Merge branch 'master' into zeeman-rework

cmake/Modules/Documentation.cmake

@@ -9,9 +9,7 @@ if(BUILD_DOC)
 
   set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
-  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
-  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
 
   add_custom_command(
     OUTPUT docenv
@@ -28,25 +26,10 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
   )
 
-  set(RST_FILES "")
-  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
-  file(MAKE_DIRECTORY ${RST_DIR})
-  foreach(TXT_FILE ${DOC_SOURCES})
-    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
-    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
-    list(APPEND RST_FILES ${RST_FILE})
-    add_custom_command(
-      OUTPUT ${RST_FILE}
-      DEPENDS requirements.txt docenv ${TXT_FILE}
-      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
-    )
-  endforeach()
-
   add_custom_command(
     OUTPUT html
-    DEPENDS ${RST_FILES}
+    DEPENDS ${DOC_SOURCES} docenv requirements.txt
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
   )
 
   add_custom_target(

doc/README

@@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
-tools           tools and settings for building the documentation
+utils           utilities and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
 LAMMPS.epub     Manual in ePUB format
@@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
 code will not, unless you update your local repository).
 
 (b) You can build the HTML and PDF files yourself, by typing "make
-html" followed by "make pdf".  Note that the PDF make requires the
+html" or by "make pdf", respectively.  This requires various tools
-HTML files already exist.  This requires various tools including
+including the Python documentation processing tool Sphinx, which the
-Sphinx, which the build process will attempt to download and install
+build process will attempt to download and install on your system into
-on your system, if not already available.  See more details below.
+a python virtual environment, if not already available.  The PDF file
-
+will require a working LaTeX installation with several add-on packages
-(c) You can genererate an older, simpler, less-fancy style of HTML
+in addition to the Python/Sphinx setup.  See more details below.
-documentation by typing "make old".  This will create an "old"
-directory.  This can be useful if (b) does not work on your box for
-some reason, or you want to quickly view the HTML version of a doc
-page you have created or edited yourself within the src directory.
-E.g. if you are planning to submit a new feature to LAMMPS.
 
 ----------------
 
@@ -46,8 +41,7 @@ Options:
 
 make html         # generate HTML in html dir using Sphinx
 make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via htmldoc and pdflatex
+                  #   in this dir via Sphinx and PDFLaTeX
-make old          # generate old-style HTML pages in old dir via txt2html
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
 make epub         # generate LAMMPS.epub in ePUB format using Sphinx
@@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
+Same as for HTML plus a compatible LaTeX installation with
-
+support for PDFLaTeX. Also the following LaTeX packages need
+to be installed (e.g. from texlive):
+- amsmath
+- babel
+- cmap
+- fncychap
+- geometry
+- hyperref
+- hypcap
+- times
 ----------------
 
 Installing prerequisites for epub build
@@ -103,7 +106,11 @@ Installing prerequisites for epub build
 ## ePUB
 
 Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
+files as the HTML tree. The ePUB format conversion currently
+does not support processing mathematical expressions via MathJAX,
+so there will be limitations on some pages. For the time being
+until this is resolved, building and using the PDF format file
+is recommended instead.
 
 For converting the generated ePUB file to a mobi format file
 (for e-book readers like Kindle, that cannot read ePUB), you

doc/src/Eqs/angle_charmm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_class2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_a + E_{bb} + E_{ba} \\
-  E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
-  E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
-  E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/angle_cosine.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [1 + \cos(\theta)] 
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_buck6d.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-$$
-  E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
-$$
-
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

doc/src/Eqs/angle_cosine_delta.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [1 - \cos(\theta - \theta_0)]
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_periodic.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]  
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_shift.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_shift_exp.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min} 
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_squared.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [\cos(\theta) - \cos(\theta_0)]^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_cross.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
-$$
-
-\end{document}

doc/src/Eqs/angle_dipole_couple.tex

@@ -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}

doc/src/Eqs/angle_dipole_gamma.tex

@@ -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}

doc/src/Eqs/angle_dipole_potential.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (\cos\gamma - \cos\gamma_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_dipole_torque.tex

@@ -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}

doc/src/Eqs/angle_fourier.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] 
-$$
-
-\end{document}

doc/src/Eqs/angle_fourier_simple.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K [ 1.0 + c \cos ( n \theta) ] 
-$$
-
-\end{document}

doc/src/Eqs/angle_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K (\theta - \theta_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_mm3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
-$$
-
-\end{document}

doc/src/Eqs/angle_quartic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
-$$
-
-\end{document}

doc/src/Eqs/bond_class2.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 
-$$
-
-\end{document}

doc/src/Eqs/bond_fene.tex

@@ -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}

doc/src/Eqs/bond_fene_expand.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = -0.5 K R_0^2
-  \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 
-  4 \epsilon \left[ \left(\frac{\sigma}{\left(r - 
-      \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - 
-      \Delta\right)}\right)^6 \right] + \epsilon
-$$
-
-\end{document}

doc/src/Eqs/bond_gromos.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-$$
-   E = K (r^2 - r_0^2)^2
-$$
-
-\end{document}

doc/src/Eqs/bond_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (r - r_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/bond_harmonic_shift.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] 
-$$
-
-\end{document}

doc/src/Eqs/bond_harmonic_shift_cut.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] 
-$$
-
-\end{document}

doc/src/Eqs/bond_mm3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
-$$
-
-\end{document}

doc/src/Eqs/bond_morse.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-%   E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2 
-   E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 
-$$
-
-\end{document}

doc/src/Eqs/bond_nonlinear.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
-$$
-
-\end{document}

doc/src/Eqs/bond_oxdna_fene.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-$$ 
-  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
-$$
-
-\end{document}

doc/src/Eqs/bond_quartic.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
-  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
-    \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}

doc/src/Install_conda.rst

@@ -32,12 +32,10 @@ install the `openkim-models` package
 
 If you have problems with the installation you can post issues to
 `this link <conda_forge_lammps_>`_.
-
+Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
-.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
-
-Thanks to Jan Janssen (Max-Planck-Institut für Eisenforschung) for setting
 up the Conda capability.
 
+.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
 
 .. _openkim: https://openkim.org
 
@@ -45,9 +43,6 @@ up the Conda capability.
 
 .. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
 
-
-
-
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html

doc/src/angle_charmm.rst

@@ -1,22 +1,22 @@
-.. index:: angle\_style charmm
+.. index:: angle_style charmm
 
-angle\_style charmm command
+angle_style charmm command
-===========================
+==========================
 
-angle\_style charmm/intel command
+angle_style charmm/intel command
-=================================
+================================
 
-angle\_style charmm/kk command
+angle_style charmm/kk command
+=============================
+
+angle_style charmm/omp command
 ==============================
 
-angle\_style charmm/omp command
-===============================
-
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style charmm
 
@@ -24,7 +24,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style charmm
    angle_coeff 1 300.0 107.0 50.0 3.0
@@ -34,12 +34,15 @@ Description
 
 The *charmm* angle style uses the potential
 
-.. image:: Eqs/angle_charmm.jpg
+.. math::
-   :align: center
 
-with an additional Urey\_Bradley term based on the distance *r* between
+   E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
-the 1st and 3rd atoms in the angle.  K, theta0, Kub, and Rub are
+
-coefficients defined for each angle type.
+
+with an additional Urey\_Bradley term based on the distance :math:`r` between
+the 1st and 3rd atoms in the angle.  :math:`K`, :math:`\theta_0`,
+:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
+type.
 
 See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
 field.
@@ -49,13 +52,13 @@ The following coefficients must be defined for each angle type via the
 the data file or restart files read by the :doc:`read\_data <read_data>`
 or :doc:`read\_restart <read_restart>` commands:
 
-* K (energy/radian\^2)
+* :math:`K` (energy/radian\^2)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
-* K\_ub (energy/distance\^2)
+* :math:`K_{ub}` (energy/distance\^2)
-* r\_ub (distance)
+* :math:`r_{ub}` (distance)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian\^2.
+internally; hence the units of :math:`K` are in energy/radian\^2.
 
 
 ----------
@@ -108,8 +111,3 @@ Related commands
 
 **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
 Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_class2.rst

@@ -1,22 +1,22 @@
-.. index:: angle\_style class2
+.. index:: angle_style class2
 
-angle\_style class2 command
+angle_style class2 command
-===========================
+==========================
 
-angle\_style class2/kk command
+angle_style class2/kk command
+=============================
+
+angle_style class2/omp command
 ==============================
 
-angle\_style class2/omp command
+angle_style class2/p6 command
-===============================
+=============================
-
-angle\_style class2/p6 command
-==============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style class2
 
@@ -24,44 +24,49 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style class2
-   angle_coeff \* 75.0
+   angle_coeff * 75.0
    angle_coeff 1 bb 10.5872 1.0119 1.5228
-   angle_coeff \* ba 3.6551 24.895 1.0119 1.5228
+   angle_coeff * ba 3.6551 24.895 1.0119 1.5228
 
 Description
 """""""""""
 
 The *class2* angle style uses the potential
 
-.. image:: Eqs/angle_class2.jpg
+.. math::
-   :align: center
 
-where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
+   E & = E_a + E_{bb} + E_{ba} \\
-bond-angle term.  Theta0 is the equilibrium angle and r1 and r2 are
+   E_a & = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4(\theta - \theta_0)^4 \\
+   E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
+   E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
+
+
+where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
+bond-angle term.  :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
 the equilibrium bond lengths.
 
 See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
 
-Coefficients for the Ea, Ebb, and Eba formulas must be defined for
+Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas 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.
 
-These are the 4 coefficients for the Ea formula:
+These are the 4 coefficients for the :math:`E_a` formula:
 
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
-* K2 (energy/radian\^2)
+* :math:`K_2` (energy/radian\^2)
-* K3 (energy/radian\^3)
+* :math:`K_3` (energy/radian\^3)
-* K4 (energy/radian\^4)
+* :math:`K_4` (energy/radian\^4)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of the various K are in per-radian.
+internally; hence the units of the various :math:`K` are in per-radian.
 
-For the Ebb formula, each line in a :doc:`angle\_coeff <angle_coeff>`
+For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
 command in the input script lists 4 coefficients, the first of which
 is "bb" to indicate they are BondBond coefficients.  In a data file,
 these coefficients should be listed under a "BondBond Coeffs" heading
@@ -69,11 +74,11 @@ and you must leave out the "bb", i.e. only list 3 coefficients after
 the angle type.
 
 * bb
-* M (energy/distance\^2)
+* :math:`M` (energy/distance\^2)
-* r1 (distance)
+* :math:`r_1` (distance)
-* r2 (distance)
+* :math:`r_2` (distance)
 
-For the Eba formula, each line in a :doc:`angle\_coeff <angle_coeff>`
+For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
 command in the input script lists 5 coefficients, the first of which
 is "ba" to indicate they are BondAngle coefficients.  In a data file,
 these coefficients should be listed under a "BondAngle Coeffs" heading
@@ -81,13 +86,13 @@ and you must leave out the "ba", i.e. only list 4 coefficients after
 the angle type.
 
 * ba
-* N1 (energy/distance\^2)
+* :math:`N_1` (energy/distance\^2)
-* N2 (energy/distance\^2)
+* :math:`N_2` (energy/distance\^2)
-* r1 (distance)
+* :math:`r_1` (distance)
-* r2 (distance)
+* :math:`r_2` (distance)
 
-The theta0 value in the Eba formula is not specified, since it is the
+The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
-same value from the Ea formula.
+since it is the same value from the :math:`E_a` formula.
 
 
 ----------
@@ -117,17 +122,19 @@ instructions on how to use the accelerated styles effectively.
 
 The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
 
-.. image:: Eqs/angle_class2_p6.jpg
+.. math::
-   :align: center
 
-In this expanded term 6 coefficients for the Ea formula need to be set:
+   E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
 
-* theta0 (degrees)
+
-* K2 (energy/radian\^2)
+In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
-* K3 (energy/radian\^3)
+
-* K4 (energy/radian\^4)
+* :math:`\theta_0` (degrees)
-* K5 (energy/radian\^5)
+* :math:`K_2` (energy/radian\^2)
-* K6 (energy/radian\^6)
+* :math:`K_3` (energy/radian\^3)
+* :math:`K_4` (energy/radian\^4)
+* :math:`K_5` (energy/radian\^5)
+* :math:`K_6` (energy/radian\^6)
 
 The bond-bond and bond-angle terms remain unchanged.
 
@@ -160,8 +167,3 @@ Related commands
 
 
 **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_coeff.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_coeff
+.. index:: angle_coeff
 
-angle\_coeff command
+angle_coeff command
-====================
+===================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_coeff N args
 
@@ -18,11 +18,11 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_coeff 1 300.0 107.0
-   angle_coeff \* 5.0
+   angle_coeff * 5.0
-   angle_coeff 2\*10 5.0
+   angle_coeff 2*10 5.0
 
 Description
 """""""""""
@@ -30,7 +30,7 @@ Description
 Specify the angle force field coefficients for one or more angle types.
 The number and meaning of the coefficients depends on the angle style.
 Angle coefficients can also be set in the data file read by the
-:doc:`read\_data <read_data>` command or in a restart file.
+:doc:`read_data <read_data>` command or in a restart file.
 
