Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/src/bond_quartic.txt
e6ac7757a374efficient_neuronet

Last Change
Raw File

bond_quartic.txt
View Options

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style quartic command :h3
bond_style quartic/omp command :h3
[Syntax:]
bond_style quartic :pre
[Examples:]
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
[Description:]
The {quartic} bond style uses the potential
:c,image(Eqs/bond_quartic.jpg)
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^4)
B1 (distance)
B2 (distance)
Rc (distance)
U0 (energy) :ul
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the "bond_coeff"_bond_coeff.html command, but
you will need to choose them carefully so they form a suitable bond
potential.
Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
are no longer bonded.
LAMMPS does the second task via a computational sleight-of-hand. It
subtracts the pairwise interaction as part of the bond computation.
When the bond breaks, the subtraction stops. For this to work, the
pairwise interaction must always be computed by the
"pair_style"_pair_style.html command, whether the bond is broken or
not. This means that "special_bonds"_special_bonds.html must be set
to 1,1,1, as indicated as a restriction below.
Note that when bonds are dumped to a file via the "dump
local"_dump.html command, bonds with type 0 are not included. The
"delete_bonds"_delete_bonds.html command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
delete_bonds all stats
delete_bonds all bond 0 remove :pre
:line
Styles with a {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 "Section 5"_Section_accelerate.html
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 GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#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 "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with {quartic} bonds.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
c4science · Help