Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/dihedral_class2.txt
37ed3d917e88efficient_neuronet

Last Change
Raw File

dihedral_class2.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
dihedral_style class2 command :h3
dihedral_style class2/omp command :h3
[Syntax:]
dihedral_style class2 :pre
[Examples:]
dihedral_style class2
dihedral_coeff 1 100 75 100 70 80 60
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
dihedral_coeff * aat -13.5271 110.2453 105.1270
dihedral_coeff * bb13 0.0 1.0119 1.1010 :pre
[Description:]
The {class2} dihedral style uses the potential
:c,image(Eqs/dihedral_class2.jpg)
where Ed is the dihedral term, Embt is a middle-bond-torsion term,
Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_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.
These are the 6 coefficients for the Ed formula:
K1 (energy)
phi1 (degrees)
K2 (energy)
phi2 (degrees)
K3 (energy)
phi3 (degrees) :ul
For the Embt formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
5 coefficients, the first of which is "mbt" to indicate they are
MiddleBondTorsion coefficients. In a data file, these coefficients
should be listed under a "MiddleBondTorsion Coeffs" heading and you
must leave out the "mbt", i.e. only list 4 coefficients after the
dihedral type.
mbt
A1 (energy/distance)
A2 (energy/distance)
A3 (energy/distance)
r2 (distance) :ul
For the Eebt formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
9 coefficients, the first of which is "ebt" to indicate they are
EndBondTorsion coefficients. In a data file, these coefficients
should be listed under a "EndBondTorsion Coeffs" heading and you must
leave out the "ebt", i.e. only list 8 coefficients after the dihedral
type.
ebt
B1 (energy/distance)
B2 (energy/distance)
B3 (energy/distance)
C1 (energy/distance)
C2 (energy/distance)
C3 (energy/distance)
r1 (distance)
r3 (distance) :ul
For the Eat formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
9 coefficients, the first of which is "at" to indicate they are
AngleTorsion coefficients. In a data file, these coefficients should
be listed under a "AngleTorsion Coeffs" heading and you must leave out
the "at", i.e. only list 8 coefficients after the dihedral type.
at
D1 (energy/radian)
D2 (energy/radian)
D3 (energy/radian)
E1 (energy/radian)
E2 (energy/radian)
E3 (energy/radian)
theta1 (degrees)
theta2 (degrees) :ul
Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of D and E are in
energy/radian.
For the Eaat formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
4 coefficients, the first of which is "aat" to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a "AngleAngleTorsion Coeffs" heading and you
must leave out the "aat", i.e. only list 3 coefficients after the
dihedral type.
aat
M (energy/radian^2)
theta1 (degrees)
theta2 (degrees) :ul
Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of M are in energy/radian^2.
For the Ebb13 formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
4 coefficients, the first of which is "bb13" to indicate they are
BondBond13 coefficients. In a data file, these coefficients should be
listed under a "BondBond13 Coeffs" heading and you must leave out the
"bb13", i.e. only list 3 coefficients after the dihedral type.
bb13
N (energy/distance^2)
r1 (distance)
r3 (distance) :ul
:line
Styles with a {cuda}, {gpu}, {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_accelerate"_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 USER-CUDA, GPU, 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_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
c4science · Help