forked from lijiext/lammps
300 lines
13 KiB
HTML
300 lines
13 KiB
HTML
|
<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/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/coul/cut/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/coul/cut/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/coul/long/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/coul/long/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/tip4p/long/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/cut/tip4p/long/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/charmm/coul/long/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style lj/charmm/coul/long/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style coul/cut/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style coul/cut/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style coul/long/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style coul/long/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style tip4p/long/soft command
|
||
|
|
</H3>
|
||
|
|
<H3>pair_style tip4p/long/soft/omp command
|
||
|
|
</H3>
|
||
|
|
<P><B>Syntax:</B>
|
||
|
|
</P>
|
||
|
|
<PRE>pair_style style args
|
||
|
|
</PRE>
|
||
|
|
<UL><LI>style = <I>lj/cut/soft</I> or <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> or <I>lj/cut/tip4p/long/soft</I> or <I>lj/charmm/coul/long/soft</I> or <I>coul/cut/soft</I> or <I>coul/long/soft</I> or <I>tip4p/long/soft</I>
|
||
|
|
<LI>args = list of arguments for a particular style
|
||
|
|
</UL>
|
||
|
|
<PRE> <I>lj/cut/soft</I> args = n alpha_lj cutoff
|
||
|
|
n, alpha_LJ = parameters of soft-core potential
|
||
|
|
cutoff = global cutoff for Lennard-Jones interactions (distance units)
|
||
|
|
<I>lj/cut/coul/cut/soft</I> 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)
|
||
|
|
<I>lj/cut/coul/long/soft</I> 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)
|
||
|
|
<I>lj/cut/tip4p/long/soft</I> 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)
|
||
|
|
<I>lj/charmm/coul/long/soft</I> 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)
|
||
|
|
<I>coul/cut/soft</I> args = n alpha_C cutoff
|
||
|
|
n, alpha_C = parameters of the soft-core potential
|
||
|
|
cutoff = global cutoff for Coulomb interactions (distance units)
|
||
|
|
<I>coul/long/soft</I> args = n alpha_C cutoff
|
||
|
|
n, alpha_C = parameters of the soft-core potential
|
||
|
|
cutoff = global cutoff for Coulomb interactions (distance units)
|
||
|
|
<I>tip4p/long/soft</I> 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)
|
||
|
|
|
||
|
|
</PRE>
|
||
|
|
<P><B>Examples:</B>
|
||
|
|
</P>
|
||
|
|
<PRE>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
|
||
|
|
</PRE>
|
||
|
|
<PRE>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
|
||
|
|
</PRE>
|
||
|
|
<PRE>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
|
||
|
|
</PRE>
|
||
|
|
<PRE>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
|
||
|
|
</PRE>
|
||
|
|
<PRE>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
|
||
|
|
</PRE>
|
||
|
|
<PRE>pair_style coul/long/soft 1.0 10.0 9.5
|
||
|
|
pair_coeff * * 1.0
|
||
|
|
pair_coeff 1 1 1.0 9.5
|
||
|
|
</PRE>
|
||
|
|
<PRE>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
|
||
|
|
</PRE>
|
||
|
|
<P><B>Description:</B>
|
||
|
|
</P>
|
||
|
|
<P>The <I>lj/cut/soft</I> 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 <A HREF = "#Beutler">(Beutler)</A>,
|
||
|
|
</P>
|
||
|
|
<CENTER><IMG SRC = "Eqs/pair_lj_soft.jpg">
|
||
|
|
</CENTER>
|
||
|
|
<P>Coulomb interactions are also damped with a soft core at short
|
||
|
|
distance,
|
||
|
|
</P>
|
||
|
|
<CENTER><IMG SRC = "Eqs/pair_coul_soft.jpg">
|
||
|
|
</CENTER>
|
||
|
|
<P>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 <A HREF = "dielectric.html">dielectric</A> command.
|
||
|
|
</P>
|
||
|
|
<P>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
|
||
|
|
<A HREF = "#Beutler">(Beutler)</A>.
|
||
|
|
</P>
|
||
|
|
<P>The paratemers n, alpha_LJ and alpha_C are set in the
|
||
|
|
<A HREF = "pair_style.html">pair_style</A> 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.
