fix doc for fix propel/self to sphinx system

doc/src/Commands_fix.rst

@@ -155,6 +155,7 @@ OPT.
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
    * :doc:`print <fix_print>`
+   * :doc:`propel/self <fix_propel_self>`
    * :doc:`property/atom (k) <fix_property_atom>`
    * :doc:`python/invoke <fix_python_invoke>`
    * :doc:`python/move <fix_python_move>`
@@ -237,4 +238,3 @@ OPT.
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
    *
-   *

doc/src/fix_propel_self.rst

@@ -0,0 +1,109 @@
+.. index:: fix propel/self
+
+fix propel/self command
+=======================
+
+Syntax
+""""""
+
+fix ID group-ID propel/self mode magnitude keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* propel/self = style name of this fix command
+* mode = velocity or quaternion
+* magnitude = magnitude of the active force
+* one or more keyword/value pairs may be appended to args
+* keyword = *types*
+
+  *types* values = one or more atom types
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix active_group all propel/self velocity 1.0
+   fix constant_velocity all viscous 1.0
+
+   fix active_group all propel/self quaternion 1.0
+
+   fix active all propel/self quaternion 1.0 types 1 2 4
+
+Description
+"""""""""""
+
+Adds a force of a constant magnitude to each atom in the group. The nature in
+which the force is added depends on the mode.
+
+For mode = velocity, the active force acts along the velocity vector of each atom. This can
+be interpreted as a velocity-dependent friction, such as proposed by :ref:`(Erdmann) <Erdmann>`.
+
+For mode = quaternion the force is along the axis obtained by rotating the x-axis along the
+atom's quaternion. In other words, the force is along the x-axis in the atom's body
+frame. This mode requires all atoms in the group to have a quaternion, so atom\_style should
+either be ellipsoid or body.  In combination with Langevin thermostat for translation and
+rotation in the overdamped regime, the quaternion mode corresponds to the active Brownian
+particle model introduced by :ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily) <Fily>`.
+
+By default, this fix is applied to all atoms in the group. You can override this
+behavior by specifying the atom types the fix should work on through the *types*
+keyword.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+This fix is not imposed  during minimization.
+
+Restrictions
+""""""""""""
+
+
+In quaternion mode, this fix makes use of per-atom quaternions to take into account the fact
+that the orientation can rotate and hence the direction of the active force can
+change. Therefore, the quaternion mode of this fix only works with atom\_styles that have a
+quaternion.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
+
+.. _Erdmann:
+
+
+
+**(Erdmann)** U. Erdmanna , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
+Eur. Phys. J. B 15, 105-113, 2000.
+
+.. _Henkes:
+
+
+
+**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
+
+.. _Bialke:
+
+
+
+**(Bialke)** J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012.
+
+.. _Fily:
+
+
+
+**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
+
+**Default:** types
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/txt/fix_propel_self.txt

@@ -76,7 +76,7 @@ quaternion.
 Eur. Phys. J. B 15, 105-113, 2000.
 
 :link(Henkes)
-[(Henkes)] Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011
+[(Henkes)] Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
 
 :link(Bialke)
 [(Bialke)] J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012.