From 5f89fde6bce07f13dc7c3561d49eee2e40b5babe Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sat, 16 Nov 2019 18:59:49 -0500
Subject: [PATCH] Update docs: bond_fene

---
 doc/src/Eqs/bond_fene.jpg | Bin 8322 -> 0 bytes
 doc/src/Eqs/bond_fene.tex |  11 -----
 doc/src/bond_fene.rst     |  45 +++++++++----------
 doc/txt/bond_fene.txt     |  88 --------------------------------------
 4 files changed, 21 insertions(+), 123 deletions(-)
 delete mode 100644 doc/src/Eqs/bond_fene.jpg
 delete mode 100644 doc/src/Eqs/bond_fene.tex
 delete mode 100644 doc/txt/bond_fene.txt

diff --git a/doc/src/Eqs/bond_fene.jpg b/doc/src/Eqs/bond_fene.jpg
deleted file mode 100644
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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) <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
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).