documentation and examples cleanup for fix propel/self

* :doc:`precession/spin <fix_precession_spin>` -

* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat

* :doc:`print <fix_print>` - print text and variables during a simulation

* :doc:`propel/self <fix_propel_self>` - model self-propelled particles

* :doc:`property/atom <fix_property_atom>` - add customized per-atom values

* :doc:`python/invoke <fix_python_invoke>` - call a Python function during a simulation

* :doc:`python/move <fix_python_move>` -  call a Python function during a simulation run

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* = *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>`.

For *mode* = *quaternion* the force is applied 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.

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.

----------

""""""""""""

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.

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. The quaternion mode

of this fix only works with atom\_style ellipsoid.

Related commands

""""""""""""""""

**(Erdmann)** U. Erdmanna , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,

**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,

Eur. Phys. J. B 15, 105-113, 2000.

.. _Henkes:

**(Bialke)** J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012.

**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.

.. _Fily:

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

fix propel/self command  :h3

[Syntax:]

fix ID group-ID propel/self mode magnitude keyword values ...

ID, group-ID are documented in "fix"_fix.html command :ulb,l

propel/self = style name of this fix command :l

mode = velocity or quaternion :l

magnitude = magnitude of the active force :l

one or more keyword/value pairs may be appended to args :l

keyword = {types} :l

  {types} values = one or more atom types

:ule

[Examples:]

fix active_group all propel/self velocity 1.0

fix constant_velocity all viscous 1.0 :pre

fix active_group all propel/self quaternion 1.0 :pre

fix active all propel/self quaternion 1.0 types 1 2 4 :pre

[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 "(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 "(Henkes)"_#Henkes, "(Bialke)"_#Bialke and "(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.

:line

[Restart, fix_modify, output, run start/stop, minimize info:]

No information about this fix is written to "binary restart

files"_restart.html.

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:]

"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html

:link(Erdmann)

[(Erdmann)] U. Erdmanna , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,

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.

:link(Bialke)

[(Bialke)] J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012.

:link(Fily)

[(Fily)] Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.

[Default:] types

Bfrac

bgq

Bh

Bialke

Biersack

bigbig

bigint

eatom

Eb

Eba

Ebeling

ebond

ebook

ebt

Equilibria

equilization

Ercolessi

Erdmann

eradius

erate

erc

Filename

filenames

Filenames

Fily

fileper

filesystem

Fincham

gcmc

gdot

GeC

Geier

gencode

georg

Georg

Hendrik

Henin

Henkelman

Henkes

henrich

Henrich

Herrmann

ln

localTemp

localvectors

Loewen

logfile

logfreq

logicals

manybody

MANYBODY

Maras

Marchetti

Marrink

Marroquin

Marsaglia

outmost

outputss

Ouyang

overdamped

overlayed

Ovito

oxdna

scaleyz

Schaik

Schilfgarde

Schimansky

Schiotz

Schlitter

Schmid