Merge pull request #1775 from rbberger/doc_updates

Update bond docs
2019-11-18 11:32:07 -05:00
parent 2e6b19ea5f 19b265f845
commit fbf280f6a3
69 changed files with 327 additions and 2755 deletions
--- a/cmake/Modules/Documentation.cmake
+++ b/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(
--- a/doc/src/Eqs/bond_class2.jpg
+++ b/doc/src/Eqs/bond_class2.jpg
--- a/doc/src/Eqs/bond_class2.tex
+++ b/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}
--- a/doc/src/Eqs/bond_fene.jpg
+++ b/doc/src/Eqs/bond_fene.jpg
--- a/doc/src/Eqs/bond_fene.tex
+++ b/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}
--- a/doc/src/Eqs/bond_fene_expand.jpg
+++ b/doc/src/Eqs/bond_fene_expand.jpg
--- a/doc/src/Eqs/bond_fene_expand.tex
+++ b/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}
--- a/doc/src/Eqs/bond_gromos.jpg
+++ b/doc/src/Eqs/bond_gromos.jpg
--- a/doc/src/Eqs/bond_gromos.tex
+++ b/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}
--- a/doc/src/Eqs/bond_harmonic.jpg
+++ b/doc/src/Eqs/bond_harmonic.jpg
--- a/doc/src/Eqs/bond_harmonic.tex
+++ b/doc/src/Eqs/bond_harmonic.tex
@ -1,9 +0,0 @@
 \documentclass[12pt]{article}
 \begin{document}
 $$
   E = K (r - r_0)^2 
 $$
 \end{document}
--- a/doc/src/Eqs/bond_harmonic_shift.jpg
+++ b/doc/src/Eqs/bond_harmonic_shift.jpg
--- a/doc/src/Eqs/bond_harmonic_shift.tex
+++ b/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}
--- a/doc/src/Eqs/bond_harmonic_shift_cut.jpg
+++ b/doc/src/Eqs/bond_harmonic_shift_cut.jpg
--- a/doc/src/Eqs/bond_harmonic_shift_cut.tex
+++ b/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}
--- a/doc/src/Eqs/bond_mm3.jpg
+++ b/doc/src/Eqs/bond_mm3.jpg
--- a/doc/src/Eqs/bond_mm3.tex
+++ b/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}
--- a/doc/src/Eqs/bond_morse.jpg
+++ b/doc/src/Eqs/bond_morse.jpg
--- a/doc/src/Eqs/bond_morse.tex
+++ b/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}
--- a/doc/src/Eqs/bond_nonlinear.jpg
+++ b/doc/src/Eqs/bond_nonlinear.jpg
--- a/doc/src/Eqs/bond_nonlinear.tex
+++ b/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}
--- a/doc/src/Eqs/bond_oxdna_fene.jpg
+++ b/doc/src/Eqs/bond_oxdna_fene.jpg
--- a/doc/src/Eqs/bond_oxdna_fene.tex
+++ b/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}
--- a/doc/src/Eqs/bond_quartic.jpg
+++ b/doc/src/Eqs/bond_quartic.jpg
--- a/doc/src/Eqs/bond_quartic.tex
+++ b/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}
--- a/doc/src/atom_modify.rst
+++ b/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
--- a/doc/src/atom_style.rst
+++ b/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
--- a/doc/src/bond_class2.rst
+++ b/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
--- a/doc/src/bond_coeff.rst
+++ b/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
--- a/doc/src/bond_fene.rst
+++ b/doc/src/bond_fene.rst
@ -1,22 +1,22 @@
-.. index:: bond\_style fene
+.. index:: bond_style fene
-bond\_style fene command
+bond_style fene command
-========================
+=======================
-bond\_style fene/intel command
+bond_style fene/intel command
-==============================
+=============================
-bond\_style fene/kk command
+bond_style fene/kk command
 ==========================
 bond_style fene/omp command
 ===========================
 bond\_style fene/omp command
 ============================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style fene
@ -24,7 +24,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style fene
   bond_coeff 1 30.0 1.5 1.0 1.0
@ -34,24 +34,26 @@ Description
 The *fene* bond style uses the potential
-.. image:: Eqs/bond_fene.jpg
+.. 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
--- a/doc/src/bond_fene_expand.rst
+++ b/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
--- a/doc/src/bond_gromos.rst
+++ b/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
--- a/doc/src/bond_harmonic.rst
+++ b/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
--- a/doc/src/bond_harmonic_shift.rst
+++ b/doc/src/bond_harmonic_shift.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style harmonic/shift
+.. index:: bond_style harmonic/shift
-bond\_style harmonic/shift command
+bond_style harmonic/shift command
-==================================
+=================================
-bond\_style harmonic/shift/omp command
+bond_style harmonic/shift/omp command
-======================================
+=====================================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style harmonic/shift
@ -18,7 +18,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style harmonic/shift
   bond_coeff 5 10.0 0.5 1.0
@ -29,23 +29,25 @@ Description
 The *harmonic/shift* bond style is a shifted harmonic bond that uses
 the potential
-.. image:: Eqs/bond_harmonic_shift.jpg
+.. math::
   :align: center
-where r0 is the equilibrium bond distance, and rc the critical distance.
+   E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
-The potential is -Umin at r0 and zero at rc. The spring constant is
+
-k = Umin / [ 2 (r0-rc)\^2].
+
 where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
 The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
 :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
 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:
-* Umin (energy)
+* :math:`U_{\text{min}}` (energy)
-* r0 (distance)
+* :math:`r_0` (distance)
-* rc (distance)
+* :math:`r_c` (distance)
 ----------
@ -88,8 +90,3 @@ Related commands
 :doc:`bond\_harmonic <bond_harmonic>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_harmonic_shift_cut.rst
+++ b/doc/src/bond_harmonic_shift_cut.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style harmonic/shift/cut
+.. index:: bond_style harmonic/shift/cut
-bond\_style harmonic/shift/cut command
+bond_style harmonic/shift/cut command
-======================================
+=====================================
-bond\_style harmonic/shift/cut/omp command
+bond_style harmonic/shift/cut/omp command
-==========================================
+=========================================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style harmonic/shift/cut
@ -18,7 +18,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style harmonic/shift/cut
   bond_coeff 5 10.0 0.5 1.0
@ -29,21 +29,23 @@ Description
 The *harmonic/shift/cut* bond style is a shifted harmonic bond that
 uses the potential
-.. image:: Eqs/bond_harmonic_shift_cut.jpg
+.. math::
   :align: center
-where r0 is the equilibrium bond distance, and rc the critical distance.
+   E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
-The bond potential is zero for distances r > rc. The potential is -Umin
+
-at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)\^2].
+
 where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
 The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
 at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
 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:
-* Umin (energy)
+* :math:`U_{\text{min}}` (energy)
-* r0 (distance)
+* :math:`r_0` (distance)
-* rc (distance)
+* :math:`r_c` (distance)
 ----------
@ -87,8 +89,3 @@ Related commands
 :doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_hybrid.rst
+++ b/doc/src/bond_hybrid.rst
@ -1,13 +1,13 @@
-.. index:: bond\_style hybrid
+.. index:: bond_style hybrid
-bond\_style hybrid command
+bond_style hybrid command
-==========================
+=========================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style hybrid style1 style2 ...
@ -17,11 +17,11 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block: LAMMPS
   bond_style hybrid harmonic fene
   bond_coeff 1 harmonic 80.0 1.2
-   bond_coeff 2\* fene 30.0 1.5 1.0 1.0
+   bond_coeff 2* fene 30.0 1.5 1.0 1.0
 Description
 """""""""""
@ -31,19 +31,19 @@ simulation.  A bond style is assigned to each bond type.  For example,
 bonds in a polymer flow (of bond type 1) could be computed with a
 *fene* potential and bonds in the wall boundary (of bond type 2) could
 be computed with a *harmonic* potential.  The assignment of bond type
-to style is made via the :doc:`bond\_coeff <bond_coeff>` command or in
+to style is made via the :doc:`bond_coeff <bond_coeff>` command or in
 the data file.
 In the bond\_coeff commands, the name of a bond style must be added
 after the bond type, with the remaining coefficients being those
 appropriate to that style.  In the example above, the 2 bond\_coeff
 commands set bonds of bond type 1 to be computed with a *harmonic*
-potential with coefficients 80.0, 1.2 for K, r0.  All other bond types
+potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`.  All other bond types
 (2-N) are computed with a *fene* potential with coefficients 30.0,
-1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
+1.5, 1.0, 1.0 for :math:`K`, :math:`R_0`, :math:`\epsilon`, :math:`\sigma`.
 If bond 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 "fene" must be added after the bond type, for each
 line in the "Bond Coeffs" section, e.g.
@ -80,11 +80,6 @@ file, you need to re-specify bond\_coeff commands.
 Related commands
 """"""""""""""""
-:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_mm3.rst
+++ b/doc/src/bond_mm3.rst
@ -1,13 +1,13 @@
-.. index:: bond\_style mm3
+.. index:: bond_style mm3
-bond\_style mm3 command
+bond_style mm3 command
-=======================
+======================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style mm3
@ -15,7 +15,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style mm3
   bond_coeff 1 100.0 107.0
@ -26,10 +26,12 @@ Description
 The *mm3* bond style uses the potential that is anharmonic in the bond
 as defined in :ref:`(Allinger) <mm3-allinger1989>`
-.. image:: Eqs/bond_mm3.jpg
+.. math::
   :align: center
-where r0 is the equilibrium value of the bond, and K is a
+   E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
 where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
 prefactor. The anharmonic prefactors have units angstrom\^(-n):
 -2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
 care of the necessary unit conversion for these factors internally.
