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

doc/src/Commands_structure.rst

@@ -10,7 +10,7 @@ A LAMMPS input script typically has 4 parts:
 
 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
@@ -58,7 +58,7 @@ using the :doc:`replicate <replicate>` command.
 
 .. _settings:
 
-Settings
+Simulation settings
 ------------------------------
 
 Once atoms and molecular topology are defined, a variety of settings

doc/src/Howto.rst

@@ -42,7 +42,7 @@ Settings howto
 
 
 .. toctree::
-   :name: settings
+   :name: settings_howto
    :maxdepth: 1
 
    Howto_2d
@@ -58,7 +58,7 @@ Analysis howto
 
 
 .. toctree::
-   :name: analysis
+   :name: analysis_howto
    :maxdepth: 1
 
    Howto_output
@@ -74,7 +74,7 @@ Force fields howto
 
 
 .. toctree::
-   :name: force
+   :name: force_howto
    :maxdepth: 1
 
    Howto_bioFF
@@ -87,7 +87,7 @@ Packages howto
 
 
 .. toctree::
-   :name: packages
+   :name: packages_howto
    :maxdepth: 1
 
    Howto_spherical