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Made requested changes to fix propel/self. Last thing to change would be to re-introduce the types keyword into this fix if that was deemed to be best.

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This commit is contained in:
Sam Cameron
2020-12-21 10:58:27 +00:00
parent 129210c7a0
commit 5a3cb38705
7 changed files with 170 additions and 161 deletions
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55
doc/src/fix_propel_self.rst
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@ -8,22 +8,19 @@ Syntax
.. parsed-literal::
fix ID group-ID propel/self magnitude keyword values
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 = *dipole* or *velocity* or *quat*
* magnitude = magnitude of self-propulsion force
* one (and only one) keyword/value pair must be appended to args
* keyword = *dipole* or *velocity* or *quat*
* zero or one keyword/value pairs may be appended
* keyword = *qvector*
.. parsed-literal::
*dipole* value = none = apply force along dipole direction
*velocity* value = none = apply force along velocity direction
*quat* values = direction vector *sx* and *sy* and *sz*
*sx* = x component of force direction in ellipsoid frame
*sy* = y component of force direction in ellipsoid frame
*sz* = z component of force direction in ellipsoid frame
*qvector* value = direction of force in ellipsoid frame
*sx*, *sy*, *sz* = components of *qvector*
Examples
@ -31,9 +28,9 @@ Examples
.. code-block:: LAMMPS
fix propel/self all 40.0 dipole
fix propel/self all 10.0 velocity
fix propel/self all 15.7 quat 1.0 0.0 0.0
fix active all propel/self dipole 40.0
fix active all propel/self velocity 10.0
fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0
Description
"""""""""""
@ -50,7 +47,7 @@ is the magnitude of the force, and :math:`e_i` is the vector direction
of the force. The specification of :math:`e_i` is based on which of the
three keywords (*dipole* or *velocity* or *quat*) one selects.
For keyword *dipole*, :math:`e_i` is just equal to
For mode *dipole*, :math:`e_i` is just equal to
the dipole vectors of the atoms in the group. Therefore, if the dipoles
are not unit vectors, the :math:`e_i` will not be unit vectors.
@ -66,21 +63,31 @@ are not unit vectors, the :math:`e_i` will not be unit vectors.
all the dipole magnitudes to 1.0 unless you have a good reason not to
(see the :doc:`set <set>` command on how to do this).
For keyword *velocity*, :math:`e_i` points in the direction
For mode *velocity*, :math:`e_i` points in the direction
of the current velocity (a unit-vector). This can be interpreted as a
velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) <Erdmann1>`.
For keyword *quat*, :math:`e_i` points in the direction of the unit
vector defined by its arguments *sx*, *sy*, and *sz*, which are
themselves defined within the coordinate frame of the atom's
For mode *quat*, :math:`e_i` points in the direction of a unit
vector, oriented in the coordinate frame of the ellipsoidal particles,
which defaults to point along the x-direction. This default behaviour
can be changed by via the *quatvec* keyword.
The optional *quatvec* keyword specifies the direction of self-propulsion
via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are
defined within the coordinate frame of the atom's
ellipsoid. For instance, for an ellipsoid with long axis along
its x-direction, if one wanted the self-propulsion force to also
be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal
to zero. For *quat*, :math:`e_i` will always be a unit vector,
so multiplying all three arguments *sx*, *sy*, and *sz* by a
positive scalar will not change the self-propulsion force
(multiplying by a negative scalar will change the sign of the
force).
to zero. This keyword may only be specified for mode *quat*.
.. note::
In using keyword *quatvec*, the three arguments *sx*,
*sy*, and *sz* will be automatically normalised to components
of a unit vector internally to avoid users having to explicitly
do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i`
will always be of unit length.
Along with adding a force contribution, this fix can also
contribute to the virial (pressure) of the system, defined as
@ -89,10 +96,10 @@ contribute to the virial (pressure) of the system, defined as
boundary conditions. See :ref:`(Winkler) <Winkler1>` for a
discussion of this active pressure contribution.
For keywords *dipole* and *quat*, this fix is by default
For modes *dipole* and *quat*, this fix is by default
included in pressure computations.
For keyword *velocity*, this fix is by default not included
For mode *velocity*, this fix is by default not included
in pressure computations.