@ -41,8 +43,8 @@ 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:
-* K (energy/distance\^2)
+* :math:`K` (energy/distance\^2)
-* r0 (distance)
+* :math:`r_0` (distance)
 Restrictions
 """"""""""""
@ -69,8 +71,3 @@ Related commands
 **(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
 (1989),
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_morse.rst
+++ b/doc/src/bond_morse.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style morse
+.. index:: bond_style morse
-bond\_style morse command
+bond_style morse command
-=========================
+========================
-bond\_style morse/omp command
+bond_style morse/omp command
-=============================
+============================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style morse
@ -18,7 +18,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style morse
   bond_coeff 5 1.0 2.0 1.2
@ -28,20 +28,22 @@ Description
 The *morse* bond style uses the potential
-.. image:: Eqs/bond_morse.jpg
+.. math::
   :align: center
-where r0 is the equilibrium bond distance, alpha is a stiffness
+   E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
-parameter, and D determines the depth of the potential well.
+
 where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness
 parameter, and :math:`D` determines the depth of the potential well.
 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:
-* D (energy)
+* :math:`D` (energy)
-* alpha (inverse distance)
+* :math:`\alpha` (inverse distance)
-* r0 (distance)
+* :math:`r_0` (distance)
 ----------
@ -83,8 +85,3 @@ 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
--- a/doc/src/bond_none.rst
+++ b/doc/src/bond_none.rst
@ -1,13 +1,13 @@
-.. index:: bond\_style none
+.. index:: bond_style none
-bond\_style none command
+bond_style none command
-========================
+=======================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style none
@ -15,7 +15,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-blocK:: LAMMPS
   bond_style none
@ -24,9 +24,9 @@ Description
 Using a bond style of none means bond forces and energies are not
 computed, even if pairs of bonded 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:`bond\_style zero <bond_zero>` command for a way to
+See the :doc:`bond_style zero <bond_zero>` command for a way to
 calculate bond statistics, but compute no bond interactions.
 Restrictions
@ -35,11 +35,6 @@ Restrictions
 **Related commands:** none
-:doc:`bond\_style zero <bond_zero>`
+:doc:`bond_style zero <bond_zero>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_nonlinear.rst
+++ b/doc/src/bond_nonlinear.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style nonlinear
+.. index:: bond_style nonlinear
-bond\_style nonlinear command
+bond_style nonlinear command
-=============================
+============================
-bond\_style nonlinear/omp command
+bond_style nonlinear/omp command
-=================================
+================================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style nonlinear
@ -18,7 +18,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style nonlinear
   bond_coeff 2 100.0 1.1 1.4
@ -28,20 +28,22 @@ Description
 The *nonlinear* bond style uses the potential
-.. image:: Eqs/bond_nonlinear.jpg
+.. math::
-   :align: center
+
   E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
 to define an anharmonic spring :ref:`(Rector) <Rector>` of equilibrium
-length r0 and maximum extension lamda.
+length :math:`r_0` and maximum extension lamda.
 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:
-* epsilon (energy)
+* :math:`\epsilon` (energy)
-* r0 (distance)
+* :math:`r_0` (distance)
-* lamda (distance)
+* :math:`\lambda` (distance)
 ----------
@ -93,8 +95,3 @@ Related commands
 **(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_oxdna.rst
+++ b/doc/src/bond_oxdna.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style oxdna/fene
+.. index:: bond_style oxdna/fene
-bond\_style oxdna/fene command
+bond_style oxdna/fene command
 =============================
 bond_style oxdna2/fene command
 ==============================
 bond\_style oxdna2/fene command
 ===============================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style oxdna/fene
@ -20,21 +20,23 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style oxdna/fene
-   bond_coeff \* 2.0 0.25 0.7525
+   bond_coeff * 2.0 0.25 0.7525
   bond_style oxdna2/fene
-   bond_coeff \* 2.0 0.25 0.7564
+   bond_coeff * 2.0 0.25 0.7564
 Description
 """""""""""
 The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
-.. image:: Eqs/bond_oxdna_fene.jpg
+.. math::
-   :align: center
+
   E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
 to define a modified finite extensible nonlinear elastic (FENE)
 potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
@ -47,9 +49,9 @@ in the data file or restart files read by the
 :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
 commands:
-* epsilon (energy)
+* :math:`\epsilon` (energy)
-* Delta (distance)
+* :math:`\Delta` (distance)
-* r0 (distance)
+* :math:`r_0` (distance)
 .. note::
@ -121,8 +123,3 @@ J. Chem. Phys. 134, 085101 (2011).
 **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
 J. Chem. Phys. 142, 234901 (2015).
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_quartic.rst
+++ b/doc/src/bond_quartic.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style quartic
+.. index:: bond_style quartic
-bond\_style quartic command
+bond_style quartic command
-===========================
+==========================
-bond\_style quartic/omp command
+bond_style quartic/omp command
-===============================
+==============================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style quartic
@ -18,7 +18,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style quartic
   bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
@ -28,11 +28,12 @@ Description
 The *quartic* bond style uses the potential
-.. image:: Eqs/bond_quartic.jpg
+.. math::
-   :align: center
+
   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
 to define a bond that can be broken as the simulation proceeds (e.g.
-due to a polymer being stretched).  The sigma and epsilon used in the
+due to a polymer being stretched).  The :math:`\sigma` and :math:`\epsilon` used in the
 LJ portion of the formula are both set equal to 1.0 by LAMMPS.
 The following coefficients must be defined for each bond type via the
@ -40,23 +41,31 @@ 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:
-* K (energy/distance\^4)
+* :math:`K` (energy/distance\^4)
-* B1 (distance)
+* :math:`B_1` (distance)
-* B2 (distance)
+* :math:`B_2` (distance)
-* Rc (distance)
+* :math:`R_c` (distance)
-* U0 (energy)
+* :math:`U_0` (energy)
 This potential was constructed to mimic the FENE bond potential for
-coarse-grained polymer chains.  When monomers with sigma = epsilon =
+coarse-grained polymer chains.  When monomers with :math:`\sigma = \epsilon = 1.0`
-1.0 are used, the following choice of parameters gives a quartic
+are used, the following choice of parameters gives a quartic potential that
-potential that looks nearly like the FENE potential: K = 1200, B1 =
+looks nearly like the FENE potential: 
 -0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878.  Different parameters
 can be specified using the :doc:`bond\_coeff <bond_coeff>` command, but
 you will need to choose them carefully so they form a suitable bond
 potential.
-Rc is the cutoff length at which the bond potential goes smoothly to a
+.. math::
-local maximum.  If a bond length ever becomes > Rc, LAMMPS "breaks"
+
   K &= 1200 \\
   B_1 &= -0.55 \\
   B_2 &= 0.25 \\
   R_c &= 1.3 \\
   U_0 &= 34.6878
 Different parameters can be specified using the :doc:`bond_coeff <bond_coeff>`
 command, but you will need to choose them carefully so they form a suitable
 bond potential.
 :math:`R_c` is the cutoff length at which the bond potential goes smoothly to a
 local maximum.  If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks"
 the bond, which means two things.  First, the bond potential is turned
 off by setting its type to 0, and is no longer computed.  Second, a
 pairwise interaction between the two atoms is turned on, since they
@ -75,7 +84,7 @@ Note that when bonds are dumped to a file via the :doc:`dump local <dump>` comma
 status of broken bonds or permanently delete them, e.g.:
-.. parsed-literal::
+.. code-block:: LAMMPS
   delete_bonds all stats
   delete_bonds all bond 0 remove
@ -124,8 +133,3 @@ 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
--- a/doc/src/bond_style.rst
+++ b/doc/src/bond_style.rst
@ -1,29 +1,27 @@
-.. index:: bond\_style
+.. index:: bond_style
-bond\_style command
+bond_style command
-===================
+==================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style style args
 * style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or         *harmonic* or *morse* or *nonlinear* or *quartic*
 * args = none for any style except *hybrid*
-.. parsed-literal::
+  * *hybrid* args = list of one or more styles
     args = none for any style except *hybrid*
     *hybrid* args = list of one or more styles
 Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style harmonic
   bond_style fene
@ -74,11 +72,11 @@ between the 2 atoms in the bond.
 Here is an alphabetic list of bond styles defined in LAMMPS.  Click on
 the style to display the formula it computes and coefficients
-specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
+specified by the associated :doc:`bond_coeff <bond_coeff>` command.
 Click on the style to display the formula it computes, any additional
 arguments specified in the bond\_style command, and coefficients
-specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
+specified by the associated :doc:`bond_coeff <bond_coeff>` command.
 There are also additional accelerated pair styles included in the
 LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@ -128,9 +126,6 @@ Related commands
 Default
 """""""
-bond\_style none
+.. code-block:: LAMMPS
-
+   bond_style none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_table.rst
+++ b/doc/src/bond_table.rst
@ -1,16 +1,16 @@
-.. index:: bond\_style table
+.. index:: bond_style table
-bond\_style table command
+bond_style table command
-=========================
+========================
-bond\_style table/omp command
+bond_style table/omp command
-=============================
+============================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style table style N
@ -21,7 +21,7 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style table linear 1000
   bond_coeff 1 file.table ENTRY1
@ -31,14 +31,14 @@ Description
 Style *table* creates interpolation tables of length *N* from bond
 potential and force values listed in a file(s) as a function of bond
-length.  The files are read by the :doc:`bond\_coeff <bond_coeff>`
+length.  The files are read by the :doc:`bond_coeff <bond_coeff>`
 command.