 N can be specified in one of two ways.  An explicit numeric value can
 be used, as in the 1st example above.  Or a wild-card asterisk can be
@@ -41,18 +41,18 @@ leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
 means all types from m to n (inclusive).
 
-Note that using an angle\_coeff command can override a previous setting
+Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
 for the same angle type.  For example, these commands set the coeffs
 for all angle types, then overwrite the coeffs for just angle type 2:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   angle_coeff \* 200.0 107.0 1.2
+   angle_coeff * 200.0 107.0 1.2
    angle_coeff 2 50.0 107.0
 
 A line in a data file that specifies angle coefficients uses the exact
-same format as the arguments of the angle\_coeff command in an input
+same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Angle Coeffs" section of a data file, the line that
@@ -63,7 +63,7 @@ corresponds to the 1st example above would be listed as
 
    1 300.0 107.0
 
-The :doc:`angle\_style class2 <angle_class2>` is an exception to this
+The :doc:`angle_style class2 <angle_class2>` is an exception to this
 rule, in that an additional argument is used in the input script to
 allow specification of the cross-term coefficients.   See its
 doc page for details.
@@ -73,13 +73,13 @@ doc page for details.
 
 
 The list of all angle styles defined in LAMMPS is given on the
-:doc:`angle\_style <angle_style>` doc page.  They are also listed in more
+:doc:`angle_style <angle_style>` doc page.  They are also listed in more
 compact form on the :ref:`Commands angle <angle>` doc
 page.
 
 On either of those pages, click on the style to display the formula it
 computes and its coefficients as specified by the associated
-angle\_coeff command.
+:doc:`angle_coeff <angle_coeff>` command.
 
 
 ----------
@@ -90,8 +90,8 @@ Restrictions
 
 
 This command must come after the simulation box is defined by a
-:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
-:doc:`create\_box <create_box>` command.
+:doc:`create_box <create_box>` command.
 
 An angle style must be defined before any angle coefficients are
 set, either in the input script or in a data file.
@@ -99,11 +99,6 @@ set, either in the input script or in a data file.
 Related commands
 """"""""""""""""
 
-:doc:`angle\_style <angle_style>`
+:doc:`angle_style <angle_style>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine.rst

@@ -1,19 +1,19 @@
-.. index:: angle\_style cosine
+.. index:: angle_style cosine
 
-angle\_style cosine command
+angle_style cosine command
-===========================
+==========================
 
-angle\_style cosine/omp command
+angle_style cosine/omp command
-===============================
-
-angle\_style cosine/kk command
 ==============================
 
+angle_style cosine/kk command
+=============================
+
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine
 
@@ -21,27 +21,29 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine
-   angle_coeff \* 75.0
+   angle_coeff * 75.0
 
 Description
 """""""""""
 
 The *cosine* angle style uses the potential
 
-.. image:: Eqs/angle_cosine.jpg
+.. math::
-   :align: center
 
-where K is defined for each angle type.
+   E = K [1 + \cos(\theta)]
+
+
+where :math:`K` is defined for each angle type.
 
 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)
+* :math:`K` (energy)
 
 
 ----------
@@ -83,8 +85,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine_buck6d.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style cosine/buck6d
+.. index:: angle_style cosine/buck6d
 
-angle\_style cosine/buck6d command
+angle_style cosine/buck6d command
-==================================
+=================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/buck6d
 
@@ -15,7 +15,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/buck6d
    angle_coeff 1  cosine/buck6d  1.978350  4  180.000000
@@ -25,22 +25,23 @@ Description
 
 The *cosine/buck6d* angle style uses the potential
 
-.. image:: Eqs/angle_cosine_buck6d.jpg
+.. math::
-   :align: center
 
-where K is the energy constant, n is the periodic multiplicity and
+   E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
-Theta0 is the equilibrium angle.
+
+where :math:`K` is the energy constant, :math:`n` is the periodic multiplicity and
+:math:`\theta_0` is the equilibrium angle.
 
 The 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 in the following order:
 
-* K (energy)
+* :math:`K` (energy)
-* n
+* :math:`n`
-* Theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
 internally.
 
 Additional to the cosine term the *cosine/buck6d* angle style computes
@@ -73,8 +74,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine_delta.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style cosine/delta
+.. index:: angle_style cosine/delta
 
-angle\_style cosine/delta command
+angle_style cosine/delta command
-=================================
+================================
 
-angle\_style cosine/delta/omp command
+angle_style cosine/delta/omp command
-=====================================
+====================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/delta
 
@@ -18,31 +18,33 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/delta
-   angle_coeff 2\*4 75.0 100.0
+   angle_coeff 2*4 75.0 100.0
 
 Description
 """""""""""
 
 The *cosine/delta* angle style uses the potential
 
-.. image:: Eqs/angle_cosine_delta.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium value of the angle, and K is a
+   E = K [1 - \cos(\theta - \theta_0)]
-prefactor.  Note that the usual 1/2 factor is included in K.
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
 
 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)
+* :math:`K` (energy)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
 internally.
 
 
@@ -85,8 +87,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_style cosine/squared <angle_cosine_squared>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine_periodic.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style cosine/periodic
+.. index:: angle_style cosine/periodic
 
-angle\_style cosine/periodic command
+angle_style cosine/periodic command
-====================================
+===================================
 
-angle\_style cosine/periodic/omp command
+angle_style cosine/periodic/omp command
-========================================
+=======================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/periodic
 
@@ -18,24 +18,26 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/periodic
-   angle_coeff \* 75.0 1 6
+   angle_coeff * 75.0 1 6
 
 Description
 """""""""""
 
 The *cosine/periodic* angle style uses the following potential, which
 is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
-particularly for organometallic systems where *n* = 4 might be used
+particularly for organometallic systems where :math:`n` = 4 might be used
-for an octahedral complex and *n* = 3 might be used for a trigonal
+for an octahedral complex and :math:`n` = 3 might be used for a trigonal
 center:
 
-.. image:: Eqs/angle_cosine_periodic.jpg
+.. math::
-   :align: center
 
-where C, B and n are coefficients defined for each angle type.
+   E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
+
+
+where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
 
 See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
 
@@ -44,13 +46,13 @@ The following coefficients must be defined for each angle type via the
 the data file or restart files read by the :doc:`read\_data <read_data>`
 or :doc:`read\_restart <read_restart>` commands:
 
-* C (energy)
+* :math:`C` (energy)
-* B = 1 or -1
+* :math:`B` = 1 or -1
-* n = 1, 2, 3, 4, 5 or 6 for periodicity
+* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
 
-Note that the prefactor C is specified and not the overall force
+Note that the prefactor :math:`C` is specified and not the overall force
-constant K = C / n\^2.  When B = 1, it leads to a minimum for the
+constant :math:`K = \frac{C}{n^2}`.  When :math:`B = 1`, it leads to a minimum for the
-linear geometry.  When B = -1, it leads to a maximum for the linear
+linear geometry.  When :math:`B = -1`, it leads to a maximum for the linear
 geometry.
 
