Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/_sources/pair_lj_soft.txt
9cf43f2a0b7fefficient_neuronet

Last Change
Raw File

pair_lj_soft.txt
View Options

.. index:: pair_style lj/cut/soft
pair_style lj/cut/soft command
==============================
pair_style lj/cut/soft/omp command
==================================
pair_style lj/cut/coul/cut/soft command
=======================================
pair_style lj/cut/coul/cut/soft/omp command
===========================================
pair_style lj/cut/coul/long/soft command
========================================
pair_style lj/cut/coul/long/soft/omp command
============================================
pair_style lj/cut/tip4p/long/soft command
=========================================
pair_style lj/cut/tip4p/long/soft/omp command
=============================================
pair_style lj/charmm/coul/long/soft command
===========================================
pair_style lj/charmm/coul/long/soft/omp command
===============================================
pair_style coul/cut/soft command
================================
pair_style coul/cut/soft/omp command
====================================
pair_style coul/long/soft command
=================================
pair_style coul/long/soft/omp command
=====================================
pair_style tip4p/long/soft command
==================================
pair_style tip4p/long/soft/omp command
======================================
Syntax
""""""
.. parsed-literal::
pair_style style args
* style = *lj/cut/soft* or *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* or *lj/cut/tip4p/long/soft* or *lj/charmm/coul/long/soft* or *coul/cut/soft* or *coul/long/soft* or *tip4p/long/soft*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/cut/soft* args = n alpha_lj cutoff
n, alpha_LJ = parameters of soft-core potential
cutoff = global cutoff for Lennard-Jones interactions (distance units)
*lj/cut/coul/cut/soft* args = n alpha_LJ alpha_C cutoff (cutoff2)
n, alpha_LJ, alpha_C = parameters of soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/long/soft* args = n alpha_LJ alpha_C cutoff
n, alpha_LJ, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/tip4p/long/soft* args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
n, alpha_LJ, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/charmm/coul/long/soft* args = n alpha_LJ alpha_C inner outer (cutoff)
n, alpha_LJ, alpha_C = parameters of the soft-core potential
inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
*coul/cut/soft* args = n alpha_C cutoff
n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units)
*coul/long/soft* args = n alpha_C cutoff
n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units)
*tip4p/long/soft* args = otype htype btype atype qdist n alpha_C cutoff
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units)
Examples
""""""""
.. parsed-literal::
pair_style lj/cut/soft 2.0 0.5 9.5
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 1.0 9.5
.. parsed-literal::
pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.5 10.0
pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
.. parsed-literal::
pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.0 10.0
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
.. parsed-literal::
pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
pair_coeff * * 0.155 3.1536 1.0
pair_coeff 1 1 0.155 3.1536 1.0 9.5
.. parsed-literal::
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
.. parsed-literal::
pair_style coul/long/soft 1.0 10.0 9.5
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
.. parsed-literal::
pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
Description
"""""""""""
The *lj/cut/soft* style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created
or anihilated :ref:`(Beutler) <Beutler>`,
.. image:: Eqs/pair_lj_soft.jpg
:align: center
Coulomb interactions are also damped with a soft core at short
distance,
.. image:: Eqs/pair_coul_soft.jpg
:align: center
In the Coulomb part C is an energy-conversion constant, q_i and q_j
are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the :doc:`dielectric <dielectric>` command.
The coefficient lambda is an activation parameter. When lambda = 1 the
pair potentiel is identical to a Lennard-Jones term or a Coulomb term
or a combination of both. When lambda = 0 the interactions are
deactivated. The transition between these two extrema is smoothed by a
soft repulsive core in order to avoid singularities in potential
energy and forces when sites are created or anihilated and can overlap
:ref:`(Beutler) <Beutler>`.
The paratemers n, alpha_LJ and alpha_C are set in the
:doc:`pair_style <pair_style>` command, before the cutoffs. Usual
choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
appropriate choices. Plots of the LJ and Coulomb terms are shown
below, for lambda ranging from 1 to 0 every 0.1.
.. image:: JPG/lj_soft.jpg
:align: center
.. image:: JPG/coul_soft.jpg
:align: center
For the *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* pair styles,
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 (energy units)
* sigma (distance units)
* lambda (activation parameter between 0 and 1)
* cutoff1 (distance units)
* cutoff2 (distance units)
The latter two coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style *lj/cut/soft*,
since it has no Coulombic terms. For the *coul/cut/soft* and
*coul/long/soft* only lambda and the optional cutoff2 are to be
specified.
Style *lj/cut/tip4p/long/soft* implements a soft-core version of the
TIP4P water model. The usage of this pair style is documented in the
:doc:`pair_lj <pair_lj>` styles. The soft-core version introduces the
lambda parameter to the list of arguments, after epsilon and sigma in
the :doc:`pair_coeff <pair_coeff>` command. The paratemers n, alpha_LJ
and alpha_C are set in the :doc:`pair_style <pair_style>` command,
before the cutoffs.
Style *lj/charmm/coul/long/soft* implements a soft-core version of the
CHARMM version of LJ interactions with an additional switching
function S(r) that ramps the energy and force smoothly to zero between
an inner and outer cutoff. The usage of this pair style is documented
in the :doc:`pair_charmm <pair_charmm>` styles. The soft-core version
introduces the lambda parameter to the list of arguments, after
epsilon and sigma in the :doc:`pair_coeff <pair_coeff>` command (and
before the optional eps14 and sigma14). The paratemers n,
alpha_LJ and alpha_C are set in the :doc:`pair_style <pair_style>`
command, before the cutoffs.
The *coul/cut/soft*, *coul/long/soft* and *tip4p/long/soft* substyles
are designed to be combined with other pair potentials via the
:doc:`pair_style hybrid/overlay <pair_hybrid>` command. This is because
they have no repulsive core. Hence, if used by themselves, there will
be no repulsion to keep two oppositely charged particles from
overlapping each other. In this case, if lambda = 1, a singularity may
occur. These substyles are suitable to represent charges embedded in
the Lennard-Jones radius of another site (for example hydrogen atoms
in several water models).
NOTES: When using the core-softed Coulomb potentials with long-range
solvers (*coul/long/soft*, *lj/cut/coul/long/soft*, etc.) in a free
energy calculation in which sites holding electrostatic charges are
being created or anihilated (using :doc:`fix_adapt/fep <fix_adapt_fep>`
and :doc:`compute_fep <compute_fep>`) it is important to adapt both the
lambda activation parameter (from 0 to 1, or the reverse) and the
value of the charge (from 0 to its final value, or the reverse). This
ensures that long-range electrostatic terms (kspace) are correct. It
is not necessary to use core-softed Coulomb potentials if the van der
Waals site is present during the free-energy route, thus avoiding
overlap of the charges. Examples are provided in the LAMMPS source
directory tree, under examples/USER/fep.
----------
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, tail correction, restart 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.
These pair styles support the :doc:`pair_modify <pair_modify>` shift
option for the energy of the Lennard-Jones portion of the pair
interaction.
These pair styles support the :doc:`pair_modify <pair_modify>` tail
option for adding a long-range tail correction to the energy and
pressure for the Lennard-Jones portion of the pair interaction.
These pair styles write 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.
----------
Restrictions
""""""""""""
To avoid division by zero do not set sigma = 0; use the lambda
parameter instead to activate/deactivate interactions, or use
epsilon = 0 and sigma = 1. Alternatively, when sites do not
interact though the Lennard-Jones term the *coul/long/soft* or
similar substyle can be used via the
:doc:`pair_style hybrid/overlay <pair_hybrid>` command.
----------
All of the plain *soft* pair styles are part of the USER-FEP package.
The *long* styles also requires the KSPACE package to be installed.
They are only enabled if LAMMPS was built with those packages. See
the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix_adapt <fix_adapt>`,
:doc:`fix_adapt/fep <fix_adapt_fep>`, :doc:`compute_fep <compute_fep>`
**Default:** none
----------
.. _Beutler:
**(Beutler)** Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
Phys Lett, 222, 529 (1994).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help