 The interpolation tables are created by fitting cubic splines to the
 file values and interpolating energy and force values at each of *N*
 distances.  During a simulation, these tables are used to interpolate
 energy and force values as needed.  The interpolation is done in one
-of 2 styles: *linear* or *spline*\ .
+of 2 styles: *linear* or *spline*.
 For the *linear* style, the bond length is used to find 2 surrounding
 table values from which an energy or force is computed by linear
@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to
 evaluate a cubic polynomial which computes the energy or force.
 The following coefficients must be defined for each bond type via the
-:doc:`bond\_coeff <bond_coeff>` command as in the example above.
+:doc:`bond_coeff <bond_coeff>` command as in the example above.
 * filename
 * keyword
@ -84,14 +84,14 @@ 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:`bond\_coeff <bond_coeff>` command.  The next line lists (in any
+:doc:`bond_coeff <bond_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:`bond\_style table <bond_style>` command.  Let
-Ntable = *N* in the bond\_style command, and Nfile = "N" in the
+Ntable = *N* in the bond_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
 uses these to interpolate as needed to generate energy and force
@ -173,11 +173,6 @@ info.
 Related commands
 """"""""""""""""
-:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_write.rst
+++ b/doc/src/bond_write.rst
@ -1,13 +1,13 @@
-.. index:: bond\_write
+.. index:: bond_write
-bond\_write command
+bond_write command
-===================
+==================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_write btype N inner outer file keyword itype jtype
@ -17,13 +17,12 @@ Syntax
 * file = name of file to write values to
 * keyword = section name in file for this set of tabulated values
 * itype,jtype = 2 atom types (optional)
 *
 Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_write 1 500 0.5 3.5 table.txt Harmonic_1
   bond_write 3 1000 0.1 6.0 table.txt Morse
@ -40,14 +39,14 @@ file.
 The energy and force values are computed at distances from inner to
 outer for 2 interacting atoms forming a bond of type btype, using the
-appropriate :doc:`bond\_coeff <bond_coeff>` coefficients. N evenly spaced
+appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly spaced
 distances are used.
 For example, for N = 7, inner = 1.0, and outer = 4.0,
 values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
 The file is written in the format used as input for the
-:doc:`bond\_style <bond_style>` *table* option with *keyword* as the
+:doc:`bond_style <bond_style>` *table* option with *keyword* as the
 section name.  Each line written to the file lists an index number
 (1-N), a distance (in distance units), an energy (in energy units),
 and a force (in force units).
@ -65,12 +64,7 @@ be specified even if the potential has a finite value at r = 0.0.
 Related commands
 """"""""""""""""
-:doc:`bond\_style table <bond_table>`,
+:doc:`bond_style table <bond_table>`,
-:doc:`bond\_style <bond_style>`, :doc:`bond\_coeff <bond_coeff>`
+:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/bond_zero.rst
+++ b/doc/src/bond_zero.rst
@ -1,26 +1,26 @@
-.. index:: bond\_style zero
+.. index:: bond_style zero
-bond\_style zero command
+bond_style zero command
-========================
+=======================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
-   bond_style zero *nocoeff*
+   bond_style zero [nocoeff]
 Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   bond_style zero
   bond_style zero nocoeff
-   bond_coeff \*
+   bond_coeff *
-   bond_coeff \* 2.14
+   bond_coeff * 2.14
 Description
 """""""""""
@ -53,8 +53,3 @@ Related commands
 :doc:`bond\_style none <bond_none>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/src/pair_list.rst
+++ b/doc/src/pair_list.rst
@ -1,13 +1,13 @@
-.. index:: pair\_style list
+.. index:: pair_style list
-pair\_style list command
+pair_style list command
-========================
+=======================
 Syntax
 """"""
-.. parsed-literal::
+.. code-block:: LAMMPS
   pair_style list listfile cutoff keyword
@ -19,14 +19,14 @@ Examples
 """"""""
-.. parsed-literal::
+.. code-block:: LAMMPS
   pair_style list restraints.txt 200.0
-   pair_coeff \* \*
+   pair_coeff * *
   pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
-   pair_coeff \* \* lj/cut 1.0 1.0
+   pair_coeff * * lj/cut 1.0 1.0
-   pair_coeff 3\* 3\* list
+   pair_coeff 3* 3* list
 Description
 """""""""""
@ -77,36 +77,41 @@ Here is an example file:
 The style *lj126* computes pairwise interactions with the formula
-.. image:: Eqs/pair_lj.jpg
+.. math::
-   :align: center
+
   E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c
 and the coefficients:
-* epsilon (energy units)
+* :math:`\epsilon` (energy units)
-* sigma (distance units)
+* :math:`\sigma` (distance units)
 The style *morse* computes pairwise interactions with the formula
-.. image:: Eqs/pair_morse.jpg
+.. math::
-   :align: center
+
   E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c
 and the coefficients:
-* D0 (energy units)
+* :math:`D_0` (energy units)
-* alpha (1/distance units)
+* :math:`\alpha` (1/distance units)
-* r0 (distance units)
+* :math:`r_0` (distance units)
 The style *harmonic* computes pairwise interactions with the formula
-.. image:: Eqs/bond_harmonic.jpg
+.. math::
-   :align: center
+
   E = K (r - r_0)^2
 and the coefficients:
-* K (energy units)
+* :math:`K` (energy units)
-* r0 (distance units)
+* :math:`r_0` (distance units)
-Note that the usual 1/2 factor is included in K.
+Note that the usual 1/2 factor is included in :math:`K`.
 ----------
@ -161,8 +166,3 @@ Related commands
 :doc:`bond\_style harmonic <bond_harmonic>`
 **Default:** none
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
 .. _lc: Commands_all.html
--- a/doc/txt/atom_modify.txt
+++ b/doc/txt/atom_modify.txt
@ -1,175 +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
 atom_modify command :h3
 [Syntax:]
 atom_modify keyword values ... :pre
 one or more keyword/value pairs may be appended :ulb,l
 keyword = {id} or {map} or {first} or {sort} :l
   {id} value = {yes} or {no}
   {map} value = {yes} or {array} or {hash}
   {first} value = group-ID = group whose atoms will appear first in internal atom lists
   {sort} values = Nfreq binsize
     Nfreq = sort atoms spatially every this many time steps
     binsize = bin size for spatial sorting (distance units) :pre
 :ule
 [Examples:]
 atom_modify map yes
 atom_modify map hash sort 10000 2.0
 atom_modify first colloid :pre
 [Description:]
 Modify certain attributes of atoms defined and stored within LAMMPS,
 in addition to what is specified by the "atom_style"_atom_style.html
 command.  The {id} and {map} keywords must be specified before a
 simulation box is defined; other keywords can be specified any time.
 The {id} keyword determines whether non-zero atom IDs can be assigned
 to each atom.  If the value is {yes}, which is the default, IDs are
 assigned, whether you use the "create atoms"_create_atoms.html or
 "read_data"_read_data.html or "read_restart"_read_restart.html
 commands to initialize atoms.  If the value is {no} the IDs for all
 atoms are assumed to be 0.
 If atom IDs are used, they must all be positive integers.  They should
 also be unique, though LAMMPS does not check for this.  Typically they
 should also be consecutively numbered (from 1 to Natoms), though this
 is not required.  Molecular "atom styles"_atom_style.html are those
 that store bond topology information (styles bond, angle, molecular,
 full).  These styles require atom IDs since the IDs are used to encode
 the topology.  Some other LAMMPS commands also require the use of atom
 IDs.  E.g. some many-body pair styles use them to avoid double
 computation of the I-J interaction between two atoms.
 The only reason not to use atom IDs is if you are running an atomic
 simulation so large that IDs cannot be uniquely assigned.  For a
 default LAMMPS build this limit is 2^31 or about 2 billion atoms.
 However, even in this case, you can use 64-bit atom IDs, allowing 2^63
 or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
 switch.  This is described on the "Build_settings"_Build_settings.html
 doc page.  If atom IDs are not used, they must be specified as 0 for
 all atoms, e.g. in a data or restart file.
 The {map} keyword determines how atoms with specific IDs are found
 when required.  An example are the bond (angle, etc) methods which
 need to find the local index of an atom with a specific global ID
 which is a bond (angle, etc) partner.  LAMMPS performs this operation
 efficiently by creating a "map", which is either an {array} or {hash}
 table, as described below.
 When the {map} keyword is not specified in your input script, LAMMPS
 only creates a map for "atom_styles"_atom_style.html for molecular
 systems which have permanent bonds (angles, etc).  No map is created
 for atomic systems, since it is normally not needed.  However some
 LAMMPS commands require a map, even for atomic systems, and will
 generate an error if one does not exist.  The {map} keyword thus
 allows you to force the creation of a map.  The {yes} value will
 create either an {array} or {hash} style map, as explained in the next
 paragraph.  The {array} and {hash} values create an atom-style or
 hash-style map respectively.
 For an {array}-style map, each processor stores a lookup table of
 length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
 for large simulations.  For a {hash}-style map, a hash table is
 created on each processor, which finds an atom ID in constant time
 (independent of the global number of atom IDs).  It can be slightly
 slower than the {array} map, but its memory cost is proportional to
 the number of atoms owned by a processor, i.e. N/P when N is the total
 number of atoms in the system and P is the number of processors.
