Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/html/_sources/dihedral_class2.txt
caf9483a0a7clammm-devel

Last Change
Raw File

dihedral_class2.txt
View Options

.. index:: dihedral_style class2
dihedral_style class2 command
=============================
dihedral_style class2/omp command
=================================
Syntax
""""""
.. parsed-literal::
dihedral_style class2
Examples
""""""""
.. parsed-literal::
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
Description
"""""""""""
The *class2* dihedral style uses the potential
.. image:: Eqs/dihedral_class2.jpg
:align: center
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 :ref:`(Sun) <dihedral-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
:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above,
or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands.
These are the 6 coefficients for the Ed formula:
* K1 (energy)
* phi1 (degrees)
* K2 (energy)
* phi2 (degrees)
* K3 (energy)
* phi3 (degrees)
For the Embt formula, each line in a
:doc:`dihedral_coeff <dihedral_coeff>` 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)
For the Eebt formula, each line in a
:doc:`dihedral_coeff <dihedral_coeff>` 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)
For the Eat formula, each line in a
:doc:`dihedral_coeff <dihedral_coeff>` 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)
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
:doc:`dihedral_coeff <dihedral_coeff>` 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)
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
:doc:`dihedral_coeff <dihedral_coeff>` 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)
----------
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 :doc:`Section_accelerate <Section_accelerate>`
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 :ref:`Making LAMMPS <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 :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
more instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
CLASS2 package. See the :ref:`Making LAMMPS <start_3>`
section for more info on packages.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
**Default:** none
----------
.. _dihedral-Sun:
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help