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rLAMMPS lammps
pair_gauss.html
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<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 gauss command
</H3>
<H3>
pair_style gauss/gpu command
</H3>
<H3>
pair_style gauss/omp command
</H3>
<H3>
pair_style gauss/cut command
</H3>
<H3>
pair_style gauss/cut/omp command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
pair_style gauss cutoff
pair_style gauss/cut cutoff
</PRE>
<UL><LI>
cutoff = global cutoff for Gauss interactions (distance units)
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
pair_style gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
</PRE>
<PRE>
pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Style
<I>
gauss
</I>
computes a tethering potential of the form
</P>
<CENTER><IMG
SRC =
"Eqs/pair_gauss.jpg"
>
</CENTER>
<P>
between an atom and its corresponding tether site which will typically
be a frozen atom in the simulation. Rc is the cutoff.
</P>
<P>
The following coefficients must be defined for each pair of atom 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:
</P>
<UL><LI>
A (energy units)
<LI>
B (1/distance^2 units)
<LI>
cutoff (distance units)
</UL>
<P>
The last coefficient is optional. If not specified, the global cutoff
is used.
</P>
<P>
Style
<I>
gauss/cut
</I>
computes a generalized Gaussian interaction potential
between pairs of particles:
</P>
<CENTER><IMG
SRC =
"Eqs/pair_gauss_cut.jpg"
>
</CENTER>
<P>
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
<A
HREF =
"#Lenart"
>
(Lenart)
</A>
and of surfactants
<A
HREF =
"#Jusufi"
>
(Jusufi)
</A>
. 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.
</P>
<P>
The following coefficients must be defined for each pair of atom types
via the
<A
HREF =
"pair_coeff.html"
>
pair_coeff
</A>
command as in the example 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:
</P>
<UL><LI>
H (energy * distance units)
<LI>
r_mh (distance units)
<LI>
sigma_h (distance units)
</UL>
<P>
The global cutoff (r_c) specified in the pair_style command is used.
</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 "-suffix command-line
switch7_Section_start.html#start_6 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>
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>
The
<I>
gauss
</I>
style does not support the
<A
HREF =
"pair_modify.html"
>
pair_modify
</A>
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.
</P>
<P>
The
<I>
gauss/cut
</I>
style supports the
<A
HREF =
"pair_modify.html"
>
pair_modify
</A>
shift
option for the energy of the Gauss-potential portion of the pair
interaction.
</P>
<P>
The
<A
HREF =
"pair_modify.html"
>
pair_modify
</A>
table and tail options are not
relevant for these pair styles.
</P>
<P>
These 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>
These pair styles can only be used via the
<I>
pair
</I>
keyword of the
<A
HREF =
"run_style.html"
>
run_style respa
</A>
command. They do not support the
<I>
inner
</I>
,
<I>
middle
</I>
,
<I>
outer
</I>
keywords.
</P>
<P>
The
<I>
gauss
</I>
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
<A
HREF =
"compute_pair.html"
>
compute
pair
</A>
command as a vector of values of length 1.
</P>
<P>
To print this quantity to the log file (with a descriptive column
heading) the following commands could be included in an input script:
</P>
<PRE>
compute gauss all pair gauss
variable occ equal c_gauss[1]
thermo_style custom step temp epair v_occ
</PRE>
<HR>
<P><B>
Restrictions:
</B>
</P>
<P>
The
<I>
gauss/cut
</I>
style is part of the "user-misc" package. It is only
enabled if LAMMPS is build with that package. See the
<A
HREF =
"Section_start.html#3"
>
Making of
LAMMPS
</A>
section for more info.
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"pair_coeff.html"
>
pair_coeff
</A>
,
<A
HREF =
"pair_coul_diel.html"
>
pair_style coul/diel
</A>
</P>
<P><B>
Default:
</B>
none
</P>
<A
NAME =
"Lenart"
></A>
<P><B>
(Lenart)
</B>
Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
044509 (2007).
</P>
<A
NAME =
"Jusufi"
></A>
<P><B>
(Jusufi)
</B>
Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
13783 (2008).
</P>
</HTML>
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