 The {first} keyword allows a "group"_group.html to be specified whose
 atoms will be maintained as the first atoms in each processor's list
 of owned atoms.  This in only useful when the specified group is a
 small fraction of all the atoms, and there are other operations LAMMPS
 is performing that will be sped-up significantly by being able to loop
 over the smaller set of atoms.  Otherwise the reordering required by
 this option will be a net slow-down.  The "neigh_modify
 include"_neigh_modify.html and "comm_modify group"_comm_modify.html
 commands are two examples of commands that require this setting to
 work efficiently.  Several "fixes"_fix.html, most notably time
 integration fixes like "fix nve"_fix_nve.html, also take advantage of
 this setting if the group they operate on is the group specified by
 this command.  Note that specifying "all" as the group-ID effectively
 turns off the {first} option.
 It is OK to use the {first} keyword with a group that has not yet been
 defined, e.g. to use the atom_modify first command at the beginning of
 your input script.  LAMMPS does not use the group until a simulation
 is run.
 The {sort} keyword turns on a spatial sorting or reordering of atoms
 within each processor's sub-domain every {Nfreq} timesteps.  If
 {Nfreq} is set to 0, then sorting is turned off.  Sorting can improve
 cache performance and thus speed-up a LAMMPS simulation, as discussed
 in a paper by "(Meloni)"_#Meloni.  Its efficacy depends on the problem
 size (atoms/processor), how quickly the system becomes disordered, and
 various other factors.  As a general rule, sorting is typically more
 effective at speeding up simulations of liquids as opposed to solids.
 In tests we have done, the speed-up can range from zero to 3-4x.
 Reordering is performed every {Nfreq} timesteps during a dynamics run
 or iterations during a minimization.  More precisely, reordering
 occurs at the first reneighboring that occurs after the target
 timestep.  The reordering is performed locally by each processor,
 using bins of the specified {binsize}.  If {binsize} is set to 0.0,
 then a binsize equal to half the "neighbor"_neighbor.html cutoff
 distance (force cutoff plus skin distance) is used, which is a
 reasonable value.  After the atoms have been binned, they are
 reordered so that atoms in the same bin are adjacent to each other in
 the processor's 1d list of atoms.
 The goal of this procedure is for atoms to put atoms close to each
 other in the processor's one-dimensional list of atoms that are also
 near to each other spatially.  This can improve cache performance when
 pairwise interactions and neighbor lists are computed.  Note that if
 bins are too small, there will be few atoms/bin.  Likewise if bins are
 too large, there will be many atoms/bin.  In both cases, the goal of
 cache locality will be undermined.
 NOTE: Running a simulation with sorting on versus off should not
 change the simulation results in a statistical sense.  However, a
 different ordering will induce round-off differences, which will lead
 to diverging trajectories over time when comparing two simulations.
 Various commands, particularly those which use random numbers
 (e.g. "velocity create"_velocity.html, and "fix
 langevin"_fix_langevin.html), may generate (statistically identical)
 results which depend on the order in which atoms are processed.  The
 order of atoms in a "dump"_dump.html file will also typically change
 if sorting is enabled.
 [Restrictions:]
 The {first} and {sort} options cannot be used together.  Since sorting
 is on by default, it will be turned off if the {first} keyword is
 used with a group-ID that is not "all".
 [Related commands:] none
 [Default:]
 By default, {id} is yes.  By default, atomic systems (no bond topology
 info) do not use a map.  For molecular systems (with bond topology
 info), a map is used.  The default map style is array if no atom ID is
 larger than 1 million, otherwise the default is hash.  By default, a
 "first" group is not defined.  By default, sorting is enabled with a
 frequency of 1000 and a binsize of 0.0, which means the neighbor
 cutoff will be used to set the bin size. If no neighbor cutoff is
 defined, sorting will be turned off.
 :line
 :link(Meloni)
 [(Meloni)] Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
--- a/doc/txt/atom_style.txt
+++ b/doc/txt/atom_style.txt
@ -1,338 +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
 atom_style command :h3
 [Syntax:]
 atom_style style args :pre
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
        {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
        {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
        {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l
  args = none for any style except the following
    {body} args = bstyle bstyle-args
      bstyle = style of body particles
      bstyle-args = additional arguments specific to the bstyle
                    see the "Howto body"_Howto_body.html doc page for details
    {tdpd} arg = Nspecies
      Nspecies = # of chemical species
    {template} arg = template-ID
      template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
    {hybrid} args = list of one or more sub-styles, each with their args :pre
 accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l
 :ule
 [Examples:]
 atom_style atomic
 atom_style bond
 atom_style full
 atom_style body nparticle 2 10
 atom_style hybrid charge bond
 atom_style hybrid charge body nparticle 2 5
 atom_style spin
 atom_style template myMols
 atom_style tdpd 2 :pre
 [Description:]
 Define what style of atoms to use in a simulation.  This determines
 what attributes are associated with the atoms.  This command must be
 used before a simulation is setup via a "read_data"_read_data.html,
 "read_restart"_read_restart.html, or "create_box"_create_box.html
 command.
 NOTE: Many of the atom styles discussed here are only enabled if
 LAMMPS was built with a specific package, as listed below in the
 Restrictions section.
 Once a style is assigned, it cannot be changed, so use a style general
 enough to encompass all attributes.  E.g. with style {bond}, angular
 terms cannot be used or added later to the model.  It is OK to use a
 style more general than needed, though it may be slightly inefficient.
 The choice of style affects what quantities are stored by each atom,
 what quantities are communicated between processors to enable forces
 to be computed, and what quantities are listed in the data file read
 by the "read_data"_read_data.html command.
 These are the additional attributes of each style and the typical
 kinds of physical systems they are used to model.  All styles store
 coordinates, velocities, atom IDs and types.  See the
 "read_data"_read_data.html, "create_atoms"_create_atoms.html, and
 "set"_set.html commands for info on how to set these various
 quantities.
 {angle} | bonds and angles | bead-spring polymers with stiffness |
 {atomic} | only the default values | coarse-grain liquids, solids, metals |
 {body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
 {bond} | bonds | bead-spring polymers |
 {charge} | charge | atomic system with charges |
 {dipole} | charge and dipole moment | system with dipolar particles |
 {dpd} | internal temperature and internal energies | DPD particles |
 {edpd} | temperature and heat capacity | eDPD particles |
 {mdpd} | density | mDPD particles |
 {tdpd} | chemical concentration | tDPD particles |
 {electron} | charge and spin and eradius | electronic force field |
 {ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
 {full} | molecular + charge | bio-molecules |
 {line} | end points, angular velocity | rigid bodies |
 {meso} | rho, e, cv | SPH particles |
 {molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
 {peri} | mass, volume | mesoscopic Peridynamic models |
 {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
 {sphere} | diameter, mass, angular velocity | granular models |
 {spin} | magnetic moment | system with magnetic particles |
 {template} | template index, template atom | small molecules with fixed topology |
 {tri} | corner points, angular momentum | rigid bodies |
 {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
 NOTE: It is possible to add some attributes, such as a molecule ID, to
 atom styles that do not have them via the "fix
 property/atom"_fix_property_atom.html command.  This command also
 allows new custom attributes consisting of extra integer or
 floating-point values to be added to atoms.  See the "fix
 property/atom"_fix_property_atom.html doc page for examples of cases
 where this is useful and details on how to initialize, access, and
 output the custom values.
 All of the above styles define point particles, except the {sphere},
 {ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
 {body} styles, which define finite-size particles.  See the "Howto
 spherical"_Howto_spherical.html doc page for an overview of using
 finite-size particle models with LAMMPS.
 All of the point-particle styles assign mass to particles on a
 per-type basis, using the "mass"_mass.html command, The finite-size
 particle styles assign mass to individual particles on a per-particle
 basis.
 For the {sphere} style, the particles are spheres and each stores a
 per-particle diameter and mass.  If the diameter > 0.0, the particle
 is a finite-size sphere.  If the diameter = 0.0, it is a point
 particle.  Note that by use of the {disc} keyword with the "fix
 nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,
 "fix nph/sphere"_fix_nph_sphere.html, "fix
 npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively
 treated as 2d discs for a 2d simulation if desired.  See also the "set
 density/disc"_set.html command.
 For the {ellipsoid} style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or
 a point particle.  If it is an ellipsoid, it also stores a shape
 vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
 with its orientation.
 For the {dipole} style, a point dipole is defined for each point
 particle.  Note that if you wish the particles to be finite-size
 spheres as in a Stockmayer potential for a dipolar fluid, so that the
 particles can rotate due to dipole-dipole interactions, then you need
 to use atom_style hybrid sphere dipole, which will assign both a
 diameter and dipole moment to each particle.
 For the {electron} style, the particles representing electrons are 3d
 Gaussians with a specified position and bandwidth or uncertainty in
 position, which is represented by the eradius = electron size.
 For the {peri} style, the particles are spherical and each stores a
 per-particle mass and volume.
 The {dpd} style is for dissipative particle dynamics (DPD) particles.
 Note that it is part of the USER-DPD package, and is not for use with
 the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can
 simply use atom_style atomic.  Atom_style dpd extends DPD particle
 properties with internal temperature (dpdTheta), internal conductive
 energy (uCond), internal mechanical energy (uMech), and internal
 chemical energy (uChem).
 The {edpd} style is for energy-conserving dissipative particle
 dynamics (eDPD) particles which store a temperature (edpd_temp), and
 heat capacity(edpd_cv).
 The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
 particles which store a density (rho) for considering
 density-dependent many-body interactions.
