forked from lijiext/lammps
264 lines
10 KiB
Plaintext
264 lines
10 KiB
Plaintext
.. index:: pair_style gayberne
|
|
|
|
pair_style gayberne command
|
|
===========================
|
|
|
|
pair_style gayberne/gpu command
|
|
===============================
|
|
|
|
pair_style gayberne/intel command
|
|
=================================
|
|
|
|
pair_style gayberne/omp command
|
|
===============================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
pair_style gayberne gamma upsilon mu cutoff
|
|
|
|
* gamma = shift for potential minimum (typically 1)
|
|
* upsilon = exponent for eta orientation-dependent energy function
|
|
* mu = exponent for chi orientation-dependent energy function
|
|
* cutoff = global cutoff for interactions (distance units)
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
pair_style gayberne 1.0 1.0 1.0 10.0
|
|
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
The *gayberne* styles compute a Gay-Berne anisotropic LJ interaction
|
|
:ref:`(Berardi) <Berardi>` between pairs of ellipsoidal particles or an
|
|
ellipsoidal and spherical particle via the formulas
|
|
|
|
.. image:: Eqs/pair_gayberne.jpg
|
|
:align: center
|
|
|
|
where A1 and A2 are the transformation matrices from the simulation
|
|
box frame to the body frame and r12 is the center to center vector
|
|
between the particles. Ur controls the shifted distance dependent
|
|
interaction based on the distance of closest approach of the two
|
|
particles (h12) and the user-specified shift parameter gamma. When
|
|
both particles are spherical, the formula reduces to the usual
|
|
Lennard-Jones interaction (see details below for when Gay-Berne treats
|
|
a particle as "spherical").
|
|
|
|
For large uniform molecules it has been shown that the energy
|
|
parameters are approximately representable in terms of local contact
|
|
curvatures :ref:`(Everaers) <Everaers>`:
|
|
|
|
.. image:: Eqs/pair_gayberne2.jpg
|
|
:align: center
|
|
|
|
The variable names utilized as potential parameters are for the most
|
|
part taken from :ref:`(Everaers) <Everaers>` in order to be consistent with
|
|
the :doc:`RE-squared pair potential <pair_resquared>`. Details on the
|
|
upsilon and mu parameters are given
|
|
`here <PDF/pair_resquared_extra.pdf>`_.
|
|
|
|
More details of the Gay-Berne formulation are given in the references
|
|
listed below and in `this supplementary document <PDF/pair_gayberne_extra.pdf>`_.
|
|
|
|
Use of this pair style requires the NVE, NVT, or NPT fixes with the
|
|
*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
|
|
order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid <atom_style>` should be used since it defines the
|
|
rotational state and the size and shape of each ellipsoidal particle.
|
|
|
|
The following coefficients must be defined for each pair of atoms
|
|
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
|
above, or in the data file or restart files read by the
|
|
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
|
commands, or by mixing as described below:
|
|
|
|
* epsilon = well depth (energy units)
|
|
* sigma = minimum effective particle radii (distance units)
|
|
* epsilon_i_a = relative well depth of type I for side-to-side interactions
|
|
* epsilon_i_b = relative well depth of type I for face-to-face interactions
|
|
* epsilon_i_c = relative well depth of type I for end-to-end interactions
|
|
* epsilon_j_a = relative well depth of type J for side-to-side interactions
|
|
* epsilon_j_b = relative well depth of type J for face-to-face interactions
|
|
* epsilon_j_c = relative well depth of type J for end-to-end interactions
|
|
* cutoff (distance units)
|
|
|
|
The last coefficient is optional. If not specified, the global
|
|
cutoff specified in the pair_style command is used.
|
|
|
|
It is typical with the Gay-Berne potential to define *sigma* as the
|
|
minimum of the 3 shape diameters of the particles involved in an I,I
|
|
interaction, though this is not required. Note that this is a
|
|
different meaning for *sigma* than the :doc:`pair_style resquared <pair_resquared>` potential uses.
|
|
|
|
The epsilon_i and epsilon_j coefficients are actually defined for atom
|
|
types, not for pairs of atom types. Thus, in a series of pair_coeff
|
|
commands, they only need to be specified once for each atom type.
|
|
|
|
Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
|
|
non-zero, the three values are assigned to atom type I. If all the
|
|
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
|
|
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
|
|
to atom type J. If all three epsilon_j values are zero, they are
|
|
ignored. Thus the typical way to define the epsilon_i and epsilon_j
|
|
coefficients is to list their values in "pair_coeff I J" commands when
|
|
I = J, but set them to 0.0 when I != J. If you do list them when I !=
|
|
J, you should insure they are consistent with their values in other
|
|
pair_coeff commands, since only the last setting will be in effect.