 
@@ -104,8 +106,3 @@ Related commands
 
 **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine_shift.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style cosine/shift
+.. index:: angle_style cosine/shift
 
-angle\_style cosine/shift command
+angle_style cosine/shift command
 =================================
 
-angle\_style cosine/shift/omp command
+angle_style cosine/shift/omp command
-=====================================
+====================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/shift
 
@@ -18,30 +18,33 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/shift
-   angle_coeff \* 10.0 45.0
+   angle_coeff * 10.0 45.0
 
 Description
 """""""""""
 
 The *cosine/shift* angle style uses the potential
 
-.. image:: Eqs/angle_cosine_shift.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium angle. The potential is bounded
+   E = -\frac{U_{\text{min}}}{2} \left[ 1 + \cos(\theta-\theta_0) \right]
-between -Umin and zero. In the neighborhood of the minimum E=- Umin +
+
-Umin/4(theta-theta0)\^2 hence the spring constant is umin/2.
+
+where :math:`\theta_0` is the equilibrium angle. The potential is bounded
+between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum
+:math:`E = - U_{\text{min}} + U_{\text{min}}/4(\theta - \theta_0)^2` hence
+the spring constant is :math:`\frac{U_{\text{min}}}{2}`.
 
 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:
 
-* umin (energy)
+* :math:`U_{\text{min}}` (energy)
-* theta (angle)
+* :math:`\theta` (angle)
 
 
 ----------
@@ -83,8 +86,3 @@ Related commands
 :doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine_shift_exp.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style cosine/shift/exp
+.. index:: angle_style cosine/shift/exp
 
-angle\_style cosine/shift/exp command
+angle_style cosine/shift/exp command
-=====================================
+====================================
 
-angle\_style cosine/shift/exp/omp command
+angle_style cosine/shift/exp/omp command
-=========================================
+========================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/shift/exp
 
@@ -18,32 +18,33 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/shift/exp
-   angle_coeff \* 10.0 45.0 2.0
+   angle_coeff * 10.0 45.0 2.0
 
 Description
 """""""""""
 
 The *cosine/shift/exp* angle style uses the potential
 
-.. image:: Eqs/angle_cosine_shift_exp.jpg
+.. math::
-   :align: center
 
-where Umin, theta, and a are defined for each angle type.
+   E = -U_{\text{min}} \frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad \text{with} \quad U(\theta,\theta_0) = -0.5 \left(1+\cos(\theta-\theta_0) \right)
 
-The potential is bounded between [-Umin:0] and the minimum is
+where :math:`U_{\text{min}}`, :math:`\theta`, and :math:`a` are defined for each angle type.
-located at the angle theta0. The a parameter can be both positive or
+
+The potential is bounded between :math:`[-U_{\text{min}}, 0]` and the minimum is
+located at the angle :math:`\theta_0`. The a parameter can be both positive or
 negative and is used to control the spring constant at the
 equilibrium.
 
-The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
+The spring constant is given by :math:`k = A \exp(A) U_{\text{min}} / [2 (\exp(a)-1)]`.
-For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
+For :math:`a > 3`, :math:`\frac{k}{U_{\text{min}}} = \frac{a}{2}` to better than 5% relative error. For negative
-values of the a parameter, the spring constant is essentially zero,
+values of the :math:`a` parameter, the spring constant is essentially zero,
 and anharmonic terms takes over. The potential is furthermore well
-behaved in the limit a -> 0, where it has been implemented to linear
+behaved in the limit :math:`a \rightarrow 0`, where it has been implemented to linear
-order in a for a < 0.001. In this limit the potential reduces to the
+order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to the
 cosineshifted potential.
 
 The following coefficients must be defined for each angle type via the
@@ -51,9 +52,9 @@ The following coefficients must be defined for each angle type via the
 the data file or restart files read by the :doc:`read\_data <read_data>`
 or :doc:`read\_restart <read_restart>` commands:
 
-* umin (energy)
+* :math:`U_min` (energy)
-* theta (angle)
+* :math:`\theta` (angle)
-* A (real number)
+* :math:`A` (real number)
 
 
 ----------
@@ -97,8 +98,3 @@ Related commands
 :doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cosine_squared.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style cosine/squared
+.. index:: angle_style cosine/squared
 
-angle\_style cosine/squared command
+angle_style cosine/squared command
-===================================
+==================================
 
-angle\_style cosine/squared/omp command
+angle_style cosine/squared/omp command
-=======================================
+======================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/squared
 
@@ -18,31 +18,33 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cosine/squared
-   angle_coeff 2\*4 75.0 100.0
+   angle_coeff 2*4 75.0 100.0
 
 Description
 """""""""""
 
 The *cosine/squared* angle style uses the potential
 
-.. image:: Eqs/angle_cosine_squared.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium value of the angle, and K is a
+   E = K [\cos(\theta) - \cos(\theta_0)]^2
-prefactor.  Note that the usual 1/2 factor is included in K.
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
 
 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)
+* :math:`K` (energy)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
 internally.
 
 
@@ -85,8 +87,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_cross.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style cross
+.. index:: angle_style cross
 
-angle\_style cross command
+angle_style cross command
 ==========================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cross
 
@@ -15,7 +15,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style cross
    angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0
@@ -26,13 +26,14 @@ Description
 The *cross* angle style uses a potential that couples the bond stretches of
 a bend with the angle stretch of that bend:
 
-.. image:: Eqs/angle_cross.jpg
+.. math::
-   :align: center
 
-where r12,0 is the rest value of the bond length between atom 1 and 2,
+   E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
-r32,0 is the rest value of the bond length between atom 2 and 2,
+
-and theta0 is the rest value of the angle. KSS is the force constant of
+where :math:`r_{12,0}` is the rest value of the bond length between atom 1 and 2,
-the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
+:math:`r_{32,0}` is the rest value of the bond length between atom 3 and 2,
+and :math:`\theta_0` is the rest value of the angle. :math:`K_{SS}` is the force constant of
+the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are the force constants
 of the bond stretch-angle stretch terms.
 
