Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/pair_lj.html
deeea254b1f0lammm-master-deprecated

Last Change
Raw File

pair_lj.html
View Options

<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/cut command
</H3>
<H3>pair_style lj/cut/cuda command
</H3>
<H3>pair_style lj/cut/experimental/cuda command
</H3>
<H3>pair_style lj/cut/gpu command
</H3>
<H3>pair_style lj/cut/opt command
</H3>
<H3>pair_style lj/cut/omp command
</H3>
<H3>pair_style lj/cut/coul/cut command
</H3>
<H3>pair_style lj/cut/coul/cut/cuda command
</H3>
<H3>pair_style lj/cut/coul/cut/gpu command
</H3>
<H3>pair_style lj/cut/coul/cut/omp command
</H3>
<H3>pair_style lj/cut/coul/debye command
</H3>
<H3>pair_style lj/cut/coul/debye/cuda command
</H3>
<H3>pair_style lj/cut/coul/debye/gpu command
</H3>
<H3>pair_style lj/cut/coul/debye/omp command
</H3>
<H3>pair_style lj/cut/coul/dsf command
</H3>
<H3>pair_style lj/cut/coul/dsf/gpu command
</H3>
<H3>pair_style lj/cut/coul/long command
</H3>
<H3>pair_style lj/cut/coul/long/cuda command
</H3>
<H3>pair_style lj/cut/coul/long/gpu command
</H3>
<H3>pair_style lj/cut/coul/long/opt command
</H3>
<H3>pair_style lj/cut/coul/long/omp command
</H3>
<H3>pair_style lj/cut/coul/msm command
</H3>
<H3>pair_style lj/cut/coul/msm/omp command
</H3>
<H3>pair_style lj/cut/tip4p/long command
</H3>
<H3>pair_style lj/cut/tip4p/long/omp command
</H3>
<H3>pair_style lj/cut/tip4p/long/opt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/dsf</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/msm</I> or <I>lj/cut/tip4p/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/cut</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/debye</I> args = kappa cutoff (cutoff2)
kappa = inverse of the Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/dsf</I> args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units)
<I>lj/cut/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/msm</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/tip4p/long</I> args = otype htype btype atype qdist 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)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
</PRE>
<PRE>pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</PRE>
<PRE>pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
</PRE>
<PRE>pair_style lj/cut/coul/dsf 0.05 2.5 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
</PRE>
<PRE>pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<PRE>pair_style lj/cut/coul/msm 10.0
pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<PRE>pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/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
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/cut</I> styles compute the standard 12/6 Lennard-Jones potential,
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <A HREF = "dielectric.html">dielectric</A> command. 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.
</P>
<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
to the Coulombic term, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
</CENTER>
<P>where kappa is the inverse of the Debye length. This potential is
another way to mimic the screening effect of a polar solvent.
</P>
<P>Style <I>lj/cut/coul/dsf</I> computes the Coulombic term via the damped
shifted force model described in <A HREF = "#Fennell">Fennell</A>, given by:
</P>
<CENTER><IMG SRC = "Eqs/pair_coul_dsf.jpg">
</CENTER>
<P>where <I>alpha</I> is the damping parameter and erfc() is the complementary
error-function. This potential is essentially a short-range,
spherically-truncated, charge-neutralized, shifted, pairwise <I>1/r</I>
summation. The potential is based on Wolf summation, proposed as an
alternative to Ewald summation for condensed phase systems where
charge screening causes electrostatic interactions to become
effectively short-ranged. In order for the electrostatic sum to be
absolutely convergent, charge neutralization within the cutoff radius
is enforced by shifting the potential through placement of image
charges on the cutoff sphere. Convergence can often be improved by
setting <I>alpha</I> to a small non-zero value.
</P>
<P>Styles <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> compute the same
Coulombic interactions as style <I>lj/cut/coul/cut</I> except that an
additional damping factor is applied to the Coulombic term so it can
be used in conjunction with the <A HREF = "kspace_style.html">kspace_style</A>
command and its <I>ewald</I> or <I>pppm</I> option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
</P>
<P>Style <I>lj/cut/tip4p/long</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, 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.
</P>
<P>IMPORTANT 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.
</P>
<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> 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.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>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.
</P>
<P>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. You cannot specify 2 cutoffs for style <I>lj/cut</I>, since it
has no Coulombic terms.
</P>
<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> and <I>lj/cut/tip4p/long</I>
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.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> 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 <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <I>geometric</I>. See the "pair_modify" command
for details.
</P>
<P>All of the lj/cut pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/tip4p/long</I> pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
</P>
<P>All of the lj/cut pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
</P>
<P>All of the lj/cut pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/cut and lj/cut/coul/long pair styles support the use of the
<I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
respa</A> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the <I>pair</I> keyword of run_style respa.
See the <A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/tip4p/long</I> styles are part of the
KSPACE package. They are only enabled if LAMMPS was built with those
packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info. Note that the KSPACE package is installed by default.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Jorgensen"></A>
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
</P>
<A NAME = "Fennell"></A>
<P><B>(Fennell)</B> C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
234104 (2006).
</P>
</HTML>
c4science · Help