 The {tdpd} style is for transport dissipative particle dynamics (tDPD)
 particles which store a set of chemical concentration. An integer
 "cc_species" is required to specify the number of chemical species
 involved in a tDPD system.
 The {meso} style is for smoothed particle hydrodynamics (SPH)
 particles which store a density (rho), energy (e), and heat capacity
 (cv).
 The {smd} style is for a general formulation of Smooth Particle
 Hydrodynamics.  Both fluids and solids can be modeled.  Particles
 store the mass and volume of an integration point, a kernel diameter
 used for calculating the field variables (e.g. stress and deformation)
 and a contact radius for calculating repulsive forces which prevent
 individual physical bodies from penetrating each other.
 For the {spin} style, a magnetic spin is associated to each atom.
 Those spins have a norm (their magnetic moment) and a direction.
 The {wavepacket} style is similar to {electron}, but the electrons may
 consist of several Gaussian wave packets, summed up with coefficients
 cs= (cs_re,cs_im).  Each of the wave packets is treated as a separate
 particle in LAMMPS, wave packets belonging to the same electron must
 have identical {etag} values.
 For the {line} style, the particles are idealized line segments and
 each stores a per-particle mass and length and orientation (i.e. the
 end points of the line segment).
 For the {tri} style, the particles are planar triangles and each
 stores a per-particle mass and size and orientation (i.e. the corner
 points of the triangle).
 The {template} style allows molecular topology (bonds,angles,etc) to be
 defined via a molecule template using the "molecule"_molecule.html
 command.  The template stores one or more molecules with a single copy
 of the topology info (bonds,angles,etc) of each.  Individual atoms
 only store a template index and template atom to identify which
 molecule and which atom-within-the-molecule they represent.  Using the
 {template} style instead of the {bond}, {angle}, {molecular} styles
 can save memory for systems comprised of a large number of small
 molecules, all of a single type (or small number of types).  See the
 paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this
 can be advantageous for large-scale coarse-grained systems.
 NOTE: When using the {template} style with a "molecule
 template"_molecule.html that contains multiple molecules, you should
 insure the atom types, bond types, angle_types, etc in all the
 molecules are consistent.  E.g. if one molecule represents H2O and
 another CO2, then you probably do not want each molecule file to
 define 2 atom types and a single bond type, because they will conflict
 with each other when a mixture system of H2O and CO2 molecules is
 defined, e.g. by the "read_data"_read_data.html command.  Rather the
 H2O molecule should define atom types 1 and 2, and bond type 1.  And
 the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
 2 if a single oxygen type is desired), and bond type 2.
 For the {body} style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
 the {bstyle} argument.  Body particles can represent complex entities,
 such as surface meshes of discrete points, collections of
 sub-particles, deformable objects, etc.
 The "Howto body"_Howto_body.html doc page describes the body styles
 LAMMPS currently supports, and provides more details as to the kind of
 body particles they represent.  For all styles, each body particle
 stores moments of inertia and a quaternion 4-vector, so that its
 orientation and position can be time integrated due to forces and
 torques.
 Note that there may be additional arguments required along with the
 {bstyle} specification, in the atom_style body command.  These
 arguments are described on the "Howto body"_Howto_body.html doc page.
 :line
 Typically, simulations require only a single (non-hybrid) atom style.
 If some atoms in the simulation do not have all the properties defined
 by a particular style, use the simplest style that defines all the
 needed properties by any atom.  For example, if some atoms in a
 simulation are charged, but others are not, use the {charge} style.
 If some atoms have bonds, but others do not, use the {bond} style.
 The only scenario where the {hybrid} style is needed is if there is no
 single style which defines all needed properties of all atoms.  For
 example, as mentioned above, if you want dipolar particles which will
 rotate due to torque, you need to use "atom_style hybrid sphere
 dipole".  When a hybrid style is used, atoms store and communicate the
 union of all quantities implied by the individual styles.
 When using the {hybrid} style, you cannot combine the {template} style
 with another molecular style that stores bond,angle,etc info on a
 per-atom basis.
 LAMMPS can be extended with new atom styles as well as new body
 styles; see the "Modify"_Modify.html doc page.
 :line
 Styles with a {kk} 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 in 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.
 Note that other acceleration packages in LAMMPS, specifically the GPU,
 USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
 styles.
 The accelerated styles are part of the KOKKOS package.  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 command cannot be used after the simulation box is defined by a
 "read_data"_read_data.html or "create_box"_create_box.html command.
 Many of the styles listed above are only enabled if LAMMPS was built
 with a specific package, as listed below.  See the "Build
 package"_Build_package.html doc page for more info.
 The {angle}, {bond}, {full}, {molecular}, and {template} styles are
 part of the MOLECULE package.
 The {line} and {tri} styles are part of the ASPHERE package.
 The {body} style is part of the BODY package.
 The {dipole} style is part of the DIPOLE package.
 The {peri} style is part of the PERI package for Peridynamics.
 The {electron} style is part of the USER-EFF package for "electronic
 force fields"_pair_eff.html.
 The {dpd} style is part of the USER-DPD package for dissipative
 particle dynamics (DPD).
 The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
 for energy-conserving dissipative particle dynamics (eDPD), many-body
 dissipative particle dynamics (mDPD), and transport dissipative particle
 dynamics (tDPD), respectively.
 The {meso} style is part of the USER-SPH package for smoothed particle
 hydrodynamics (SPH).  See "this PDF
 guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
 The {spin} style is part of the SPIN package.
 The {wavepacket} style is part of the USER-AWPMD package for the
 "antisymmetrized wave packet MD method"_pair_awpmd.html.
 [Related commands:]
 "read_data"_read_data.html, "pair_style"_pair_style.html
 [Default:]
 atom_style atomic
 :line
 :link(Grime)
 [(Grime)] Grime and Voth, to appear in J Chem Theory & Computation
 (2014).
--- a/doc/txt/bond_class2.txt
+++ b/doc/txt/bond_class2.txt
@ -1,81 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style class2 command :h3
 bond_style class2/omp command :h3
 bond_style class2/kk command :h3
 [Syntax:]
 bond_style class2 :pre
 [Examples:]
 bond_style class2
 bond_coeff 1 1.0 100.0 80.0 80.0 :pre
 [Description:]
 The {class2} bond style uses the potential
 :c,image(Eqs/bond_class2.jpg)
 where r0 is the equilibrium bond distance.
 See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 R0 (distance)
 K2 (energy/distance^2)
 K3 (energy/distance^3)
 K4 (energy/distance^4) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the CLASS2
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
 :line
 :link(bond-Sun)
 [(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
--- a/doc/txt/bond_coeff.txt
+++ b/doc/txt/bond_coeff.txt
@ -1,82 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_coeff command :h3
 [Syntax:]
 bond_coeff N args :pre
 N = bond type (see asterisk form below)
 args = coefficients for one or more bond types :ul
 [Examples:]
 bond_coeff 5 80.0 1.2
 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 harmonic 200.0 1.0 :pre
 [Description:]
 Specify the bond force field coefficients for one or more bond types.
 The number and meaning of the coefficients depends on the bond style.
 Bond coefficients can also be set in the data file read by the
 "read_data"_read_data.html 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
 used to set the coefficients for multiple bond types.  This takes the
 form "*" or "*n" or "n*" or "m*n".  If N = the number of bond types,
 then an asterisk with no numeric values means all types from 1 to N.  A
 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 a bond_coeff command can override a previous setting
 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:
 bond_coeff * 100.0 1.2
 bond_coeff 2 200.0 1.2 :pre
 A line in a data file that specifies bond coefficients uses the exact
 same format as the arguments of the bond_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 "Bond Coeffs" section of a data file, the line that
 corresponds to the 1st example above would be listed as
 5 80.0 1.2 :pre
 :line
 The list of all bond styles defined in LAMMPS is given on the
 "bond_style"_bond_style.html doc page.  They are also listed in more
 compact form on the "Commands bond"_Commands_bond.html 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
 bond_coeff command.
 :line
 [Restrictions:]
 This command must come after the simulation box is defined by a
 "read_data"_read_data.html, "read_restart"_read_restart.html, or
 "create_box"_create_box.html command.
 A bond style must be defined before any bond coefficients are set,
 either in the input script or in a data file.
