From 954be8483a4d3bb085cec702c956d7a226f80cc2 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 14 Nov 2019 20:44:22 -0500
Subject: [PATCH] Update docs: angle_dipole

---
 doc/src/Eqs/angle_dipole_couple.jpg    | Bin 2930 -> 0 bytes
 doc/src/Eqs/angle_dipole_couple.tex    |  10 --
 doc/src/Eqs/angle_dipole_gamma.jpg     | Bin 2709 -> 0 bytes
 doc/src/Eqs/angle_dipole_gamma.tex     |   9 --
 doc/src/Eqs/angle_dipole_potential.jpg | Bin 2616 -> 0 bytes
 doc/src/Eqs/angle_dipole_potential.tex |   9 --
 doc/src/Eqs/angle_dipole_torque.jpg    | Bin 5110 -> 0 bytes
 doc/src/Eqs/angle_dipole_torque.tex    |   9 --
 doc/src/angle_dipole.rst               |  87 +++++++++--------
 doc/txt/angle_dipole.txt               | 126 -------------------------
 10 files changed, 46 insertions(+), 204 deletions(-)
 delete mode 100644 doc/src/Eqs/angle_dipole_couple.jpg
 delete mode 100644 doc/src/Eqs/angle_dipole_couple.tex
 delete mode 100644 doc/src/Eqs/angle_dipole_gamma.jpg
 delete mode 100644 doc/src/Eqs/angle_dipole_gamma.tex
 delete mode 100644 doc/src/Eqs/angle_dipole_potential.jpg
 delete mode 100644 doc/src/Eqs/angle_dipole_potential.tex
 delete mode 100644 doc/src/Eqs/angle_dipole_torque.jpg
 delete mode 100644 doc/src/Eqs/angle_dipole_torque.tex
 delete mode 100644 doc/txt/angle_dipole.txt

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diff --git a/doc/src/Eqs/angle_dipole_couple.tex b/doc/src/Eqs/angle_dipole_couple.tex
deleted file mode 100644
index a857d83d7a..0000000000
--- a/doc/src/Eqs/angle_dipole_couple.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
--\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
-\vec{F_j} & = & -\vec{F_i} \\
-\end{eqnarray*}                           
-
-\end{document}
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diff --git a/doc/src/Eqs/angle_dipole_gamma.tex b/doc/src/Eqs/angle_dipole_gamma.tex
deleted file mode 100644
index 965b74ad96..0000000000
--- a/doc/src/Eqs/angle_dipole_gamma.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   \cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_dipole_potential.jpg b/doc/src/Eqs/angle_dipole_potential.jpg
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diff --git a/doc/src/Eqs/angle_dipole_potential.tex b/doc/src/Eqs/angle_dipole_potential.tex
deleted file mode 100644
index 8949835eb7..0000000000
--- a/doc/src/Eqs/angle_dipole_potential.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (\cos\gamma - \cos\gamma_0)^2 
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_dipole_torque.jpg b/doc/src/Eqs/angle_dipole_torque.jpg
deleted file mode 100644
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diff --git a/doc/src/Eqs/angle_dipole_torque.tex b/doc/src/Eqs/angle_dipole_torque.tex
deleted file mode 100644
index 9527459fdc..0000000000
--- a/doc/src/Eqs/angle_dipole_torque.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
-           \vec{r_{ij}} \times \vec{\mu_j}
-$$
-\end{document}
\ No newline at end of file
diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst
index dac03c03b5..0ad7da5069 100644
--- a/doc/src/angle_dipole.rst
+++ b/doc/src/angle_dipole.rst
@@ -1,16 +1,16 @@
-.. index:: angle\_style dipole
+.. index:: angle_style dipole
 
-angle\_style dipole command
-===========================
+angle_style dipole command
+==========================
 
-angle\_style dipole/omp command
-===============================
+angle_style dipole/omp command
+==============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style dipole
 
@@ -18,7 +18,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style dipole
    angle_coeff 6 2.1 180.0
@@ -28,53 +28,63 @@ Description
 
 The *dipole* angle style is used to control the orientation of a dipolar
 atom within a molecule :ref:`(Orsi) <Orsi>`. Specifically, the *dipole* angle
-style restrains the orientation of a point dipole mu\_j (embedded in atom
-'j') with respect to a reference (bond) vector r\_ij = r\_i - r\_j, where 'i'
-is another atom of the same molecule (typically, 'i' and 'j' are also
-covalently bonded).
+style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom
+:math:`j`) with respect to a reference (bond) vector
+:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of
+the same molecule (typically, :math:`i` and :math:`j` are also covalently bonded).
 
-It is convenient to define an angle gamma between the 'free' vector mu\_j
-and the reference (bond) vector r\_ij:
+It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}`
+and the reference (bond) vector :math:`\vec{r_{ij}}`:
+
+.. math::
+
+   \cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}}
 
-.. image:: Eqs/angle_dipole_gamma.jpg
-   :align: center
 
 The *dipole* angle style uses the potential:
 
-.. image:: Eqs/angle_dipole_potential.jpg
-   :align: center
+.. math::
 
-where K is a rigidity constant and gamma0 is an equilibrium (reference)
+   E = K (\cos\gamma - \cos\gamma_0)^2
+
+
+where :math:`K` is a rigidity constant and gamma0 is an equilibrium (reference)
 angle.
 