 The following coefficients must be defined for each angle type via the
@@ -40,15 +41,15 @@ The following coefficients must be defined for each angle type via the
 the data file or restart files read by the :doc:`read\_data <read_data>`
 or :doc:`read\_restart <read_restart>` commands:
 
-* KSS (energy/distance\^2)
+* :math:`K_{SS}` (energy/distance\^2)
-* KBS0 (energy/distance/rad)
+* :math:`K_{BS0}` (energy/distance/rad)
-* KBS1 (energy/distance/rad)
+* :math:`K_{BS1}` (energy/distance/rad)
-* r12,0 (distance)
+* :math:`r_{12,0}` (distance)
-* r32,0 (distance)
+* :math:`r_{32,0}` (distance)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
+internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
 
 Restrictions
 """"""""""""
@@ -64,12 +65,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-----------
-
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

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
+style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom
-'j') with respect to a reference (bond) vector r\_ij = r\_i - r\_j, where 'i'
+:math:`j`) with respect to a reference (bond) vector
-is another atom of the same molecule (typically, 'i' and 'j' are also
+:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of
-covalently bonded).
+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
+It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}`
-and the reference (bond) vector r\_ij:
+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
+.. math::
-   :align: center
 
-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
+.. math::
-   :align: center
 
-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
+direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is
-restrained to point towards atom 'i').
+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
+.. math::
-   :align: center
 
-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)
+* :math:`K` (energy)
-* gamma0 (degrees)
+* :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
+   definition. This atom ID :math:`k` should be chosen to be that of an atom
-   bonded to atom 'i' to avoid errors with "lost angle atoms" when running
+   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

doc/src/angle_fourier.rst

@@ -1,42 +1,46 @@
-.. index:: angle\_style fourier
+.. index:: angle_style fourier
 
-angle\_style fourier command
+angle_style fourier command
-============================
+===========================
 
-angle\_style fourier/omp command
+angle_style fourier/omp command
-================================
+===============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style fourier
 
 Examples
 """"""""
 
-angle\_style fourier
+.. code-block:: LAMMPS
-angle\_coeff 75.0 1.0 1.0 1.0
+
+   angle_style fourier
+   angle_coeff 75.0 1.0 1.0 1.0
 
 Description
 """""""""""
 
 The *fourier* angle style uses the potential
 
-.. image:: Eqs/angle_fourier.jpg
+.. math::
-   :align: center
+
+   E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
+
 
 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)
+* :math:`K` (energy)
-* C0 (real)
+* :math:`C_0` (real)
-* C1 (real)
+* :math:`C_1` (real)
-* C2 (real)
+* :math:`C_2` (real)
 
 
 ----------
@@ -78,8 +82,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_fourier_simple.rst

@@ -1,41 +1,45 @@
-.. index:: angle\_style fourier/simple
+.. index:: angle_style fourier/simple
 
-angle\_style fourier/simple command
+angle_style fourier/simple command
-===================================
+==================================
 
-angle\_style fourier/simple/omp command
+angle_style fourier/simple/omp command
-=======================================
+======================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style fourier/simple
 
 Examples
 """"""""
 
-angle\_style fourier/simple
+.. code-block:: LAMMPS
-angle\_coeff 100.0 -1.0 1.0
+
+   angle_style fourier/simple
+   angle_coeff 100.0 -1.0 1.0
 
 Description
 """""""""""
 
 The *fourier/simple* angle style uses the potential
 
-.. image:: Eqs/angle_fourier_simple.jpg
+.. math::
-   :align: center
+
+   E = K [ 1.0 + c \cos ( n \theta) ]
+
 
 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)
+* :math:`K` (energy)
-* c (real)
+* :math:`c` (real)
-* n (real)
+* :math:`n` (real)
 
 
 ----------
@@ -77,8 +81,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_harmonic.rst

@@ -1,22 +1,22 @@
-.. index:: angle\_style harmonic
+.. index:: angle_style harmonic
 
-angle\_style harmonic command
+angle_style harmonic command
-=============================
+============================
 
-angle\_style harmonic/intel command
+angle_style harmonic/intel command
-===================================
+==================================
 
-angle\_style harmonic/kk command
+angle_style harmonic/kk command
+===============================
+
+angle_style harmonic/omp command
 ================================
 
-angle\_style harmonic/omp command
-=================================
-
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style harmonic
 
@@ -24,7 +24,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style harmonic
    angle_coeff 1 300.0 107.0
@@ -34,22 +34,24 @@ Description
 
 The *harmonic* angle style uses the potential
 
-.. image:: Eqs/angle_harmonic.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium value of the angle, and K is a
+   E = K (\theta - \theta_0)^2
-prefactor.  Note that the usual 1/2 factor is included in K.
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
 
 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/radian\^2)
+* :math:`K` (energy/radian\^2)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian\^2.
+internally; hence the units of :math:`K` are in energy/radian\^2.
 
 
 ----------
@@ -91,8 +93,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_hybrid.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style hybrid
+.. index:: angle_style hybrid
 
-angle\_style hybrid command
+angle_style hybrid command
-===========================
+==========================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style hybrid style1 style2 ...
 
@@ -17,11 +17,11 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style hybrid harmonic cosine
    angle_coeff 1 harmonic 80.0 30.0
-   angle_coeff 2\* cosine 50.0
+   angle_coeff 2* cosine 50.0
 
 Description
 """""""""""
@@ -31,19 +31,19 @@ simulation.  An angle style is assigned to each angle type.  For
 example, angles in a polymer flow (of angle type 1) could be computed
 with a *harmonic* potential and angles in the wall boundary (of angle
 type 2) could be computed with a *cosine* potential.  The assignment
-of angle type to style is made via the :doc:`angle\_coeff <angle_coeff>`
+of angle type to style is made via the :doc:`angle_coeff <angle_coeff>`
 command or in the data file.
 
-In the angle\_coeff commands, the name of an angle style must be added
+In the :doc:`angle_coeff <angle_coeff>` commands, the name of an angle style must be added
 after the angle type, with the remaining coefficients being those
 appropriate to that style.  In the example above, the 2 angle\_coeff
 commands set angles of angle type 1 to be computed with a *harmonic*
-potential with coefficients 80.0, 30.0 for K, theta0.  All other angle
+potential with coefficients 80.0, 30.0 for :math:`K`, :math:`\theta_0`.  All other angle
-types (2-N) are computed with a *cosine* potential with coefficient
+types :math:`(2 - N)` are computed with a *cosine* potential with coefficient
-50.0 for K.
+50.0 for :math:`K`.
 
 If angle coefficients are specified in the data file read via the
-:doc:`read\_data <read_data>` command, then the same rule applies.
+:doc:`read_data <read_data>` command, then the same rule applies.
 E.g. "harmonic" or "cosine", must be added after the angle type, for each
 line in the "Angle Coeffs" section, e.g.
 
