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.. index:: pair_style gauss
pair_style gauss command
========================
pair_style gauss/gpu command
============================
pair_style gauss/omp command
============================
pair_style gauss/cut command
============================
pair_style gauss/cut/omp command
================================
Syntax
""""""
.. parsed-literal::
pair_style gauss cutoff
pair_style gauss/cut cutoff
* cutoff = global cutoff for Gauss interactions (distance units)
Examples
""""""""
.. parsed-literal::
pair_style gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
.. parsed-literal::
pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
Description
"""""""""""
Style *gauss* computes a tethering potential of the form
.. image:: Eqs/pair_gauss.jpg
:align: center
between an atom and its corresponding tether site which will typically
be a frozen atom in the simulation. Rc is the cutoff.
The following coefficients must be defined for each pair of atom 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:
* A (energy units)
* B (1/distance^2 units)
* cutoff (distance units)
The last coefficient is optional. If not specified, the global cutoff
is used.
Style *gauss/cut* computes a generalized Gaussian interaction potential
between pairs of particles:
.. image:: Eqs/pair_gauss_cut.jpg
:align: center
where H determines together with the standard deviation sigma_h the
peak height of the Gaussian function, and r_mh the peak position.
Examples of the use of the Gaussian potentials include implicit
solvent simulations of salt ions :ref:`(Lenart) <Lenart>` and of surfactants
:ref:`(Jusufi) <Jusufi>`. In these instances the Gaussian potential mimics
the hydration barrier between a pair of particles. The hydration
barrier is located at r_mh and has a width of sigma_h. The prefactor
determines the hight of the potential barrier.
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff <pair_coeff>` command as in the example above,
or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* H (energy * distance units)
* r_mh (distance units)
* sigma_h (distance units)
The global cutoff (r_c) specified in the pair_style command is used.
----------
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 "-suffix command-line
switch7_Section_start.html#start_6 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**:
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
The *gauss* style does not support the :doc:`pair_modify <pair_modify>`
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.
The *gauss/cut* style supports the :doc:`pair_modify <pair_modify>` shift
option for the energy of the Gauss-potential portion of the pair
interaction.
The :doc:`pair_modify <pair_modify>` table and tail options are not
relevant for these pair styles.
These pair styles write their 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.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well
sites have an atom within the distance at which the force is a maximum
= sqrt(0.5/b). This quantity can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 1.
To print this quantity to the log file (with a descriptive column
heading) the following commands could be included in an input script:
.. parsed-literal::
compute gauss all pair gauss
variable occ equal c_gauss[1]
thermo_style custom step temp epair v_occ
----------
Restrictions
""""""""""""
The *gauss/cut* style is part of the "user-misc" package. It is only
enabled if LAMMPS is build with that package. See the :ref:`Making of LAMMPS <3>` section for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_style coul/diel <pair_coul_diel>`
**Default:** none
.. _Lenart:
**(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
044509 (2007).
.. _Jusufi:
**(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
13783 (2008).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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