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reformat, remove accelerator info, correct restrictions

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Axel Kohlmeyer
2022-10-18 14:35:22 -04:00
parent 45713e97d4
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doc/src/pair_ylz.rst
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@ -1,13 +1,8 @@
.. index:: pair_style ylz
.. index:: pair_style ylz/gpu
.. index:: pair_style ylz/intel
.. index:: pair_style ylz/omp
pair_style ylc command
===========================
Accelerator Variants: *ylz/gpu*, *ylz/intel*, *ylz/omp*
Syntax
""""""
@ -30,14 +25,29 @@ Examples
Description
"""""""""""
The *ylz* (Yuan-Li-Zhang)
:ref:`(Yuan) <Yuan>` style computes anisotropic interactions between pairs of particles considering the relative particle orientations via the formulas
The *ylz* (Yuan-Li-Zhang) :ref:`(Yuan) <Yuan>` style computes
anisotropic interactions between pairs of particles considering the
relative particle orientations via the formulas
.. math::
U ( \mathbf{r}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) =\left\{\begin{matrix} \mathbf{u}_R(r)+\left [ 1-\phi (\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) \right ]\epsilon, ~~ r<\mathbf{r}_{min} \\ \mathbf{u}_A(r)\phi (\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ),~~ \mathbf{r}_{min}<r<\mathbf{r}_{c} \\ \end{matrix}\right.\\\\ \phi (\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=1+\mu (a(\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )-1) \\\\ a(\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=(\mathbf{n}_i\times\mathbf{r\hat{}}_{ij} )\cdot (\mathbf{n}_j\times\mathbf{r\hat{}}_{ij} )+sin\mathbf{\theta}_0(\mathbf{n}_i-\mathbf{n}_j)\cdot \mathbf{r\hat{}}_{ij}\\\\ \mathbf{u}_R(r)=\epsilon \left [ \left ( \frac{{r}_{min}}{r} \right )^{4}-2\left ( \frac{{r}_{min}}{r}\right )^{2} \right ] \\\\ \mathbf{u}_A(r)=-\epsilon\;cos^{2\zeta }\left ( \frac{\pi}{2}\frac{\left ( {r}-{r}_{min} \right )}{\left ( {r}_{c}-{r}_{min} \right )} \right ) \\
where :math:`r_{i}` and :math:`r_{j}` are the center position vectors of particles i and j, respectively, :math:`r_{ij}=r_{i}-r_{j}` is the inter-particle distance vector, :math:`r=\left|r_{ij} \right|` and :math:`{r\hat{}}_{ij}=\mathbf{r}_{ij}/r`. The unit vectors :math:`n_{i}` and :math:`n_{j}` represent the axes of symmetry of particles i and j, respectively. :math:`u_R` and :math:`u_A` are the repulsive and attractive potentials. :math:`\phi` is an angular function which depends on the relative orientation between pair particles. :math:`\mu` is the parameter related to bending rigidity, :math:`\theta_{0}` is the parameter related to the spontaneous curvature, and :math:`\epsilon` is the energy unit, respectively. The :math:`\zeta` controls the slope of the attractive branch and :math:`{r}_{c}`is the cutoff radius. :math:`r_{min}` is the distance which minimizes the potential energy :math:`u_{A}(r)`and :math:`r_{min}=2^{1/6}\sigma`, where :math:`\sigma` is the length unit.
where :math:`r_{i}` and :math:`r_{j}` are the center position vectors of
particles i and j, respectively, :math:`r_{ij}=r_{i}-r_{j}` is the
inter-particle distance vector, :math:`r=\left|r_{ij} \right|` and
:math:`{r\hat{}}_{ij}=\mathbf{r}_{ij}/r`. The unit vectors :math:`n_{i}`
and :math:`n_{j}` represent the axes of symmetry of particles i and j,
respectively. :math:`u_R` and :math:`u_A` are the repulsive and
attractive potentials. :math:`\phi` is an angular function which depends
on the relative orientation between pair particles. :math:`\mu` is the
parameter related to bending rigidity, :math:`\theta_{0}` is the
parameter related to the spontaneous curvature, and :math:`\epsilon` is
the energy unit, respectively. The :math:`\zeta` controls the slope of
the attractive branch and :math:`{r}_{c}`is the cutoff
radius. :math:`r_{min}` is the distance which minimizes the potential
energy :math:`u_{A}(r)`and :math:`r_{min}=2^{1/6}\sigma`, where
:math:`\sigma` is the length unit.
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 of each particle.
@ -53,29 +63,28 @@ The following coefficients must be defined for each pair of atoms types via the
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair_modify" command for details.
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is *geometric*\ . See the "pair_modify" command for details.
The :doc:`pair_modify <pair_modify>` table option is not relevant for this pair style.
The :doc:`pair_modify <pair_modify>` table option is not relevant for
this pair style.
This pair style does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
This pair style does not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file.
This pair style writes its information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the :doc:`run_style respa <run_style>` command. It does not support the
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
----------
@ -83,24 +92,26 @@ This pair style can only be used via the *pair* keyword of the :doc:`run_style r
Restrictions
""""""""""""
The *ylz* style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
The *ylz* style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These pair styles require that atoms store torque and a quaternion to represent their orientation, as defined by the :doc:`atom_style <atom_style>`. It also require they store a per-type :doc:`shape <set>`. The particles cannot store a per-particle diameter.
This pair style requires that atoms store torque and a quaternion to
represent their orientation, as defined by the :doc:`atom_style
<atom_style>`. It also requires they store a per-atom :doc:`shape
<set>`. The particles cannot store a per-particle diameter.
This pair style requires that atoms be ellipsoids as defined by the
:doc:`atom_style ellipsoid <atom_style>` command.
Particles acted on by the potential can be finite-size aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
This pair style requires that **all** atoms are ellipsoids as defined by
the :doc:`atom_style ellipsoid <atom_style>` command.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere <fix_nve_asphere>`,
:doc:`compute temp/asphere <compute_temp_asphere>`, :doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style gayberne <pair_resquared>`
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere
:doc:<fix_nve_asphere>`, `compute temp/asphere <compute_temp_asphere>`,
:doc::doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style
:doc:gayberne <pair_resquared>`
Default
"""""""