Homec4science
Diffusion lammps (master) Browse

lammps/doc/_sources/pair_lj_long.txt
9cf43f2a0b7fmaster

Last Change
Raw File

pair_lj_long.txt
View Options

.. index:: pair_style lj/long/coul/long
pair_style lj/long/coul/long command
====================================
pair_style lj/long/coul/long/omp command
========================================
pair_style lj/long/coul/long/opt command
========================================
pair_style lj/long/tip4p/long command
=====================================
Syntax
""""""
.. parsed-literal::
pair_style style args
* style = *lj/long/coul/long* or *lj/long/tip4p/long*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/long/coul/long* args = flag_lj flag_coul cutoff (cutoff2)
flag_lj = *long* or *cut* or *off*
*long* = use Kspace long-range summation for dispersion 1/r^6 term
*cut* = use a cutoff on dispersion 1/r^6 term
*off* = omit disperion 1/r^6 term entirely
flag_coul = *long* or *off*
*long* = use Kspace long-range summation for Coulombic 1/r term
*off* = omit Coulombic term
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/long/tip4p/long* args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
flag_lj = *long* or *cut*
*long* = use Kspace long-range summation for dispersion 1/r^6 term
*cut* = use a cutoff
flag_coul = *long* or *off*
*long* = use Kspace long-range summation for Coulombic 1/r term
*off* = omit Coulombic term
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)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
Examples
""""""""
.. parsed-literal::
pair_style lj/long/coul/long cut off 2.5
pair_style lj/long/coul/long cut long 2.5 4.0
pair_style lj/long/coul/long long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
.. parsed-literal::
pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description
"""""""""""
Style *lj/long/coul/long* computes the standard 12/6 Lennard-Jones and
Coulombic potentials, given by
.. image:: Eqs/pair_lj.jpg
:align: center
.. image:: Eqs/pair_coulomb.jpg
:align: center
where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, epsilon is the dielectric constant which can be set by
the :doc:`dielectric <dielectric>` command, and Rc is the cutoff. If
one cutoff is specified in the pair_style command, it is used for both
the LJ and Coulombic terms. If two cutoffs are specified, they are
used as cutoffs for the LJ and Coulombic terms respectively.
The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r
interactions. This is done by use of the *flag_lj* and *flag_coul*
settings. The :ref:`In 't Veld <Veld>` paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
Style *lj/long/tip4p/long* implements the TIP4P water model of
:ref:`(Jorgensen) <Jorgensen>`, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :ref:`howto section <howto_8>` for more
information on how to use the TIP4P pair style. Note that the
neighobr list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
the offset distance of the fictitious charges on O atoms in water
molecules. Thus it is typically best in an efficiency sense to use a
LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
neighbor list. This leads to slightly larger cost for the long-range
calculation, so you can test the trade-off for your model.
If *flag_lj* is set to *long*, no cutoff is used on the LJ 1/r^6
dispersion term. The long-range portion can be calculated by using
the :doc:`kspace_style ewald/disp or pppm/disp <kspace_style>` commands.
The specified LJ cutoff then determines which portion of the LJ
interactions are computed directly by the pair potential versus which
part is computed in reciprocal space via the Kspace style. If
*flag_lj* is set to *cut*, the LJ interactions are simply cutoff, as
with :doc:`pair_style lj/cut <pair_lj>`.
If *flag_coul* is set to *long*, no cutoff is used on the Coulombic
interactions. The long-range portion can calculated by using any of
several :doc:`kspace_style <kspace_style>` command options such as
*pppm* or *ewald*. Note that if *flag_lj* is also set to long, then
the *ewald/disp* or *pppm/disp* Kspace style needs to be used to
perform the long-range calculations for both the LJ and Coulombic
interactions. If *flag_coul* is set to *off*, Coulombic interactions
are not computed.
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)
* cutoff1 (distance units)
* cutoff2 (distance units)
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
The latter 2 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.
Note that if you are using *flag_lj* set to *long*, you
cannot specify a LJ cutoff for an atom type pair, since only one
global LJ cutoff is allowed. Similarly, if you are using *flag_coul*
set to *long*, you cannot specify a Coulombic cutoff for an atom type
pair, since only one global Coulombic cutoff is allowed.
For *lj/long/tip4p/long* only the LJ cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
----------
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 all of the lj/long pair styles 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, assuming *flag_lj* is *cut*.
These pair styles support the :doc:`pair_modify <pair_modify>` table and
table/disp options since they can tabulate the short-range portion of
the long-range Coulombic and dispersion interactions.
Thes pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding a long-range tail correction to the
Lennard-Jones portion of the energy and pressure.
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.
The pair lj/long/coul/long styles support the use of the *inner*,
*middle*, and *outer* keywords of the :doc:`run_style respa <run_style>`
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. See the
:doc:`run_style <run_style>` command for details.
----------
Restrictions
""""""""""""
These styles are part of the KSPACE package. They are only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info. Note that
the KSPACE package is installed by default.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
**Default:** none
----------
.. _Veld:
**(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help