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Update docs: bond_fene

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Richard Berger
2019-11-16 18:59:49 -05:00
parent 98bd975e90
commit 5f89fde6bc
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doc/src/Eqs/bond_fene.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

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doc/src/bond_fene.rst
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.. index:: bond\_style fene
.. index:: bond_style fene
bond\_style fene command
========================
bond_style fene command
=======================
bond\_style fene/intel command
==============================
bond_style fene/intel command
=============================
bond\_style fene/kk command
bond_style fene/kk command
==========================
bond_style fene/omp command
===========================
bond\_style fene/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
@ -34,24 +34,26 @@ Description
The *fene* bond style uses the potential
.. image:: Eqs/bond_fene.jpg
:align: center
.. math::
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential.
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_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:
* K (energy/distance\^2)
* R0 (distance)
* epsilon (energy)
* sigma (distance)
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
----------
@ -107,8 +109,3 @@ Related commands
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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doc/txt/bond_fene.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style fene command :h3
bond_style fene/intel command :h3
bond_style fene/kk command :h3
bond_style fene/omp command :h3
[Syntax:]
bond_style fene :pre
[Examples:]
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0 :pre
[Description:]
The {fene} bond style uses the potential
:c,image(Eqs/bond_fene.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#fene-Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
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^2)
R0 (distance)
epsilon (energy)
sigma (distance) :ul
: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 on the "Speed packages"_Speed_packages.html doc
page. 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 "Build
package"_Build_package.html doc page 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"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page 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. See the "Build package"_Build_package.html doc page for more
info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(fene-Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).