Merge pull request #1847 from pdebuyl/fix-active

   * :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>`

   *

   *

   *

   *

* :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

.. 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 quat

* 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 quat 1.0

   fix active all propel/self quat 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* = *quat* 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.

----------

**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 quat 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 quat mode

of this fix only works with atom\_style ellipsoid.

Related commands

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

:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`

.. _Erdmann:

**(Erdmann)** U. Erdmann , 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. Bialke, T. Speck, and H Loewen, 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

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

quadrupolar

Quant

quartic

quat

quaternion

quaternions

quati

scaleyz

Schaik

Schilfgarde

Schimansky

Schiotz

Schlitter

Schmid

dimension 2

boundary p p p

variable L equal 20

region total block -$L $L -$L $L -0.5 0.5

lattice hex 0.3

create_box 2 total

create_atoms 1 box

# Set random fraction to passive:

set type 1 type/fraction 2 0.5 1337

# Purely repulsive particles:

variable rc equal "2^(1.0/6.0)"

pair_style lj/cut ${rc}

pair_coeff * * 1.0 1.0

pair_modify shift yes

mass * 1.0

fix step all nve

fix temp all langevin 1.0 1.0 1.0 13

fix twod all enforce2d

neighbor 0.6 bin

dump traj all custom 250 2d_active.dump.bin id type x y z

thermo_style custom time step pe ke etotal temp

thermo 1000

run 5000

group one type 1

group two type 2

compute ke1 one ke

compute ke2 two ke

thermo_style custom step pe ke etotal temp c_ke1 c_ke2

fix active all propel/self velocity 1.0

# With active force there is more motion so increase bin size:

neighbor 1.0 bin

run 10000

# Only make type 1 active:

fix active all propel/self velocity 1.0 types 1

# With active force there is more motion so increase bin size:

neighbor 1.0 bin

run 10000