@@ -77,7 +77,7 @@ input script, since BondBond (or BondAngle) coefficients need not be
 specified at all for angle types that are not *class2*\ .
 
 An angle style of *none* with no additional coefficients can be used
-in place of an angle style, either in a input script angle\_coeff
+in place of an angle style, either in a input script :doc:`angle_coeff <angle_coeff>`
 command or in the data file, if you desire to turn off interactions
 for specific angle types.
 
@@ -95,16 +95,11 @@ for more info.
 
 Unlike other angle styles, the hybrid angle style does not store angle
 coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`.  Thus when restarting a simulation from a restart
-file, you need to re-specify angle\_coeff commands.
+file, you need to re-specify :doc:`angle_coeff <angle_coeff>` commands.
 
 Related commands
 """"""""""""""""
 
-:doc:`angle\_coeff <angle_coeff>`
+:doc:`angle_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_mm3.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style mm3
+.. index:: angle_style mm3
 
-angle\_style mm3 command
+angle_style mm3 command
-========================
+=======================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style mm3
 
@@ -15,7 +15,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style mm3
    angle_coeff 1 100.0 107.0
@@ -26,23 +26,25 @@ Description
 The *mm3* angle style uses the potential that is anharmonic in the angle
 as defined in :ref:`(Allinger) <mm3-allinger1989>`
 
-.. image:: Eqs/angle_mm3.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium value of the angle, and K is a
+   E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
-prefactor. The anharmonic prefactors have units deg\^(-n), for example
+
--0.014 deg\^(-1), 5.6(10)\^(-5) deg\^(-2), ...
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
+:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
 
 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/radian\^2)
+* :math:`K` (energy/radian\^2)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian\^2.
+internally; hence the units of :math:`K` are in energy/radian\^2.
 
 Restrictions
 """"""""""""
@@ -58,12 +60,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-----------
-
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_none.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style none
+.. index:: angle_style none
 
-angle\_style none command
+angle_style none command
-=========================
+========================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style none
 
@@ -15,7 +15,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style none
 
@@ -24,23 +24,19 @@ Description
 
 Using an angle style of none means angle forces and energies are not
 computed, even if triplets of angle atoms were listed in the data file
-read by the :doc:`read\_data <read_data>` command.
+read by the :doc:`read_data <read_data>` command.
 
-See the :doc:`angle\_style zero <angle_zero>` command for a way to
+See the :doc:`angle_style zero <angle_zero>` command for a way to
 calculate angle statistics, but compute no angle interactions.
 
 Restrictions
 """"""""""""
- none
+
+none
 
 Related commands
 """"""""""""""""
 
-:doc:`angle\_style zero <angle_zero>`
+:doc:`angle_style zero <angle_zero>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_quartic.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style quartic
+.. index:: angle_style quartic
 
-angle\_style quartic command
+angle_style quartic command
-============================
+===========================
 
-angle\_style quartic/omp command
+angle_style quartic/omp command
-================================
+===============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style quartic
 
@@ -18,7 +18,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style quartic
    angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
@@ -28,24 +28,26 @@ Description
 
 The *quartic* angle style uses the potential
 
-.. image:: Eqs/angle_quartic.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium value of the angle, and K is a
+   E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
-prefactor.  Note that the usual 1/2 factor is included in K.
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
 
 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:
 
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
-* K2 (energy/radian\^2)
+* :math:`K_2` (energy/radian\^2)
-* K3 (energy/radian\^3)
+* :math:`K_3` (energy/radian\^3)
-* K4 (energy/radian\^4)
+* :math:`K_4` (energy/radian\^4)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian\^2.
+internally; hence the units of :math:`K` are in energy/radian\^2.
 
 
 ----------
@@ -87,8 +89,3 @@ Related commands
 :doc:`angle\_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_sdk.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style sdk
+.. index:: angle_style sdk
 
-angle\_style sdk command
+angle_style sdk command
-========================
+=======================
 
-angle\_style sdk/omp command
+angle_style sdk/omp command
-============================
+===========================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style sdk
 
@@ -20,7 +20,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style sdk
    angle_coeff 1 300.0 107.0
@@ -30,25 +30,27 @@ Description
 
 The *sdk* angle style is a combination of the harmonic angle potential,
 
-.. image:: Eqs/angle_harmonic.jpg
+.. math::
-   :align: center
 
-where theta0 is the equilibrium value of the angle and K a prefactor,
+   E = K (\theta - \theta_0)^2 
+
+
+where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor,
 with the *repulsive* part of the non-bonded *lj/sdk* pair style
 between the atoms 1 and 3.  This angle potential is intended for
 coarse grained MD simulations with the CMM parameterization using the
 :doc:`pair\_style lj/sdk <pair_sdk>`.  Relative to the pair\_style
 *lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden
-jumps.  Note that the usual 1/2 factor is included in K.
+jumps.  Note that the usual 1/2 factor is included in :math:`K`.
 
 The following coefficients must be defined for each angle type via the
 :doc:`angle\_coeff <angle_coeff>` command as in the example above:
 
-* K (energy/radian\^2)
+* :math:`K` (energy/radian\^2)
-* theta0 (degrees)
+* :math:`\theta_0` (degrees)
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian\^2.
+internally; hence the units of :math:`K` are in energy/radian\^2.
 The also required *lj/sdk* parameters will be extracted automatically
 from the pair\_style.
 
@@ -93,8 +95,3 @@ Related commands
 :doc:`pair\_style lj/sdk/coul/long <pair_sdk>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_style.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style
+.. index:: angle_style
 
-angle\_style command
+angle_style command
-====================
+===================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style style
 
@@ -17,7 +17,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style harmonic
    angle_style charmm
@@ -29,19 +29,19 @@ Description
 Set the formula(s) LAMMPS uses to compute angle interactions between
 triplets of atoms, which remain in force for the duration of the
 simulation.  The list of angle triplets is read in by a
-:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` command
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
 from a data or restart file.
 
 Hybrid models where angles are computed using different angle
 potentials can be setup using the *hybrid* angle style.
 
 The coefficients associated with a angle style can be specified in a
-data or restart file or via the :doc:`angle\_coeff <angle_coeff>` command.
+data or restart file or via the :doc:`angle_coeff <angle_coeff>` command.
 