|
||
|
|
</P>
|
||
|
|
<CENTER><IMG SRC = "JPG/lj_soft.jpg"><IMG SRC = "JPG/coul_soft.jpg">
|
||
|
|
</CENTER>
|
||
|
|
<P>For the <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> pair styles,
|
||
|
|
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>lambda (activation parameter between 0 and 1)
|
||
|
|
<LI>cutoff1 (distance units)
|
||
|
|
<LI>cutoff2 (distance units)
|
||
|
|
</UL>
|
||
|
|
<P>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 <I>lj/cut/soft</I>,
|
||
|
|
since it has no Coulombic terms. For the <I>coul/cut/soft</I> and
|
||
|
|
<I>coul/long/soft</I> only lambda and the optional cutoff2 are to be
|
||
|
|
specified.
|
||
|
|
</P>
|
||
|
|
<P>Style <I>lj/cut/tip4p/long/soft</I> implements a soft-core version of the
|
||
|
|
TIP4P water model. The usage of this pair style is documented in the
|
||
|
|
<A HREF = "pair_lj.html">pair_lj</A> styles. The soft-core version introduces the
|
||
|
|
lambda parameter to the list of arguments, after epsilon and sigma in
|
||
|
|
the <A HREF = "pair_coeff.html">pair_coeff</A> command. The paratemers n, alpha_LJ
|
||
|
|
and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A> command,
|
||
|
|
before the cutoffs.
|
||
|
|
</P>
|
||
|
|
<P>Style <I>lj/charmm/coul/long/soft</I> 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 <A HREF = "pair_charmm.html">pair_charmm</A> styles. The soft-core version
|
||
|
|
introduces the lambda parameter to the list of arguments, after
|
||
|
|
epsilon and sigma in the <A HREF = "pair_coeff.html">pair_coeff</A> command (and
|
||
|
|
before the optional eps14 and sigma14). The paratemers n,
|
||
|
|
alpha_LJ and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A>
|
||
|
|
command, before the cutoffs.
|
||
|
|
</P>
|
||
|
|
<P>The <I>coul/cut/soft</I>, <I>coul/long/soft</I> and <I>tip4p/long/soft</I> substyles
|
||
|
|
are designed to be combined with other pair potentials via the
|
||
|
|
<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> 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).
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTES: When using the core-softed Coulomb potentials with
|
||
|
|
long-range solvers (<I>coul/long/soft</I>, <I>lj/cut/coul/long/soft</I>, etc.)
|
||
|
|
in a free energy calculation in which sites holding electrostatic
|
||
|
|
charges are being created or anihilated (using
|
||
|
|
<A HREF = "fix_adapt_fep.html">fix_adapt/fep</A> and <A HREF = "compute_fep.html">compute_fep</A>)
|
||
|
|
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.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</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-INTEL,
|
||
|
|
KOKKOS, 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, tail correction, restart info</B>:
|
||
|
|
</P>
|
||
|
|
<P>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 <I>geometric</I>. See the "pair_modify" command
|
||
|
|
for details.
|
||
|
|
</P>
|
||
|
|
<P>These 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>These 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>These pair styles write 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>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P><B>Restrictions:</B>
|
||
|
|
</P>
|
||
|
|
<P>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 <I>coul/long/soft</I> or
|
||
|
|
similar substyle can be used via the
|
||
|
|
<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P>All of the plain <I>soft</I> pair styles are part of the USER-FEP package.
|
||
|
|
The <I>long</I> styles also requires the KSPACE package to be installed.
|
||
|
|
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><B>Related commands:</B>
|
||
|
|
</P>
|
||
|
|
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_adapt.html">fix_adapt</A>,
|
||
|
|
<A HREF = "fix_adapt_fep.html">fix_adapt/fep</A>, <A HREF = "compute_fep.html">compute_fep</A>
|
||
|
|
</P>
|
||
|
|
<P><B>Default:</B> none
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<A NAME = "Beutler"></A>
|
||
|
|
|
||
|
|
<P><B>(Beutler)</B> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
|
||
|
|
Phys Lett, 222, 529 (1994).
|
||
|
|
</P>
|
||
|
|
</HTML>
|