diff --git a/doc/src/Eqs/bond_fene.jpg b/doc/src/Eqs/bond_fene.jpg deleted file mode 100644 index e8b909c08f..0000000000 Binary files a/doc/src/Eqs/bond_fene.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_fene.tex b/doc/src/Eqs/bond_fene.tex deleted file mode 100644 index ec4dd8efa2..0000000000 --- a/doc/src/Eqs/bond_fene.tex +++ /dev/null @@ -1,11 +0,0 @@ -\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} \ No newline at end of file diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index cd25419544..d952321c20 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -1,22 +1,22 @@ -.. 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) `, 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`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 diff --git a/doc/txt/bond_fene.txt b/doc/txt/bond_fene.txt deleted file mode 100644 index 9ec4017d00..0000000000 --- a/doc/txt/bond_fene.txt +++ /dev/null @@ -1,88 +0,0 @@ -"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).