 All angle potentials store their coefficient data in binary restart
-files which means angle\_style and :doc:`angle\_coeff <angle_coeff>`
+files which means angle_style and :doc:`angle_coeff <angle_coeff>`
 commands do not need to be re-specified in an input script that
-restarts a simulation.  See the :doc:`read\_restart <read_restart>`
+restarts a simulation.  See the :doc:`read_restart <read_restart>`
 command for details on how to do this.  The one exception is that
 angle\_style *hybrid* only stores the list of sub-styles in the restart
 file; angle coefficients need to be re-specified.
@@ -49,7 +49,7 @@ file; angle coefficients need to be re-specified.
 .. note::
 
    When both an angle and pair style is defined, the
-   :doc:`special\_bonds <special_bonds>` command often needs to be used to
+   :doc:`special_bonds <special_bonds>` command often needs to be used to
    turn off (or weight) the pairwise interaction that would otherwise
    exist between 3 bonded atoms.
 
@@ -62,11 +62,11 @@ between the 3 atoms in the angle.
 
 Here is an alphabetic list of angle styles defined in LAMMPS.  Click on
 the style to display the formula it computes and coefficients
-specified by the associated :doc:`angle\_coeff <angle_coeff>` command.
+specified by the associated :doc:`angle_coeff <angle_coeff>` command.
 
 Click on the style to display the formula it computes, any additional
 arguments specified in the angle\_style command, and coefficients
-specified by the associated :doc:`angle\_coeff <angle_coeff>` command.
+specified by the associated :doc:`angle_coeff <angle_coeff>` command.
 
 There are also additional accelerated pair styles included in the
 LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@@ -115,17 +115,12 @@ individual bond potentials tell if it is part of a package.
 Related commands
 """"""""""""""""
 
-:doc:`angle\_coeff <angle_coeff>`
+:doc:`angle_coeff <angle_coeff>`
 
 Default
 """""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_table.rst

@@ -1,16 +1,16 @@
-.. index:: angle\_style table
+.. index:: angle_style table
 
-angle\_style table command
+angle_style table command
-==========================
+=========================
 
-angle\_style table/omp command
+angle_style table/omp command
-==============================
+=============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style table style N
 
@@ -21,7 +21,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style table linear 1000
    angle_coeff 3 file.table ENTRY1
@@ -31,7 +31,7 @@ Description
 
 Style *table* creates interpolation tables of length *N* from angle
 potential and derivative values listed in a file(s) as a function of
-angle The files are read by the :doc:`angle\_coeff <angle_coeff>`
+angle The files are read by the :doc:`angle_coeff <angle_coeff>`
 command.
 
 The interpolation tables are created by fitting cubic splines to the
@@ -50,7 +50,7 @@ find the appropriate set of coefficients which are used to evaluate a
 cubic polynomial which computes the energy or derivative.
 
 The following coefficients must be defined for each angle type via the
-:doc:`angle\_coeff <angle_coeff>` command as in the example above.
+:doc:`angle_coeff <angle_coeff>` command as in the example above.
 
 * filename
 * keyword
@@ -85,13 +85,13 @@ A section begins with a non-blank line whose 1st character is not a
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
 initial text must match the argument specified in the
-:doc:`angle\_coeff <angle_coeff>` command.  The next line lists (in any
+:doc:`angle_coeff <angle_coeff>` command.  The next line lists (in any
 order) one or more parameters for the table.  Each parameter is a
 keyword followed by one or more numeric values.
 
 The parameter "N" is required and its value is the number of table
 entries that follow.  Note that this may be different than the *N*
-specified in the :doc:`angle\_style table <angle_style>` command.  Let
+specified in the :doc:`angle_style table <angle_style>` command.  Let
 Ntable = *N* in the angle\_style command, and Nfile = "N" in the
 tabulated file.  What LAMMPS does is a preliminary interpolation by
 creating splines using the Nfile tabulated values as nodal points.  It
@@ -176,11 +176,6 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`angle\_coeff <angle_coeff>`
+:doc:`angle_coeff <angle_coeff>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/angle_zero.rst

@@ -1,13 +1,13 @@
-.. index:: angle\_style zero
+.. index:: angle_style zero
 
-angle\_style zero command
+angle_style zero command
-=========================
+========================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style zero *nocoeff*
 
@@ -15,12 +15,12 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    angle_style zero
    angle_style zero nocoeff
-   angle_coeff \*
+   angle_coeff *
-   angle_coeff \* 120.0
+   angle_coeff * 120.0
 
 Description
 """""""""""
@@ -32,14 +32,14 @@ other commands.
 As an example, the :doc:`compute angle/local <compute_angle_local>`
 command can be used to compute the theta values for the list of
 triplets of angle atoms listed in the data file read by the
-:doc:`read\_data <read_data>` command.  If no angle style is defined,
+:doc:`read_data <read_data>` command.  If no angle style is defined,
 this command cannot be used.
 
 The optional *nocoeff* flag allows to read data files with AngleCoeff
-section for any angle style. Similarly, any angle\_coeff commands
+section for any angle style. Similarly, any :doc:`angle_coeff <angle_coeff>` commands
 will only be checked for the angle type number and the rest ignored.
 
-Note that the :doc:`angle\_coeff <angle_coeff>` command must be used for
+Note that the :doc:`angle_coeff <angle_coeff>` command must be used for
 all angle types. If specified, there can be only one value, which is
 going to be used to assign an equilibrium angle, e.g. for use with
 :doc:`fix shake <fix_shake>`.
@@ -51,11 +51,6 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`angle\_style none <angle_none>`
+:doc:`angle_style none <angle_none>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/atom_modify.rst

@@ -1,13 +1,13 @@
-.. index:: atom\_modify
+.. index:: atom_modify
 
-atom\_modify command
+atom_modify command
-====================
+===================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    atom_modify keyword values ...
 
@@ -29,7 +29,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    atom_modify map yes
    atom_modify map hash sort 10000 2.0
@@ -188,8 +188,3 @@ defined, sorting will be turned off.
 
 
 **(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/atom_style.rst

@@ -1,13 +1,13 @@
-.. index:: atom\_style
+.. index:: atom_style
 
-atom\_style command
+atom_style command
-===================
+==================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    atom_style style args
 
@@ -33,7 +33,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    atom_style atomic
    atom_style bond
@@ -371,8 +371,3 @@ atom\_style atomic
 
 **(Grime)** Grime and Voth, to appear in J Chem Theory & Computation
 (2014).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/bond_class2.rst

@@ -1,19 +1,19 @@
-.. index:: bond\_style class2
+.. index:: bond_style class2
 
-bond\_style class2 command
+bond_style class2 command
-==========================
+=========================
 
-bond\_style class2/omp command
+bond_style class2/omp command
-==============================
-
-bond\_style class2/kk command
 =============================
 
+bond_style class2/kk command
+============================
+
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style class2
 
@@ -21,7 +21,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style class2
    bond_coeff 1 1.0 100.0 80.0 80.0
@@ -31,10 +31,12 @@ Description
 
 The *class2* bond style uses the potential
 
-.. image:: Eqs/bond_class2.jpg
+.. math::
-   :align: center
 
-where r0 is the equilibrium bond distance.
+   E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
+
+
+where :math:`r_0` is the equilibrium bond distance.
 
