (either gas, dark, or star) that the particles in the gas group of the
+    GADGET file will be saved under.
+    
+.. cmdoption:: --t1tree, --halotree
+
+    Tree (either gas, dark, or star) that the particles in the halo group of
+    the GADGET file will be saved under.
+
+.. cmdoption:: --t2tree, --disktree
+
+    Tree (either gas, dark, or star) that the particles in the disk group of
+    the GADGET file will be saved under.
+    
+.. cmdoption:: --t3tree, --bulgetree
+
+    Tree (either gas, dark, or star) that the particles in the bulge group of
+    the GADGET file will be saved under.
+
+.. cmdoption:: --t4tree, --startree
+
+    Tree (either gas, dark, or star) that the particles in the star group of
+    the GADGET file will be saved under.
+    
+.. cmdoption:: --t5tree, --bndrytree
+
+    Tree (either gas, dark, or star) that the particles in the boundary group 
+    of the GADGET file will be saved under.
+    
+.. cmdoption:: --t0name, --gasname
+
+    Name of the group that the particles in the gas group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t1name, --haloname
+
+    Name of the group that the particles in the halo group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t2name, --diskname
+
+    Name of the group that the particles in the disk group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t3name, --bulgename
+
+    Name of the group that the particles in the bulge group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t4name, --starname
+
+    Name of the group that the particles in the star group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t5name, --bndryname
+
+    Name of the group that the particles in the boundary group of the GADGET 
+    file is given, under the specified tree.
+
+
+Gadget HDF5 -> IRATE
+--------------------
+
+.. program:: gh52irate
+
+The ``gb2irate`` script converts files in the Gadget HDF5 format to IRATE.
+Use it as ``gh52irate input-file [output-file] [options]``.  If `outfile`
+is not specified, it will be the same as infile with '-irate.hdf5' added.
+
+Options:
+
+.. cmdoption:: --t0tree, --gastree
+
+    Tree (either gas, dark, or star) that the particles in the gas group of the
+    GADGET file will be saved under.
+    
+.. cmdoption:: --t1tree, --halotree
+
+    Tree (either gas, dark, or star) that the particles in the halo group of
+    the GADGET file will be saved under.
+
+.. cmdoption:: --t2tree, --disktree
+
+    Tree (either gas, dark, or star) that the particles in the disk group of
+    the GADGET file will be saved under.
+    
+.. cmdoption:: --t3tree, --bulgetree
+
+    Tree (either gas, dark, or star) that the particles in the bulge group of
+    the GADGET file will be saved under.
+
+.. cmdoption:: --t4tree, --startree
+
+    Tree (either gas, dark, or star) that the particles in the star group of
+    the GADGET file will be saved under.
+    
+.. cmdoption:: --t5tree, --bndrytree
+
+    Tree (either gas, dark, or star) that the particles in the boundary group 
+    of the GADGET file will be saved under.
+    
+.. cmdoption:: --t0name, --gasname
+
+    Name of the group that the particles in the gas group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t1name, --haloname
+
+    Name of the group that the particles in the halo group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t2name, --diskname
+
+    Name of the group that the particles in the disk group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t3name, --bulgename
+
+    Name of the group that the particles in the bulge group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t4name, --starname
+
+    Name of the group that the particles in the star group of the GADGET file
+    is given, under the specified tree.
+    
+.. cmdoption:: --t5name, --bndryname
+
+    Name of the group that the particles in the boundary group of the GADGET 
+    file is given, under the specified tree.
+
+
+EnBiD -> IRATE
+--------------
+
+.. program:: enbid2irate
+
 The ``gb2irate`` script converts files in the tipsy binary format to IRATE.
 Use it as ``gb2irate input-file output-file [options]``. 
 
 Options:
 
 *add options*
+
+
+Gadget Binary + EnBiD -> IRATE
+------------------------------
+
+.. program:: gb-enbid2irate
+
+The ``gb2irate`` script converts files in the tipsy binary format to IRATE.
+Use it as ``gb2irate input-file output-file [options]``. 
+
+Options:
+
+*add options*
+
+
+AHF ASCII -> IRATE
+------------------
+
+.. program:: ahf2irate
+
+The ``gb2irate`` script converts files in the tipsy binary format to IRATE.
+Use it as ``gb2irate input-file output-file [options]``. 
+
+Options:
+
+*add options*
+
+
+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]``. 
+
+Options:
+
+*add options*
+
+
+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]``. 
+
+Options:
+
+*add options*
 parser.add_option("-d",action="store_true",dest="dir",help="Specifies that the given output argument is the output directory, in which case the file is saved in that directory with the default name.  Default = %default",default=False)
 parser.add_option("-i","--inits",action="store_true",dest="ics",help="Specifies that the input file is an initial conditions file, in which case the gas densities and smoothing lengths are assumed to be absent.  Note that if this is incorrectly turned on and there is gas present, the code will fail.  Default = %default.",default=False)
 parser.add_option("-p","--potential",action="store_true",dest="potential",help="Specifies that gravitational potential is included in the Gadget binary file (enabled in the Makefile).  Default = %default",default=False)
-parser.add_option("-a","--acceleartion",action="store_true",dest="accel",help="Specifies that acceleration is included in the Gadget binary file (enabled in the Makefile).  Default = %default",default=False)
+parser.add_option("-a","--acceleration",action="store_true",dest="accel",help="Specifies that acceleration is included in the Gadget binary file (enabled in the Makefile).  Default = %default",default=False)
 parser.add_option("-s","--entropy",action="store_true",dest="entropy",help="Specifies that the rate of change of entropy of gas particles is included in the Gadget binary file (enabled in the Makefile).  Default = %default",default=False)
 parser.add_option("-t","--timestep",action="store_true",dest="timestep",help="Specifies that the timestep of each particle is included in the Gadget binary file (enabled in the Makefile).  Default = %default",default=False)