 The torque on the dipole can be obtained by differentiating the
 potential using the 'chain rule' as in appendix C.3 of
 :ref:`(Allen) <Allen1>`:
 
-.. image:: Eqs/angle_dipole_torque.jpg
-   :align: center
+.. math::
 
-Example: if gamma0 is set to 0 degrees, the torque generated by
+   \vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j}
+
+
+Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by
 the potential will tend to align the dipole along the reference
-direction defined by the (bond) vector r\_ij (in other words, mu\_j is
-restrained to point towards atom 'i').
+direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is
+restrained to point towards atom :math:`i`).
 
-The dipolar torque T\_j must be counterbalanced in order to conserve
+The dipolar torque :math:`\vec{T_j}` must be counterbalanced in order to conserve
 the local angular momentum. This is achieved via an additional force
-couple generating a torque equivalent to the opposite of T\_j:
+couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`:
 
-.. image:: Eqs/angle_dipole_couple.jpg
-   :align: center
+.. math::
 
-where F\_i and F\_j are applied on atoms i and j, respectively.
+   -\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
+   \vec{F_j} & = & -\vec{F_i} \\
+
+
+where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i`
+and :math:`j`, respectively.
 
 The following coefficients must be defined for each angle type via the
 :doc:`angle\_coeff <angle_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)
-* gamma0 (degrees)
+* :math:`K` (energy)
+* :math:`\gamma_0` (degrees)
 
 
 ----------
@@ -108,17 +118,17 @@ page for more info.
 
 .. note::
 
-   In the "Angles" section of the data file, the atom ID 'j'
+   In the "Angles" section of the data file, the atom ID :math:`j`
    defining the direction of the dipole vector to restrain must come
-   before the atom ID of the reference atom 'i'. A third atom ID 'k' must
+   before the atom ID of the reference atom :math:`i`. A third atom ID :math:`k` must
    also be provided to comply with the requirement of a valid angle
-   definition. This atom ID k should be chosen to be that of an atom
-   bonded to atom 'i' to avoid errors with "lost angle atoms" when running
+   definition. This atom ID :math:`k` should be chosen to be that of an atom
+   bonded to atom :math:`i` to avoid errors with "lost angle atoms" when running
    in parallel. Since the LAMMPS code checks for valid angle definitions,
-   cannot use the same atom ID of either 'i' or 'j' (this was allowed
+   cannot use the same atom ID of either :math:`i` or :math:`j` (this was allowed
    and recommended with older LAMMPS versions).
 
-The "newton" command for intramolecular interactions must be "on"
+The :doc:`newton <newton>` command for intramolecular interactions must be "on"
 (which is the default except when using some accelerator packages).
 
 This angle style should not be used with SHAKE.
@@ -147,8 +157,3 @@ lipid membranes, PloS ONE 6(12): e28637, 2011.
 
 **(Allen)** Allen & Tildesley, Computer Simulation of Liquids,
 Clarendon Press, Oxford, 1987.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/txt/angle_dipole.txt b/doc/txt/angle_dipole.txt
deleted file mode 100644
index cdb11972ec..0000000000
--- a/doc/txt/angle_dipole.txt
+++ /dev/null
@@ -1,126 +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
-
-angle_style dipole command :h3
-angle_style dipole/omp command :h3
-
-[Syntax:]
-
-angle_style dipole :pre
-
-[Examples:]
-
-angle_style dipole
-angle_coeff 6 2.1 180.0 :pre
-
-[Description:]
-
-The {dipole} angle style is used to control the orientation of a dipolar
-atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
-style restrains the orientation of a point dipole mu_j (embedded in atom
-'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
-is another atom of the same molecule (typically, 'i' and 'j' are also
-covalently bonded).
-
-It is convenient to define an angle gamma between the 'free' vector mu_j
-and the reference (bond) vector r_ij:
-
-:c,image(Eqs/angle_dipole_gamma.jpg)
-
-The {dipole} angle style uses the potential:
-
-:c,image(Eqs/angle_dipole_potential.jpg)
-
-where K is a rigidity constant and gamma0 is an equilibrium (reference)
-angle.
-
-The torque on the dipole can be obtained by differentiating the
-potential using the 'chain rule' as in appendix C.3 of
-"(Allen)"_#Allen1:
-
-:c,image(Eqs/angle_dipole_torque.jpg)
-
-Example: if gamma0 is set to 0 degrees, the torque generated by
-the potential will tend to align the dipole along the reference
-direction defined by the (bond) vector r_ij (in other words, mu_j is
-restrained to point towards atom 'i').
-
-The dipolar torque T_j must be counterbalanced in order to conserve
-the local angular momentum. This is achieved via an additional force
-couple generating a torque equivalent to the opposite of T_j:
-
-:c,image(Eqs/angle_dipole_couple.jpg)
-
-where F_i and F_j are applied on atoms i and j, respectively.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_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)
-gamma0 (degrees) :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.
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER-MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-NOTE: In the "Angles" section of the data file, the atom ID 'j'
-defining the direction of the dipole vector to restrain must come
-before the atom ID of the reference atom 'i'. A third atom ID 'k' must
-also be provided to comply with the requirement of a valid angle
-definition. This atom ID k should be chosen to be that of an atom
-bonded to atom 'i' to avoid errors with "lost angle atoms" when running
-in parallel. Since the LAMMPS code checks for valid angle definitions,
-cannot use the same atom ID of either 'i' or 'j' (this was allowed
-and recommended with older LAMMPS versions).
-
-The "newton" command for intramolecular interactions must be "on"
-(which is the default except when using some accelerator packages).
-
-This angle style should not be used with SHAKE.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html
-
-[Default:] none
-
-:line
-
-:link(Orsi)
-[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
-lipid membranes, PloS ONE 6(12): e28637, 2011.
-
-:link(Allen1)
-[(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
-Clarendon Press, Oxford, 1987.