 [Related commands:]
 "bond_style"_bond_style.html
 [Default:] none
--- a/doc/txt/bond_fene.txt
+++ b/doc/txt/bond_fene.txt
@ -1,88 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style fene command :h3
 bond_style fene/intel command :h3
 bond_style fene/kk command :h3
 bond_style fene/omp command :h3
 [Syntax:]
 bond_style fene :pre
 [Examples:]
 bond_style fene
 bond_coeff 1 30.0 1.5 1.0 1.0 :pre
 [Description:]
 The {fene} bond style uses the potential
 :c,image(Eqs/bond_fene.jpg)
 to define a finite extensible nonlinear elastic (FENE) potential
 "(Kremer)"_#fene-Kremer, used for bead-spring polymer models.  The first
 term is attractive, the 2nd Lennard-Jones term is repulsive.  The
 first term extends to R0, the maximum extent of the bond.  The 2nd
 term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 K (energy/distance^2)
 R0 (distance)
 epsilon (energy)
 sigma (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
 :line
 :link(fene-Kremer)
 [(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
--- a/doc/txt/bond_fene_expand.txt
+++ b/doc/txt/bond_fene_expand.txt
@ -1,91 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style fene/expand command :h3
 bond_style fene/expand/omp command :h3
 [Syntax:]
 bond_style fene/expand :pre
 [Examples:]
 bond_style fene/expand
 bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre
 [Description:]
 The {fene/expand} bond style uses the potential
 :c,image(Eqs/bond_fene_expand.jpg)
 to define a finite extensible nonlinear elastic (FENE) potential
 "(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
 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
 + delta.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 K (energy/distance^2)
 R0 (distance)
 epsilon (energy)
 sigma (distance)
 delta (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
 :line
 :link(feneexpand-Kremer)
 [(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
--- a/doc/txt/bond_gromos.txt
+++ b/doc/txt/bond_gromos.txt
@ -1,72 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style gromos command :h3
 bond_style gromos/omp command :h3
 [Syntax:]
 bond_style gromos :pre
 [Examples:]
 bond_style gromos
 bond_coeff 5 80.0 1.2 :pre
 [Description:]
 The {gromos} bond style uses the potential
 :c,image(Eqs/bond_gromos.jpg)
 where r0 is the equilibrium bond distance.  Note that the usual 1/4
 factor is included in K.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 K (energy/distance^4)
 r0 (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
--- a/doc/txt/bond_harmonic.txt
+++ b/doc/txt/bond_harmonic.txt
@ -1,74 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style harmonic command :h3
 bond_style harmonic/intel command :h3
 bond_style harmonic/kk command :h3
 bond_style harmonic/omp command :h3
 [Syntax:]
 bond_style harmonic :pre
 [Examples:]
 bond_style harmonic
 bond_coeff 5 80.0 1.2 :pre
 [Description:]
 The {harmonic} bond style uses the potential
 :c,image(Eqs/bond_harmonic.jpg)
 where r0 is the equilibrium bond distance.  Note that the usual 1/2
 factor is included in K.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 K (energy/distance^2)
 r0 (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
--- a/doc/txt/bond_harmonic_shift.txt
+++ b/doc/txt/bond_harmonic_shift.txt
@ -1,76 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style harmonic/shift command :h3
 bond_style harmonic/shift/omp command :h3
 [Syntax:]
 bond_style harmonic/shift :pre
 [Examples:]
 bond_style harmonic/shift
 bond_coeff 5 10.0 0.5 1.0 :pre
 [Description:]
 The {harmonic/shift} bond style is a shifted harmonic bond that uses
 the potential
 :c,image(Eqs/bond_harmonic_shift.jpg)
 where r0 is the equilibrium bond distance, and rc the critical distance.
 The potential is -Umin at r0 and zero at rc. The spring constant is
 k = Umin / \[ 2 (r0-rc)^2\].
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 Umin (energy) :ul
 r0 (distance) :ul
 rc (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the
 USER-MISC package.  See the "Build package"_Build_package.html doc
 page for more info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
 "bond_harmonic"_bond_harmonic.html
 [Default:] none
--- a/doc/txt/bond_harmonic_shift_cut.txt
+++ b/doc/txt/bond_harmonic_shift_cut.txt
@ -1,77 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style harmonic/shift/cut command :h3
 bond_style harmonic/shift/cut/omp command :h3
 [Syntax:]
 bond_style harmonic/shift/cut :pre
 [Examples:]
 bond_style harmonic/shift/cut
 bond_coeff 5 10.0 0.5 1.0 :pre
 [Description:]
 The {harmonic/shift/cut} bond style is a shifted harmonic bond that
 uses the potential
 :c,image(Eqs/bond_harmonic_shift_cut.jpg)
 where r0 is the equilibrium bond distance, and rc the critical distance.
 The bond potential is zero for distances r > rc. The potential is -Umin
 at r0 and zero at rc. The spring constant is k = Umin / \[ 2 (r0-rc)^2\].
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 Umin (energy)
 r0 (distance)
 rc (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the
 USER-MISC package.  See the "Build package"_Build_package.html doc
 page for more info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
 "bond_harmonic"_bond_harmonic.html,
 "bond_harmonic_shift"_bond_harmonic_shift.html
 [Default:] none
--- a/doc/txt/bond_hybrid.txt
+++ b/doc/txt/bond_hybrid.txt
@ -1,74 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style hybrid command :h3
 [Syntax:]
 bond_style hybrid style1 style2 ... :pre
 style1,style2 = list of one or more bond styles :ul
 [Examples:]
 bond_style hybrid harmonic fene
 bond_coeff 1 harmonic 80.0 1.2
 bond_coeff 2* fene 30.0 1.5 1.0 1.0 :pre
 [Description:]
 The {hybrid} style enables the use of multiple bond styles in one
 simulation.  A bond style is assigned to each bond type.  For example,
 bonds in a polymer flow (of bond type 1) could be computed with a
 {fene} potential and bonds in the wall boundary (of bond type 2) could
 be computed with a {harmonic} potential.  The assignment of bond type
 to style is made via the "bond_coeff"_bond_coeff.html command or in
 the data file.
 In the bond_coeff commands, the name of a bond style must be added
 after the bond type, with the remaining coefficients being those
 appropriate to that style.  In the example above, the 2 bond_coeff
 commands set bonds of bond type 1 to be computed with a {harmonic}
 potential with coefficients 80.0, 1.2 for K, r0.  All other bond types
 (2-N) are computed with a {fene} potential with coefficients 30.0,
 1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
 If bond coefficients are specified in the data file read via the
 "read_data"_read_data.html command, then the same rule applies.
 E.g. "harmonic" or "fene" must be added after the bond type, for each
 line in the "Bond Coeffs" section, e.g.
 Bond Coeffs :pre
 1 harmonic 80.0 1.2
 2 fene 30.0 1.5 1.0 1.0
 ... :pre
 A bond style of {none} with no additional coefficients can be used in
 place of a bond style, either in a input script bond_coeff command or
 in the data file, if you desire to turn off interactions for specific
 bond types.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 Unlike other bond styles, the hybrid bond style does not store bond
 coefficient info for individual sub-styles in a "binary restart
 files"_restart.html.  Thus when restarting a simulation from a restart
 file, you need to re-specify bond_coeff commands.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
--- a/doc/txt/bond_mm3.txt
+++ b/doc/txt/bond_mm3.txt
@ -1,58 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style mm3 command :h3
 [Syntax:]
 bond_style mm3 :pre
 [Examples:]
 bond_style mm3
 bond_coeff 1 100.0 107.0 :pre
 [Description:]
 The {mm3} bond style uses the potential that is anharmonic in the bond
 as defined in "(Allinger)"_#mm3-allinger1989
 :c,image(Eqs/bond_mm3.jpg)
 where r0 is the equilibrium value of the bond, and K is a
 prefactor. The anharmonic prefactors have units angstrom^(-n):
 -2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
 care of the necessary unit conversion for these factors internally.
 Note that the MM3 papers contains an error in Eq (1):
 (7/12)2.55 should be replaced with (7/12)2.55^2
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 K (energy/distance^2)
 r0 (distance) :ul
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the
 USER_YAFF package.  See the "Build package"_Build_package.html doc
 page for more info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html
 [Default:] none
 :line
 :link(mm3-allinger1989)
 [(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
 (1989),
--- a/doc/txt/bond_morse.txt
+++ b/doc/txt/bond_morse.txt
@ -1,73 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style morse command :h3
 bond_style morse/omp command :h3
 [Syntax:]
 bond_style morse :pre
 [Examples:]
 bond_style morse
 bond_coeff 5 1.0 2.0 1.2 :pre
 [Description:]
 The {morse} bond style uses the potential
 :c,image(Eqs/bond_morse.jpg)
 where r0 is the equilibrium bond distance, alpha is a stiffness
 parameter, and D determines the depth of the potential well.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 D (energy)
 alpha (inverse distance)
 r0 (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
--- a/doc/txt/bond_none.txt
+++ b/doc/txt/bond_none.txt
@ -1,34 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style none command :h3
 [Syntax:]
 bond_style none :pre
 [Examples:]
 bond_style none :pre
 [Description:]
 Using a bond style of none means bond forces and energies are not
 computed, even if pairs of bonded atoms were listed in the data file
 read by the "read_data"_read_data.html command.
 See the "bond_style zero"_bond_zero.html command for a way to
 calculate bond statistics, but compute no bond interactions.
 [Restrictions:] none
 [Related commands:] none
 "bond_style zero"_bond_zero.html
 [Default:] none
--- a/doc/txt/bond_nonlinear.txt
+++ b/doc/txt/bond_nonlinear.txt
@ -1,78 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style nonlinear command :h3
 bond_style nonlinear/omp command :h3
 [Syntax:]
 bond_style nonlinear :pre
 [Examples:]
 bond_style nonlinear
 bond_coeff 2 100.0 1.1 1.4 :pre
 [Description:]
 The {nonlinear} bond style uses the potential
 :c,image(Eqs/bond_nonlinear.jpg)
 to define an anharmonic spring "(Rector)"_#Rector of equilibrium
 length r0 and maximum extension lamda.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 epsilon (energy)
 r0 (distance)
 lamda (distance) :ul
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
 :line
 :link(Rector)
 [(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
--- a/doc/txt/bond_oxdna.txt
+++ b/doc/txt/bond_oxdna.txt
@ -1,99 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style oxdna/fene command :h3
 bond_style oxdna2/fene command :h3
 [Syntax:]
 bond_style oxdna/fene :pre
 bond_style oxdna2/fene :pre
 [Examples:]
 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525 :pre
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564 :pre
 [Description:]
 The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
 :c,image(Eqs/bond_oxdna_fene.jpg)
 to define a modified finite extensible nonlinear elastic (FENE)
 potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
 phosphate backbone in the oxDNA force field for coarse-grained
 modelling of DNA.
