small fixes of documentation

doc/RTD/source/CommandLineOptions/index.rst

 .. Command line options
    Matthieu Schaller, 21st October 2018
 
+.. _cmdline-options:
+
 Command line options
 ====================
 
+SWIFT requires a number of runtime options to run and get any sensible output.
+For instance, just running the ``swift`` binary will not use any SPH or gravity;
+the particles will just sit still!
+
+Below is a list of the command line options and when they should be used. The same list
+can be found by typing ``./swift -h``.
+
++ ``-a``: Pin runners using processor affinity.
++ ``-c``: Run with cosmological time integration.
++ ``-C``: Run with cooling.
++ ``-d``: Dry run. Read the parameter file, allocate memory but does not read
+  the particles from ICs and exit before the start of time integration. Allows
+  user to check validity of parameter and IC files as well as memory limits.
++ ``-D``: Always drift all particles even the ones far from active particles.
+  This emulates Gadget-[23] and GIZMO's default behaviours.
++ ``-e``: Enable floating-point exceptions (debugging mode).
++ ``-f``: {int} Overwrite the CPU frequency (Hz) to be used for time measurements.
++ ``-g``: Run with an external gravitational potential.
++ ``-G``: Run with self-gravity.
++ ``-M``: Reconstruct the multipoles every time-step.
++ ``-n``: {int} Execute a fixed number of time steps. When unset use the
+  time_end parameter to stop.
++ ``-o``: {str} Generate a default output parameter file.
++ ``-P``: {sec:par:val} Set parameter value and overwrites values read from the
+  parameters file. Can be used more than once.
++ ``-s``: Run with hydrodynamics.
++ ``-S``: Run with stars.
++ ``-t``: {int} The number of threads to use on each MPI rank. Defaults to 1 if
+  not specified.
++ ``-T``: Print timers every time-step.
++ ``-v``: [12] Increase the level of verbosity: 1, MPI-rank 0 writes, 2, All
+  MPI-ranks write.
++ ``-y``: {int} Time-step frequency at which task graphs are dumped.
++ ``-Y``: {int} Time-step frequency at which threadpool tasks are dumped.
++ ``-h``: Print a help message and exit.

doc/RTD/source/GettingStarted/running_example.rst

@@ -19,14 +19,14 @@ as ``wget`` for grabbing the glass).
 
 
 This will run the 'SodShock' in 3D and produce a nice plot that shows you
-how the density has varied. Try running with GIZMO (this will take
+how the density has varied. Try running with GIZMO-MFV (this will take
 _significantly_ longer than with SPH) to see the difference. For that, you
 will need to reconfigure with the following options:
 
 .. code-block:: bash
    
    ./configure \
-   --with-hydro=gizmo \
+   --with-hydro=gizmo-mfv \
    --with-riemann-solver=hllc
 
 

doc/RTD/source/GettingStarted/runtime_options.rst

@@ -8,34 +8,5 @@ SWIFT requires a number of runtime options to run and get any sensible output.
 For instance, just running the ``swift`` binary will not use any SPH or gravity;
 the particles will just sit still!
 
-Below is a list of the runtime options and when they should be used. The same list
-can be found by typing ``./swift -h``.
+A list of available command line options can be found on the :ref:`cmdline-options` page.
 
-+ ``-a``: Pin runners using processor affinity.
-+ ``-c``: Run with cosmological time integration.
-+ ``-C``: Run with cooling.
-+ ``-d``: Dry run. Read the parameter file, allocate memory but does not read
-  the particles from ICs and exit before the start of time integration. Allows
-  user to check validity of parameter and IC files as well as memory limits.
-+ ``-D``: Always drift all particles even the ones far from active particles.
-  This emulates Gadget-[23] and GIZMO's default behaviours.
-+ ``-e``: Enable floating-point exceptions (debugging mode).
-+ ``-f``: {int} Overwrite the CPU frequency (Hz) to be used for time measurements.
-+ ``-g``: Run with an external gravitational potential.
-+ ``-G``: Run with self-gravity.
-+ ``-M``: Reconstruct the multipoles every time-step.
-+ ``-n``: {int} Execute a fixed number of time steps. When unset use the
-  time_end parameter to stop.
-+ ``-o``: {str} Generate a default output parameter file.
-+ ``-P``: {sec:par:val} Set parameter value and overwrites values read from the
-  parameters file. Can be used more than once.
-+ ``-s``: Run with hydrodynamics.
-+ ``-S``: Run with stars.
-+ ``-t``: {int} The number of threads to use on each MPI rank. Defaults to 1 if
-  not specified.
-+ ``-T``: Print timers every time-step.
-+ ``-v``: [12] Increase the level of verbosity: 1, MPI-rank 0 writes, 2, All
-  MPI-ranks write.
-+ ``-y``: {int} Time-step frequency at which task graphs are dumped.
-+ ``-Y``: {int} Time-step frequency at which threadpool tasks are dumped.
-+ ``-h``: Print a help message and exit.

doc/RTD/source/NewOption/index.rst

-.. Equation of State
+.. Adding new schemes
    Loic Hausammann, 7th April 2018
 
 .. _new_option: