186 lines
6.7 KiB
ReStructuredText
186 lines
6.7 KiB
ReStructuredText
.. index:: fix wall/ees
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.. index:: fix wall/region/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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.. code-block:: LAMMPS
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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
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the group by generating a force on the atom in a direction
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perpendicular to the wall and a torque parallel with the wall. The
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energy of 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
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\sigma_{n}^2+3 r \sigma_{n}^4\right) }{945
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\left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r
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\sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{
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\left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12
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\sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n
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< r < r_c
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Introduced by Babadi and Ejtehadi in :ref:`(Babadi)
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<BabadiEjtehadi>`. Here, *r* is the distance from the particle to the
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wall at position *coord*, and Rc is the *cutoff* distance at which
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the particle and wall no longer interact. Also, :math:`\sigma_n` is
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the distance between center of ellipsoid and the nearest point of its
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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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prefactor is
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.. math::
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8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon
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\quad \sigma_a \quad \sigma_b \quad \sigma_c
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where :math:`\epsilon` is the LJ energy parameter for the constituent
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LJ particles and :math:`\sigma_a`, :math:`\sigma_b`, and
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:math:`\sigma_c` are the radii of the ellipsoidal
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particles. :math:`\rho_{wall}` and :math:`\rho_{ellipsoid}` are the
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number density of the constituent particles, in the wall and ellipsoid
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respectively, in units of 1/volume.
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.. note::
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You must ensure 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
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wall/region <fix_wall_region>` command. One may also find an example
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of using this fix in the examples/PACKAGES/ees/ directory.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about these fixes are written to :doc:`binary restart
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files <restart>`.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by
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these fixes to add the energy of interaction between atoms and all the
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specified walls or region wall to the global potential energy of the
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system as part of :doc:`thermodynamic output <thermo_style>`. The
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default settings for these fixes are :doc:`fix_modify energy no
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<fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *respa* option is supported by
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these fixes. This allows to set at which level of the :doc:`r-RESPA
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<run_style>` integrator the fix is adding its forces. Default is the
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outermost level.
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These fixes computes a global scalar and a global vector of forces,
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which can be accessed by various :doc:`output commands
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<Howto_output>`. See the :doc:`fix wall <fix_wall>` command for a
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description of the scalar and vector.
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No parameter of these fixes can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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The forces due to these fixes are imposed during an energy
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minimization, invoked by the :doc:`minimize <minimize>` command.
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.. note::
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If you want the atom/wall interaction energy to be included in
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the total potential energy of the system (the quantity being
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minimized), you MUST enable the :doc:`fix_modify <fix_modify>` *energy*
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option for this fix.
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Restrictions
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""""""""""""
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These fixes are part of the EXTRA-FIX package. They are only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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These fixes 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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