136 lines
5.1 KiB
ReStructuredText
136 lines
5.1 KiB
ReStructuredText
.. index:: fix wall/ees
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fix wall/ees command
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====================
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fix wall/region/ees command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID style args
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* style = *wall/ees* or *wall/region/ees*
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.. parsed-literal::
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args for style *wall/ees*\ : one or more *face parameters* groups may be appended
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face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
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parameters = coord epsilon sigma cutoff
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coord = position of wall = EDGE or constant or variable
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EDGE = current lo or hi edge of simulation box
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constant = number like 0.0 or -30.0 (distance units)
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variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
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epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units)
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epsilon can be a variable (see below)
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sigma = size factor for wall-particle interaction (distance units)
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sigma can be a variable (see below)
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cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
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.. parsed-literal::
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args for style *wall/region/ees*\ : *region-ID* *epsilon* *sigma* *cutoff*
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region-ID = region whose boundary will act as wall
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epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units)
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sigma = size factor for wall-particle interaction (distance units)
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cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box
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fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5
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fix wallhi all wall/ees v_wiggle 23.2 1.0 1.0 2.5
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fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
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fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5
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Description
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"""""""""""
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Fix *wall/ees* bounds the simulation domain on one or more of its
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faces with a flat wall that interacts with the ellipsoidal atoms in the
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group by generating a force on the atom in a direction perpendicular to
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the wall and a torque parallel with the wall. The energy of
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wall-particle interactions E is given by:
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.. math::
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E = \epsilon \left[ \frac{2 \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
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Introduced by Babadi and Ejtehadi in :ref:`(Babadi) <BabadiEjtehadi>`. Here,
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*r* is the distance from the particle to the wall at position *coord*\ ,
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and Rc is the *cutoff* distance at which the particle and wall no
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longer interact. Also, :math:`\sigma_n` is the distance between center of
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ellipsoid and the nearest point of its surface to the wall as shown below.
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.. image:: JPG/fix_wall_ees_image.jpg
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:align: center
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Details of using this command and specifications are the same as
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fix/wall command. You can also find an example in USER/ees/ under
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examples/ directory.
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The prefactor :math:`\epsilon` can be thought of as an
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effective Hamaker constant with energy units for the strength of the
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ellipsoid-wall interaction. More specifically, the :math:`\epsilon`
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pre-factor is
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.. math::
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8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon \quad \sigma_a \quad \sigma_b \quad \sigma_c
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where :math:`\epsilon` is the LJ energy parameter for the constituent LJ
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particles and :math:`\sigma_a`, :math:`\sigma_b`, and :math:`\sigma_c`
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are the radii of the ellipsoidal particles. :math:`\rho_{wall}` and
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:math:`\rho_{ellipsoid}` are the number density of the constituent
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particles, in the wall and ellipsoid respectively, in units of 1/volume.
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.. note::
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You must insure that r is always bigger than :math:`\sigma_n` for
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all particles in the group, or LAMMPS will generate an error. This
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means you cannot start your simulation with particles touching the wall
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position *coord* (:math:`r = \sigma_n`) or with particles penetrating
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the wall (:math:`0 =< r < \sigma_n`) or with particles on the wrong
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side of the wall (:math:`r < 0`).
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Fix *wall/region/ees* treats the surface of the geometric region defined
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by the *region-ID* as a bounding wall which interacts with nearby
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ellipsoidal particles according to the EES potential introduced above.
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Other details of this command are the same as for the :doc:`fix wall/region <fix_wall_region>` command. One may also find an example
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of using this fix in the examples/USER/misc/ees/ directory.
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Restrictions
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""""""""""""
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This fix is part of the USER-MISC package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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This fix requires that atoms be ellipsoids as defined by the
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:doc:`atom_style ellipsoid <atom_style>` command.
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Related commands
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""""""""""""""""
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:doc:`fix wall <fix_wall>`,
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:doc:`pair resquared <pair_resquared>`
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Default
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"""""""
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none
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----------
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.. _BabadiEjtehadi:
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**(Babadi)** Babadi and Ejtehadi, EPL, 77 (2007) 23002.
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