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additional formatting updates

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Axel Kohlmeyer
2022-09-21 15:54:25 -04:00
parent ad76bb2997
commit 0343ad09ea
1 changed files with 12 additions and 10 deletions
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22
doc/src/pair_gayberne.rst
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@ -44,14 +44,15 @@ ellipsoidal and spherical particle via the formulas
U_r = & 4 \epsilon ( \varrho^{12} - \varrho^6) \\
\varrho = & \frac{\sigma}{ h_{12} + \gamma \sigma}
where A1 and A2 are the transformation matrices from the simulation box
frame to the body frame and :math:`r_{12}` is the center to center
vector between the particles. :math:`U_r` controls the shifted distance
dependent interaction based on the distance of closest approach of the
two particles (:math:`h_{12}`) and the user-specified shift parameter
gamma. When both particles are spherical, the formula reduces to the
usual Lennard-Jones interaction (see details below for when Gay-Berne
treats a particle as "spherical").
where :math:`\mathbf{A}_1` and :math:`\mathbf{A}_2` are the
transformation matrices from the simulation box frame to the body frame
and :math:`r_{12}` is the center to center vector between the particles.
:math:`U_r` controls the shifted distance dependent interaction based on
the distance of closest approach of the two particles (:math:`h_{12}`)
and the user-specified shift parameter :math:`\gamma`. When both
particles are spherical, the formula reduces to the usual Lennard-Jones
interaction (see details below for when Gay-Berne treats a particle as
"spherical").
For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
@ -74,8 +75,9 @@ listed below and in `this supplementary document <PDF/pair_gayberne_extra.pdf>`_
Use of this pair style requires the NVE, NVT, or NPT fixes with the
*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid <atom_style>` should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.
order to integrate particle rotation. Additionally, :doc:`atom_style
ellipsoid <atom_style>` should be used since it defines the rotational
state and the size and shape of each ellipsoidal particle.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples