Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F93631079
pair_airebo.html
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Nov 30, 07:14
Size
8 KB
Mime Type
text/html
Expires
Mon, Dec 2, 07:14 (2 d)
Engine
blob
Format
Raw Data
Handle
22680120
Attached To
rLAMMPS lammps
pair_airebo.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 airebo command
</H3>
<H3>
pair_style airebo/omp command
</H3>
<H3>
pair_style rebo command
</H3>
<H3>
pair_style rebo/omp command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
pair_style style cutoff LJ_flag TORSION_flag
</PRE>
<UL><LI>
style =
<I>
airebo
</I>
or
<I>
rebo
</I>
<LI>
cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
<LI>
LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
<LI>
TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional)
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
pair_style airebo 3.0
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C
</PRE>
<PRE>
pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C
</PRE>
<P><B>
Description:
</B>
</P>
<P>
The
<I>
airebo
</I>
pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of
<A
HREF =
"#Stuart"
>
(Stuart)
</A>
for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
<I>
rebo
</I>
pair style computes the Reactive Empirical Bond Order (REBO)
Potential of
<A
HREF =
"#Brenner"
>
(Brenner)
</A>
. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.
</P>
<P>
The AIREBO potential consists of three terms:
</P>
<CENTER><IMG
SRC =
"Eqs/pair_airebo.jpg"
>
</CENTER>
<P>
By default, all three terms are included. For the
<I>
airebo
</I>
style, if
the two optional flag arguments to the pair_style command are
included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
with no additional arguments.
</P>
<P>
The detailed formulas for this potential are given in
<A
HREF =
"#Stuart"
>
(Stuart)
</A>
; here we provide only a brief description.
</P>
<P>
The E_REBO term has the same functional form as the hydrocarbon REBO
potential developed in
<A
HREF =
"#Brenner"
>
(Brenner)
</A>
. The coefficients for
E_REBO in AIREBO are essentially the same as Brenner's potential, but
a few fitted spline values are slightly different. For most cases the
E_REBO term in AIREBO will produce the same energies, forces and
statistical averages as the original REBO potential from which it was
derived. The E_REBO term in the AIREBO potential gives the model its
reactive capabilities and only describes short-ranged C-C, C-H and H-H
interactions (r
< 2
Angstroms
).
These
interactions
have
strong
coordination-dependence
through
a
bond
order
parameter
,
which
adjusts
the
attraction
between
the
I
,
J
atoms
based
on
the
position
of
other
nearby
atoms
and
thus
has
3-
and
4-body
dependence
.
</
P
>
<P>
The E_LJ term adds longer-ranged interactions (2
< r
<
cutoff
)
using
a
form
similar
to
the
standard
<
A
HREF =
"pair_lj.html"
>
Lennard Jones potential
</A>
.
The E_LJ term in AIREBO contains a series of switching functions so
that the short-ranged LJ repulsion (1/r^12) does not interfere with
the energetics captured by the E_REBO term. The extent of the E_LJ
interactions is determined by the
<I>
cutoff
</I>
argument to the pair_style
command which is a scale factor. For each type pair (C-C, C-H, H-H)
the cutoff is obtained by multiplying the scale factor by the sigma
value defined in the potential file for that type pair. In the
standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale
factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms.
</P>
<P>
The E_TORSION term is an explicit 4-body potential that describes
various dihedral angle preferences in hydrocarbon configurations.
</P>
<HR>
<P>
Only a single pair_coeff command is used with the
<I>
airebo
</I>
or
<I>
rebo
</I>
style which specifies an AIREBO potential file with parameters for C
and H. Note that the
<I>
rebo
</I>
style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
</P>
<UL><LI>
filename
<LI>
N element names = mapping of AIREBO elements to atom types
</UL>
<P>
See the
<A
HREF =
"pair_coeff.html"
>
pair_coeff
</A>
doc page for alternate ways
to specify the path for the potential file.
</P>
<P>
As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:
</P>
<PRE>
pair_coeff * * CH.airebo C C C H
</PRE>
<P>
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
type 4 to the H element in the SW file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a
<I>
airebo
</I>
potential is used as part of the
<I>
hybrid
</I>
pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.
</P>
<P>
The parameters/coefficients for the AIREBO potentials are listed in
the CH.airebo file to agree with the original
<A
HREF =
"#Stuart"
>
(Stuart)
</A>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.
</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, table, tail correction, restart, rRESPA info
</B>
:
</P>
<P>
These pair styles do not support the
<A
HREF =
"pair_modify.html"
>
pair_modify
</A>
mix, shift, table, and tail options.
</P>
<P>
These pair styles do not write their information to
<A
HREF =
"restart.html"
>
binary restart
files
</A>
, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands 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><B>
Restrictions:
</B>
</P>
<P>
These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package (which it is by
default). See the
<A
HREF =
"Section_start.html#start_3"
>
Making LAMMPS
</A>
section
for more info.
</P>
<P>
These pair potentials require the
<A
HREF =
"newton.html"
>
newton
</A>
setting to be
"on" for pair interactions.
</P>
<P>
The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal
<A
HREF =
"units.html"
>
units
</A>
. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn't use "metal" units.
</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 =
"Stuart"
></A>
<P><B>
(Stuart)
</B>
Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
(2000).
</P>
<A
NAME =
"Brenner"
></A>
<P><B>
(Brenner)
</B>
Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).
</P>
</HTML>
Event Timeline
Log In to Comment