 The following coefficients must be defined for the bond type via the
 "bond_coeff"_bond_coeff.html command as given in the above example, or
 in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
 commands:
 epsilon (energy)
 Delta (distance)
 r0 (distance) :ul
 NOTE: The oxDNA bond style has to be used together with the
 corresponding oxDNA pair styles for excluded volume interaction
 {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
 coaxial stacking interaction {oxdna/coaxstk} as well as
 hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
 "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an
 additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
 The coefficients in the above example have to be kept fixed and cannot
 be changed without reparameterizing the entire model.
 Example input and data files for DNA duplexes can be found in
 examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.  A simple python
 setup tool which creates single straight or helical DNA strands, DNA
 duplexes or arrays of DNA duplexes can be found in
 examples/USER/cgdna/util/.
 Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
 any publication that uses this implementation.  The article contains
 more information on the model, the structure of the input file, the
 setup tool and the performance of the LAMMPS-implementation of oxDNA.
 The preprint version of the article can be found
 "here"_PDF/USER-CGDNA.pdf.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the
 USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 "Build package"_Build_package.html doc page for more info.
 [Related commands:]
 "pair_style oxdna/excv"_pair_oxdna.html, "pair_style
 oxdna2/excv"_pair_oxdna2.html, "fix
 nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "bond_coeff"_bond_coeff.html
 [Default:] none
 :line
 :link(Henrich2)
 [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
 T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 :link(oxdna_fene)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
 J. Chem. Phys. 134, 085101 (2011).
 :link(oxdna2)
 [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
 J. Chem. Phys. 142, 234901 (2015).
--- a/doc/txt/bond_quartic.txt
+++ b/doc/txt/bond_quartic.txt
@ -1,112 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style quartic command :h3
 bond_style quartic/omp command :h3
 [Syntax:]
 bond_style quartic :pre
 [Examples:]
 bond_style quartic
 bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
 [Description:]
 The {quartic} bond style uses the potential
 :c,image(Eqs/bond_quartic.jpg)
 to define a bond that can be broken as the simulation proceeds (e.g.
 due to a polymer being stretched).  The sigma and epsilon used in the
 LJ portion of the formula are both set equal to 1.0 by LAMMPS.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 K (energy/distance^4)
 B1 (distance)
 B2 (distance)
 Rc (distance)
 U0 (energy) :ul
 This potential was constructed to mimic the FENE bond potential for
 coarse-grained polymer chains.  When monomers with sigma = epsilon =
 1.0 are used, the following choice of parameters gives a quartic
 potential that looks nearly like the FENE potential: K = 1200, B1 =
 -0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878.  Different parameters
 can be specified using the "bond_coeff"_bond_coeff.html command, but
 you will need to choose them carefully so they form a suitable bond
 potential.
 Rc is the cutoff length at which the bond potential goes smoothly to a
 local maximum.  If a bond length ever becomes > Rc, LAMMPS "breaks"
 the bond, which means two things.  First, the bond potential is turned
 off by setting its type to 0, and is no longer computed.  Second, a
 pairwise interaction between the two atoms is turned on, since they
 are no longer bonded.
 LAMMPS does the second task via a computational sleight-of-hand.  It
 subtracts the pairwise interaction as part of the bond computation.
 When the bond breaks, the subtraction stops.  For this to work, the
 pairwise interaction must always be computed by the
 "pair_style"_pair_style.html command, whether the bond is broken or
 not.  This means that "special_bonds"_special_bonds.html must be set
 to 1,1,1, as indicated as a restriction below.
 Note that when bonds are dumped to a file via the "dump
 local"_dump.html command, bonds with type 0 are not included.  The
 "delete_bonds"_delete_bonds.html command can also be used to query the
 status of broken bonds or permanently delete them, e.g.:
 delete_bonds all stats
 delete_bonds all bond 0 remove :pre
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 The {quartic} style requires that "special_bonds"_special_bonds.html
 parameters be set to 1,1,1.  Three- and four-body interactions (angle,
 dihedral, etc) cannot be used with {quartic} bonds.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
--- a/doc/txt/bond_style.txt
+++ b/doc/txt/bond_style.txt
@ -1,115 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style command :h3
 [Syntax:]
 bond_style style args :pre
 style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \
        {harmonic} or {morse} or {nonlinear} or {quartic} :ul
  args = none for any style except {hybrid}
  {hybrid} args = list of one or more styles :pre
 [Examples:]
 bond_style harmonic
 bond_style fene
 bond_style hybrid harmonic fene :pre
 [Description:]
 Set the formula(s) LAMMPS uses to compute bond interactions between
 pairs of atoms.  In LAMMPS, a bond differs from a pairwise
 interaction, which are set via the "pair_style"_pair_style.html
 command.  Bonds are defined between specified pairs of atoms and
 remain in force for the duration of the simulation (unless the bond
 breaks which is possible in some bond potentials).  The list of bonded
 atoms is read in by a "read_data"_read_data.html or
 "read_restart"_read_restart.html command from a data or restart file.
 By contrast, pair potentials are typically defined between all pairs
 of atoms within a cutoff distance and the set of active interactions
 changes over time.
 Hybrid models where bonds are computed using different bond potentials
 can be setup using the {hybrid} bond style.
 The coefficients associated with a bond style can be specified in a
 data or restart file or via the "bond_coeff"_bond_coeff.html command.
 All bond potentials store their coefficient data in binary restart
 files which means bond_style and "bond_coeff"_bond_coeff.html commands
 do not need to be re-specified in an input script that restarts a
 simulation.  See the "read_restart"_read_restart.html command for
 details on how to do this.  The one exception is that bond_style
 {hybrid} only stores the list of sub-styles in the restart file; bond
 coefficients need to be re-specified.
 NOTE: When both a bond and pair style is defined, the
 "special_bonds"_special_bonds.html command often needs to be used to
 turn off (or weight) the pairwise interaction that would otherwise
 exist between 2 bonded atoms.
 In the formulas listed for each bond style, {r} is the distance
 between the 2 atoms in the bond.
 :line
 Here is an alphabetic list of bond styles defined in LAMMPS.  Click on
 the style to display the formula it computes and coefficients
 specified by the associated "bond_coeff"_bond_coeff.html command.
 Click on the style to display the formula it computes, any additional
 arguments specified in the bond_style command, and coefficients
 specified by the associated "bond_coeff"_bond_coeff.html command.
 There are also additional accelerated pair styles included in the
 LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
 The individual style names on the "Commands bond"_Commands_bond.html
 doc page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 "none"_bond_none.html - turn off bonded interactions
 "zero"_bond_zero.html - topology but no interactions
 "hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
 "class2"_bond_class2.html - COMPASS (class 2) bond
 "fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
 "fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
 "gromos"_bond_gromos.html - GROMOS force field bond
 "harmonic"_bond_harmonic.html - harmonic bond
 "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
 "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
 "mm3"_bond_mm3.html - MM3 anharmonic bond
 "morse"_bond_morse.html - Morse bond
 "nonlinear"_bond_nonlinear.html - nonlinear bond
 "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
 "oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
 "quartic"_bond_quartic.html - breakable quartic bond
 "table"_bond_table.html - tabulated by bond length :ul
 :line
 [Restrictions:]
 Bond styles can only be set for atom styles that allow bonds to be
 defined.
 Most bond styles are part of the MOLECULE package.  They are only
 enabled if LAMMPS was built with that package.  See the "Build
 package"_Build_package.html doc page for more info.  The doc pages for
 individual bond potentials tell if it is part of a package.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:]
 bond_style none
--- a/doc/txt/bond_table.txt
+++ b/doc/txt/bond_table.txt
@ -1,163 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style table command :h3
 bond_style table/omp command :h3
 [Syntax:]
 bond_style table style N :pre
 style = {linear} or {spline} = method of interpolation
 N = use N values in table :ul
 [Examples:]
 bond_style table linear 1000
 bond_coeff 1 file.table ENTRY1 :pre
 [Description:]
 Style {table} creates interpolation tables of length {N} from bond
 potential and force values listed in a file(s) as a function of bond
 length.  The files are read by the "bond_coeff"_bond_coeff.html
 command.
 The interpolation tables are created by fitting cubic splines to the
 file values and interpolating energy and force values at each of {N}
 distances.  During a simulation, these tables are used to interpolate
 energy and force values as needed.  The interpolation is done in one
 of 2 styles: {linear} or {spline}.
 For the {linear} style, the bond length is used to find 2 surrounding
 table values from which an energy or force is computed by linear
 interpolation.
 For the {spline} style, a cubic spline coefficients are computed and
 stored at each of the {N} values in the table.  The bond length is
 used to find the appropriate set of coefficients which are used to
 evaluate a cubic polynomial which computes the energy or force.
 The following coefficients must be defined for each bond type via the
 "bond_coeff"_bond_coeff.html command as in the example above.
 filename
 keyword :ul
 The filename specifies a file containing tabulated energy and force
 values.  The keyword specifies a section of the file.  The format of
 this file is described below.
 :line
 The format of a tabulated file is as follows (without the
 parenthesized comments):
 # Bond potential for harmonic (one or more comment or blank lines) :pre
 HAM                           (keyword is the first text on line)
 N 101 FP 0 0 EQ 0.5           (N, FP, EQ  parameters)
                              (blank line)
 1 0.00 338.0000 1352.0000     (index, bond-length, energy, force)
 2 0.01 324.6152 1324.9600
 ...
