update documentation

documentation/_static/overview.rst

@@ -184,16 +184,17 @@ available, called ``bfps``, that you can execute.
 Just executing it will run a small test DNS on a real space grid of size
 :math:`32 \times 32 \times 32`, in the current
 folder, with the simulation name ``test``.
-So, open a console, and type ``bfps NavierStokes``:
+So, open a console, and type ``bfps DNS NSVE``:
 
 .. code:: bash
 
     # depending on how curious you are, you may have a look at the
     # options first:
     bfps --help
-    bfps NavierStokes --help
+    bfps DNS --help
+    bfps DNS NS --help
     # or you may just run it:
-    bfps NavierStokes
+    bfps DNS NSVE
 
 The simulation itself should not take more than a few seconds, since
 this is just a :math:`32^3` simulation run for 8 iterations.
@@ -205,9 +206,9 @@ the following:
 .. code:: python
 
     import numpy as np
-    from bfps import NavierStokes
+    from bfps import DNS
 
-    c = NavierStokes(
+    c = DNS(
             work_dir = '/location/of/simulation/data',
             simname = 'simulation_name_goes_here')
     c.compute_statistics()
@@ -223,7 +224,7 @@ the following:
             data_file['iteration'].value*c.parameters['dt'] / c.statistics['Tint'],
             data_file['iteration'].value*c.parameters['dt'] / c.statistics['tauK']))
 
-:func:`compute_statistics <bfps.NavierStokes.NavierStokes.compute_statistics>`
+:func:`compute_statistics <bfps.DNS.DNS.compute_statistics>`
 will read the data
 file generated by the DNS, compute a bunch of basic statistics, for
 example the Taylor scale Reynolds number :math:`R_\lambda` that we're
@@ -233,7 +234,7 @@ What happens is that the DNS will have generated an ``HDF5`` file
 containing a bunch of specific datasets (spectra, moments of real space
 representations, etc).
 The function
-:func:`compute_statistics <bfps.NavierStokes.NavierStokes.compute_statistics>`
+:func:`compute_statistics <bfps.DNS.DNS.compute_statistics>`
 performs simple postprocessing that may however be expensive, therefore
 it also saves some data into a ``<simname>_postprocess.h5`` file, and
 then it also performs some time averages, yielding the ``statistics``
@@ -242,6 +243,8 @@ dictionary that is used in the above code.
 Behind the scenes
 -----------------
 
+TODO FIXME obsolete documentation
+
 In brief the following takes place:
 
     1. An instance ``c`` of