|
|
|
|
Note that if this potential is being used as a sub-style of
|
|
:doc:`pair_style hybrid <pair_hybrid>`, and there is no "pair_coeff I I"
|
|
setting made for Gay-Berne for a particular type I (because I-I
|
|
interactions are computed by another hybrid pair potential), then you
|
|
still need to insure the epsilon a,b,c coefficients are assigned to
|
|
that type. e.g. in a "pair_coeff I J" command.
|
|
|
|
.. note::
|
|
|
|
If the epsilon a = b = c for an atom type, and if the shape of
|
|
the particle itself is spherical, meaning its 3 shape parameters are
|
|
all the same, then the particle is treated as an LJ sphere by the
|
|
Gay-Berne potential. This is significant because if two LJ spheres
|
|
interact, then the simple Lennard-Jones formula is used to compute
|
|
their interaction energy/force using the specified epsilon and sigma
|
|
as the standard LJ parameters. This is much cheaper to compute than
|
|
the full Gay-Berne formula. To treat the particle as a LJ sphere with
|
|
sigma = D, you should normally set epsilon a = b = c = 1.0, set the
|
|
pair_coeff sigma = D, and also set the 3 shape parameters for the
|
|
particle to D. The one exception is that if the 3 shape parameters
|
|
are set to 0.0, which is a valid way in LAMMPS to specify a point
|
|
particle, then the Gay-Berne potential will treat that as shape
|
|
parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
|
|
requires finite-size particles. In this case you should still set the
|
|
pair_coeff sigma to 1.0 as well.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
|
|
of the manual. The accelerated styles take the same arguments and
|
|
should produce the same results, except for round-off and precision
|
|
issues.
|
|
|
|
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
|
|
|
You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
|
|
use the :doc:`suffix <suffix>` command in your input script.
|
|
|
|
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
|
|
more instructions on how to use the accelerated styles effectively.
|
|
|
|
|
|
----------
|
|
|
|
|
|
**Mixing, shift, table, tail correction, restart, rRESPA info**:
|
|
|
|
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
|
and cutoff distance for this pair style can be mixed. The default mix
|
|
value is *geometric*. See the "pair_modify" command for details.
|
|
|
|
This pair styles supports the :doc:`pair_modify <pair_modify>` shift
|
|
option for the energy of the Lennard-Jones portion of the pair
|
|
interaction, but only for sphere-sphere interactions. There is no
|
|
shifting performed for ellipsoidal interactions due to the anisotropic
|
|
dependence of the interaction.
|
|
|
|
The :doc:`pair_modify <pair_modify>` table option is not relevant
|
|
for this pair style.
|
|
|
|
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
|
tail option for adding long-range tail corrections to energy and
|
|
pressure.
|
|
|
|
This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
|
|
to be specified in an input script that reads a restart file.
|
|
|
|
This pair style can only be used via the *pair* keyword of the
|
|
:doc:`run_style respa <run_style>` command. It does not support the
|
|
*inner*, *middle*, *outer* keywords.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
|
|
The *gayberne* style is part of the ASPHERE package. It is only
|
|
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
|
|
|
These pair style require that atoms store torque and a quaternion to
|
|
represent their orientation, as defined by the
|
|
:doc:`atom_style <atom_style>`. It also require they store a per-type
|
|
:doc:`shape <shape>`. The particles cannot store a per-particle
|
|
diameter.
|
|
|
|
This pair style requires that atoms be ellipsoids as defined by the
|
|
:doc:`atom_style ellipsoid <atom_style>` command.
|
|
|
|
Particles acted on by the potential can be finite-size aspherical or
|
|
spherical particles, or point particles. Spherical particles have all
|
|
3 of their shape parameters equal to each other. Point particles have
|
|
all 3 of their shape parameters equal to 0.0.
|
|
|
|
The Gay-Berne potential does not become isotropic as r increases
|
|
:ref:`(Everaers) <Everaers>`. The distance-of-closest-approach
|
|
approximation used by LAMMPS becomes less accurate when high-aspect
|
|
ratio ellipsoids are used.
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere <fix_nve_asphere>`,
|
|
:doc:`compute temp/asphere <compute_temp_asphere>`, :doc:`pair_style resquared <pair_resquared>`
|
|
|
|
**Default:** none
|
|
|
|
|
|
----------
|
|
|
|
|
|
.. _Everaers:
|
|
|
|
|
|
|
|
**(Everaers)** Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
|
|
|
|
.. _Berardi:
|
|
|
|
|
|
|
|
**(Berardi)** Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
|
|
Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
|
|
|
|
.. _Perram:
|
|
|
|
|
|
|
|
**(Perram)** Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
|
|
|
|
.. _Allen:
|
|
|
|
|
|
|
|
**(Allen)** Allen and Germano, Mol Phys 104, 3225-3235 (2006).
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|