Update running_caesar and units docs

docs/source/running.rst

@@ -6,30 +6,44 @@ Running CAESAR
    :local:
    :depth: 3
 
+``CAESAR`` offers three basic functions:
+
+[1] Identify galaxies and halos, compute a wide range of properties for each object, and cross-match them;
+
+[2] Compute photometry accounting for the line-of-sight dust extinction to each star in the object; and
+
+[3] Compute the most massive progenitors/descendant for any galaxy or halo in another snapshot [UNDER CONSTRUCTION].
+
 ----
 
 Command Line
 ============
 
-Running ``CAESAR`` has been made extremely simple!  There is a nifty
-command line interface (CLI) which allows you to quickly execute
-``CAESAR`` on a single snapshot.  This is done by:
+Running ``CAESAR``'s first (and primary) functionality is very simple.  
+The command line interface (CLI) allows you to quickly execute
+``CAESAR`` on a single snapshot:
 
 .. code-block:: bash
 
    $> caesar snapshot
 
-This will run the code, an output a file named
-``caesar_snapshot.hdf5``.
+This will run the code, an output a catalog file named ``caesar_snapshot.hdf5``.
+
+CLI OPTIONS
+-----------
+
+* LIST OPTIONS HERE [TODO]
 
 ----
 
 Scripted
 ========
 
-Scripting ``CAESAR`` is also quite simple.  The following is a simple
-example of how one might write a script to perform the same action as
-was done in the above section (Command Line):
+It is also possible to run ``CAESAR`` within a script.  This is 
+useful e.g. for running over multiple snapshots.
+
+Here is a simple example of how one might write a script to perform the same action as
+the CLI command above; it also details what the CLI command does:
 
 .. code-block:: python
 
@@ -51,4 +65,24 @@ was done in the above section (Command Line):
 
    # now we save the output
    obj.save('caesar_snapshot.hdf5')
-   
+  
+member_search() options
+----------------------- 
+
+* **nproc**:  Number of cores for OpenMP parallelization.  This follows the ``joblib`` convention that negative numbers correspond to using all except ``nproc+1`` cores, e.g. ``nproc=-2`` uses all but 1 core. *Default:* 1
+
+* **haloid**:  Source for halo ID's.  *Default:* 'fof'
+
+  * ``haloid='fof'`` uses a 3D Friends-of-Friends (3DFOF) with b=0.2 to identify halos.  
+
+  * ``haloid='snap'`` instead reads halo membership info for each particle from the snapshot variable ``HaloID``.  
+
+* **fof6d_file**:  Stores results of 6DFOF galaxy finder in a file for future retrieval.  If file does not exist, it is created; if it exists, the galaxy membership information is read from this file instead of running the 6DFOF.  *Default:* *None*
+
+* **fsps_bands**:  Triggers optional photometry computation, in specified bands. The ``fsps.list_filters()`` command under ``python-fsps`` lists the available bands.  One can also specify a string that will be matched to all available bands, e.g. ``fsps_bands=['sdss']`` will compute all bands that include the phrase ``sdss``. *Default:* *None*
+
+* **ssp_table_file**: Path to lookup table for FSPS photometry.  If this file does not exist or this keyword is unspecified, it will be generated (this takes some time).  If it exists, ``CAESAR`` will read it in. *Default:* *None*
+
+
+
+

docs/source/units.rst

@@ -43,7 +43,9 @@ or to physical *kpc/h* (using ``obj.simulation.hubble_constant=0.7``):
    In [3]: obj.galaxies[0].radii['total'].to('kpc/h')
    Out[3]: 5.19577490116 kpc/h
 
-That was easy!
+When adding and subtracting quantities, they will be all be converted 
+to the units of the first quantity.  You don't have to worry about
+homegenizing the units yourself!
 
 Working with units
 ******************
@@ -63,8 +65,16 @@ To assign a unit, you can use the yt functions ``YTQuantity`` and ``YTArray``:
    Out[6]: 10000.0 kpc
 
 Similarly, use ``YTArray`` for arrays.  
+
 If you need to get rid of the units and return a value for any reason,
-simply append ``.d`` to the quantity.
+simply append ``.d`` to the quantity:
+
+.. code-block:: python
+
+   In [7]: print(x.d)
+   Out[7]: 10
+   In [8]: print(x.to('kpc').d)
+   Out[8]: 10000.0
 
 For further information and tutorials regarding yt's units
 please visit the `symbolic unit