 101 1.00 338.0000 -1352.0000 :pre
 A section begins with a non-blank line whose 1st character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 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
 "bond_coeff"_bond_coeff.html 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 "bond_style table"_bond_style.html command.  Let
 Ntable = {N} in the bond_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
 uses these to interpolate as needed to generate energy and force
 values at Ntable different points.  The resulting tables of length
 Ntable are then used as described above, when computing energy and
 force for individual bond lengths.  This means that if you want the
 interpolation tables of length Ntable to match exactly what is in the
 tabulated file (with effectively no preliminary interpolation), you
 should set Ntable = Nfile.
 The "FP" parameter is optional.  If used, it is followed by two values
 fplo and fphi, which are the derivatives of the force at the innermost
 and outermost bond lengths.  These values are needed by the spline
 construction routines.  If not specified by the "FP" parameter, they
 are estimated (less accurately) by the first two and last two force
 values in the table.
 The "EQ" parameter is also optional.  If used, it is followed by a the
 equilibrium bond length, which is used, for example, by the "fix
 shake"_fix_shake.html command.  If not used, the equilibrium bond
 length is to the distance in the table with the lowest potential energy.
 Following a blank line, the next N lines list the tabulated values.
 On each line, the 1st value is the index from 1 to N, the 2nd value is
 the bond length r (in distance units), the 3rd value is the energy (in
 energy units), and the 4th is the force (in force units).  The bond
 lengths must range from a LO value to a HI value, and increase from
 one line to the next.  If the actual bond length is ever smaller than
 the LO value or larger than the HI value, then the bond energy and
 force is evaluated as if the bond were the LO or HI length.
 Note that one file can contain many sections, each with a tabulated
 potential.  LAMMPS reads the file section by section until it finds
 one that matches the specified keyword.
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the "Speed packages"_Speed_packages.html doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Build
 package"_Build_package.html doc page for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Run_options.html when you invoke LAMMPS, or you can use the
 "suffix"_suffix.html command in your input script.
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 :line
 [Restart info:]
 This bond style writes the settings for the "bond_style table"
 command to "binary restart files"_restart.html, so a bond_style
 command does not need to specified in an input script that reads a
 restart file.  However, the coefficient information is not stored in
 the restart file, since it is tabulated in the potential files.  Thus,
 bond_coeff commands do need to be specified in the restart input
 script.
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the MOLECULE
 package.  See the "Build package"_Build_package.html doc page for more
 info.
 [Related commands:]
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
 [Default:] none
--- a/doc/txt/bond_write.txt
+++ b/doc/txt/bond_write.txt
@ -1,64 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_write command :h3
 [Syntax:]
 bond_write btype N inner outer file keyword itype jtype :pre
 btype = bond types
 N = # of values
 inner,outer = inner and outer bond length (distance units)
 file = name of file to write values to
 keyword = section name in file for this set of tabulated values
 itype,jtype = 2 atom types (optional)
 :ul
 [Examples:]
 bond_write 1 500 0.5 3.5 table.txt Harmonic_1
 bond_write 3 1000 0.1 6.0 table.txt Morse :pre
 [Description:]
 Write energy and force values to a file as a function of distance for
 the currently defined bond potential.  This is useful for plotting the
 potential function or otherwise debugging its values.  If the file
 already exists, the table of values is appended to the end of the file
 to allow multiple tables of energy and force to be included in one
 file.
 The energy and force values are computed at distances from inner to
 outer for 2 interacting atoms forming a bond of type btype, using the
 appropriate "bond_coeff"_bond_coeff.html coefficients. N evenly spaced
 distances are used.
 For example, for N = 7, inner = 1.0, and outer = 4.0,
 values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
 The file is written in the format used as input for the
 "bond_style"_bond_style.html {table} option with {keyword} as the
 section name.  Each line written to the file lists an index number
 (1-N), a distance (in distance units), an energy (in energy units),
 and a force (in force units).
 [Restrictions:]
 All force field coefficients for bond and other kinds of interactions
 must be set before this command can be invoked.
 Due to how the bond force is computed, an inner value > 0.0 must
 be specified even if the potential has a finite value at r = 0.0.
 [Related commands:]
 "bond_style table"_bond_table.html,
 "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html
 [Default:] none
--- a/doc/txt/bond_zero.txt
+++ b/doc/txt/bond_zero.txt
@ -1,48 +0,0 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 :line
 bond_style zero command :h3
 [Syntax:]
 bond_style zero {nocoeff} :pre
 [Examples:]
 bond_style zero
 bond_style zero nocoeff
 bond_coeff *
 bond_coeff * 2.14 :pre
 [Description:]
 Using an bond style of zero means bond forces and energies are not
 computed, but the geometry of bond pairs is still accessible to other
 commands.
 As an example, the "compute bond/local"_compute_bond_local.html
 command can be used to compute distances for the list of pairs of bond
 atoms listed in the data file read by the "read_data"_read_data.html
 command.  If no bond style is defined, this command cannot be used.
 The optional {nocoeff} flag allows to read data files with a BondCoeff
 section for any bond style. Similarly, any bond_coeff commands
 will only be checked for the bond type number and the rest ignored.
 Note that the "bond_coeff"_bond_coeff.html command must be used for
 all bond types. If specified, there can be only one value, which is
 going to be used to assign an equilibrium distance, e.g. for use with
 "fix shake"_fix_shake.html.
 [Restrictions:] none
 [Related commands:]
 "bond_style none"_bond_none.html
 [Default:] none
--- a/doc/txt/pair_list.txt
+++ b/doc/txt/pair_list.txt
@ -1,144 +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
 pair_style list command :h3
 [Syntax:]
 pair_style list listfile cutoff keyword :pre
 listfile = name of file with list of pairwise interactions
 cutoff = global cutoff (distance units)
 keyword = optional flag {nocheck} or {check} (default is {check}) :ul
 [Examples:]
 pair_style list restraints.txt 200.0
 pair_coeff * * :pre
 pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
 pair_coeff * * lj/cut 1.0 1.0
 pair_coeff 3* 3* list :pre
 [Description:]
 Style {list} computes interactions between explicitly listed pairs of
 atoms with the option to select functional form and parameters for
 each individual pair.  Because the parameters are set in the list
 file, the pair_coeff command has no parameters (but still needs to be
 provided).  The {check} and {nocheck} keywords enable/disable a test
 that checks whether all listed bonds were present and computed.
 This pair style can be thought of as a hybrid between bonded,
 non-bonded, and restraint interactions.  It will typically be used as
 an additional interaction within the {hybrid/overlay} pair style.  It
 currently supports three interaction styles: a 12-6 Lennard-Jones, a
 Morse and a harmonic potential.
 The format of the list file is as follows:
 one line per pair of atoms :ulb,l
 empty lines will be ignored :l
 comment text starts with a '#' character :l
 line syntax: {ID1 ID2 style coeffs cutoff} :l
  ID1 = atom ID of first atom
  ID2 = atom ID of second atom
  style = style of interaction
  coeffs = list of coeffs
  cutoff = cutoff for interaction (optional) :pre
 :ule
 The cutoff parameter is optional. If not specified, the global cutoff
 is used.
 Here is an example file:
 # this is a comment :pre
 15 259 lj126     1.0 1.0      50.0
 15 603 morse    10.0 1.2 2.0  10.0 # and another comment
 18 470 harmonic 50.0 1.2       5.0  :pre
 The style {lj126} computes pairwise interactions with the formula
 :c,image(Eqs/pair_lj.jpg)
 and the coefficients:
 epsilon (energy units)
 sigma (distance units) :ul
 The style {morse} computes pairwise interactions with the formula
 :c,image(Eqs/pair_morse.jpg)
 and the coefficients:
 D0 (energy units)
 alpha (1/distance units)
 r0 (distance units) :ul
 The style {harmonic} computes pairwise interactions with the formula
 :c,image(Eqs/bond_harmonic.jpg)
 and the coefficients:
 K (energy units)
 r0 (distance units) :ul
 Note that the usual 1/2 factor is included in K.
 :line
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 This pair style does not support mixing since all parameters are
 explicit for each pair.
 The "pair_modify"_pair_modify.html shift option is supported by this
 pair style.
 The "pair_modify"_pair_modify.html table and tail options are not
 relevant for this pair style.
 This pair style does not write its information to "binary restart
 files"_restart.html, so pair_style and pair_coeff commands need
 to be specified in an input script that reads a restart file.
 This pair style can only be used via the {pair} keyword of the
 "run_style respa"_run_style.html command.  It does not support the
 {inner}, {middle}, {outer} keywords.
 :line
 [Restrictions:]
 This pair style does not use a neighbor list and instead identifies
 atoms by their IDs. This has two consequences: 1) The cutoff has to be
 chosen sufficiently large, so that the second atom of a pair has to be
 a ghost atom on the same node on which the first atom is local;
 otherwise the interaction will be skipped. You can use the {check}
 option to detect, if interactions are missing. 2) Unlike other pair
 styles in LAMMPS, an atom I will not interact with multiple images of
 atom J (assuming the images are within the cutoff distance), but only
 with the nearest image.
 This style is part of the USER-MISC package. It is only enabled if
 LAMMPS is build with that package. See the "Build
 package"_Build_package.html doc page on for more info.
 [Related commands:]
 "pair_coeff"_pair_coeff.html,
 "pair_style hybrid/overlay"_pair_hybrid.html,
 "pair_style lj/cut"_pair_lj.html,
 "pair_style morse"_pair_morse.html,
 "bond_style harmonic"_bond_harmonic.html
 [Default:] none