make names/lables more consistent and avoid reference errors in sphinx

1. :ref:`Initialization <init>`

2. :ref:`System definition <system>` 

3. :ref:`Settings <settings>`

3. :ref:`Simulation settings <settings>`

4. :ref:`Run a simulation <run>`

The last 2 parts can be repeated as many times as desired.  I.e. run a

.. _settings:

Settings

Simulation settings

------------------------------

Once atoms and molecular topology are defined, a variety of settings

.. toctree::

   :name: settings

   :name: settings_howto

   :maxdepth: 1

   Howto_2d

.. toctree::

   :name: analysis

   :name: analysis_howto

   :maxdepth: 1

   Howto_output

.. toctree::

   :name: force

   :name: force_howto

   :maxdepth: 1

   Howto_bioFF

.. toctree::

   :name: packages

   :name: packages_howto

   :maxdepth: 1

   Howto_spherical