 See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
 
@@ -43,10 +45,10 @@ The following coefficients must be defined for each bond type via the
 the data file or restart files read by the :doc:`read\_data <read_data>`
 or :doc:`read\_restart <read_restart>` commands:
 
-* R0 (distance)
+* :math:`r_0` (distance)
-* K2 (energy/distance\^2)
+* :math:`K_2` (energy/distance\^2)
-* K3 (energy/distance\^3)
+* :math:`K_3` (energy/distance\^3)
-* K4 (energy/distance\^4)
+* :math:`K_4` (energy/distance\^4)
 
 
 ----------
@@ -98,8 +100,3 @@ Related commands
 
 
 **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/bond_coeff.rst

@@ -1,13 +1,13 @@
-.. index:: bond\_coeff
+.. index:: bond_coeff
 
-bond\_coeff command
+bond_coeff command
-===================
+==================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_coeff N args
 
@@ -18,11 +18,11 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_coeff 5 80.0 1.2
-   bond_coeff \* 30.0 1.5 1.0 1.0
+   bond_coeff * 30.0 1.5 1.0 1.0
-   bond_coeff 1\*4 30.0 1.5 1.0 1.0
+   bond_coeff 1*4 30.0 1.5 1.0 1.0
    bond_coeff 1 harmonic 200.0 1.0
 
 Description
@@ -47,9 +47,9 @@ for the same bond type.  For example, these commands set the coeffs
 for all bond types, then overwrite the coeffs for just bond type 2:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   bond_coeff \* 100.0 1.2
+   bond_coeff * 100.0 1.2
    bond_coeff 2 200.0 1.2
 
 A line in a data file that specifies bond coefficients uses the exact
@@ -97,8 +97,3 @@ Related commands
 :doc:`bond\_style <bond_style>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

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
+.. math::
-   :align: center
+
+   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
+first term extends to :math:`R_0`, the maximum extent of the bond.  The 2nd
-term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential.
+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)
+* :math:`K` (energy/distance\^2)
-* R0 (distance)
+* :math:`R_0` (distance)
-* epsilon (energy)
+* :math:`\epsilon` (energy)
-* sigma (distance)
+* :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

doc/src/bond_fene_expand.rst

@@ -1,16 +1,16 @@
-.. index:: bond\_style fene/expand
+.. index:: bond_style fene/expand
 
-bond\_style fene/expand command
+bond_style fene/expand command
-===============================
+==============================
 
-bond\_style fene/expand/omp command
+bond_style fene/expand/omp command
-===================================
+==================================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style fene/expand
 
@@ -18,7 +18,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style fene/expand
    bond_coeff 1 30.0 1.5 1.0 1.0 0.5
@@ -28,29 +28,30 @@ Description
 
 The *fene/expand* bond style uses the potential
 
-.. image:: Eqs/bond_fene_expand.jpg
+.. math::
-   :align: center
+
+   E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon
+
 
 to define a finite extensible nonlinear elastic (FENE) potential
 :ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models.  The first
 term is attractive, the 2nd Lennard-Jones term is repulsive.
 
 The *fene/expand* bond style is similar to *fene* except that an extra
-shift factor of delta (positive or negative) is added to *r* to
+shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
 effectively change the bead size of the bonded atoms.  The first term
-now extends to R0 + delta and the 2nd term is cutoff at 2\^(1/6) sigma
+now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
-+ delta.
 
 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)
+* :math:`K` (energy/distance\^2)
-* R0 (distance)
+* :math:`R_0` (distance)
-* epsilon (energy)
+* :math:`\epsilon` (energy)
-* sigma (distance)
+* :math:`\sigma` (distance)
-* delta (distance)
+* :math:`\Delta` (distance)
 
 
 ----------
@@ -106,8 +107,3 @@ Related commands
 
 
 **(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/bond_gromos.rst

@@ -1,16 +1,16 @@
-.. index:: bond\_style gromos
+.. index:: bond_style gromos
 
-bond\_style gromos command
+bond_style gromos command
-==========================
+=========================
 
-bond\_style gromos/omp command
+bond_style gromos/omp command
-==============================
+=============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style gromos
 
@@ -18,7 +18,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style gromos
    bond_coeff 5 80.0 1.2
@@ -28,19 +28,21 @@ Description
 
 The *gromos* bond style uses the potential
 
-.. image:: Eqs/bond_gromos.jpg
+.. math::
-   :align: center
 
-where r0 is the equilibrium bond distance.  Note that the usual 1/4
+   E = K (r^2 - r_0^2)^2
-factor is included in K.
+
+
+where :math:`r_0` is the equilibrium bond distance.  Note that the usual 1/4
+factor is included in :math:`K`.
 
 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\^4)
+* :math:`K` (energy/distance\^4)
-* r0 (distance)
+* :math:`r_0` (distance)
 
 
 ----------
@@ -82,8 +84,3 @@ Related commands
 :doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/bond_harmonic.rst

@@ -1,22 +1,22 @@
-.. index:: bond\_style harmonic
+.. index:: bond_style harmonic
 
-bond\_style harmonic command
+bond_style harmonic command
-============================
+===========================
 
-bond\_style harmonic/intel command
+bond_style harmonic/intel command
-==================================
+=================================
 
-bond\_style harmonic/kk command
+bond_style harmonic/kk command
+==============================
+
+bond_style harmonic/omp command
 ===============================
 
-bond\_style harmonic/omp command
-================================
-
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style harmonic
 
@@ -24,7 +24,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    bond_style harmonic
    bond_coeff 5 80.0 1.2
@@ -34,19 +34,21 @@ Description
 
 The *harmonic* bond style uses the potential
 
-.. image:: Eqs/bond_harmonic.jpg
+.. math::
-   :align: center
 
-where r0 is the equilibrium bond distance.  Note that the usual 1/2
+   E = K (r - r_0)^2
-factor is included in K.
+
+
+where :math:`r_0` is the equilibrium bond distance.  Note that the usual 1/2
+factor is included in :math:`K`.
 
 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)
+* :math:`K` (energy/distance\^2)
-* r0 (distance)
+* :math:`r_0` (distance)
 
 
 ----------
@@ -88,8 +90,3 @@ Related commands
 :doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
 
 **Default:** none
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html