docs: update commands section

doc/src/Commands_all.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -12,12 +14,14 @@
       * :doc:`KSpace styles <Commands_kspace>`
       * :doc:`Dump styles <Commands_dump>`
    
+.. raw:: latex
+
+   \clearpage
+
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.  Note that style
+An alphabetic list of general LAMMPS commands.
-commands with many variants, can be more easily accessed via the small
-table above.
 
 .. table_from_list::
    :columns: 5

doc/src/Commands_bond.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -14,8 +16,8 @@
    
 .. _bond:
 
-Bond_style potentials
+Bonds styles
-=====================
+============
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -60,8 +62,8 @@ OPT.
 
 .. _angle:
 
-Angle_style potentials
+Angle styles
-======================
+============
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -106,8 +108,8 @@ OPT.
 
 .. _dihedral:
 
-Dihedral_style potentials
+Dihedral styles
-=========================
+===============
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -144,8 +146,8 @@ OPT.
 
 .. _improper:
 
-Improper_style potentials
+Improper styles
-=========================
+===============
 
 All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in

doc/src/Commands_category.rst

@@ -1,3 +1,7 @@
+.. raw:: latex
+
+   \clearpage
+
 Commands by category
 ====================
 
@@ -6,8 +10,8 @@ This page lists most of the LAMMPS commands, grouped by category.  The
 alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 
-Initialization:
+Initialization
-------------------------------
+--------------
 
 .. table_from_list::
    :columns: 5
@@ -18,8 +22,8 @@ Initialization:
    * :doc:`suffix <suffix>`
    * :doc:`units <units>`
 
-Setup simulation box:
+Setup simulation box
-------------------------------
+--------------------
 
 .. table_from_list::
    :columns: 4
@@ -31,8 +35,8 @@ Setup simulation box:
    * :doc:`lattice <lattice>`
    * :doc:`region <region>`
 
-Setup atoms:
+Setup atoms
-------------------------------
+-----------
 
 .. table_from_list::
    :columns: 4
@@ -55,8 +59,8 @@ Setup atoms:
    * :doc:`set <set>`
    * :doc:`velocity <velocity>`
 
-Force fields:
+Force fields
-------------------------------
+------------
 
 .. table_from_list::
    :columns: 4
@@ -79,8 +83,8 @@ Force fields:
    * :doc:`pair_write <pair_write>`
    * :doc:`special_bonds <special_bonds>`
 
-Settings:
+Settings
-------------------------------
+--------
 
 .. table_from_list::
    :columns: 4
@@ -98,8 +102,8 @@ Settings:
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
 
-Operations within timestepping (fixes) and diagnostics (computes):
+Operations within timestepping (fixes) and diagnostics (computes)
-------------------------------------------------------------------------------------------
+-----------------------------------------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -111,8 +115,8 @@ Operations within timestepping (fixes) and diagnostics (computes):
    * :doc:`uncompute <uncompute>`
    * :doc:`unfix <unfix>`
 
-Output:
+Output
-------------------------------
+------
 
 .. table_from_list::
    :columns: 4
@@ -131,8 +135,8 @@ Output:
    * :doc:`write_dump <write_dump>`
    * :doc:`write_restart <write_restart>`
 
-Actions:
+Actions
-------------------------------
+-------
 
 .. table_from_list::
    :columns: 6
@@ -146,8 +150,8 @@ Actions:
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
 
-Input script control:
+Input script control
-------------------------------
+--------------------
 
 .. table_from_list::
    :columns: 7

doc/src/Commands_compute.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -12,8 +14,8 @@
       * :doc:`KSpace styles <Commands_kspace>`
       * :doc:`Dump styles <Commands_dump>`
 
-Compute commands
+Compute styles
-================
+==============
 
 An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
 Some styles have accelerated versions.  This is indicated by
@@ -21,7 +23,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
 KOKKOS, o = OPENMP, t = OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`ackland/atom <compute_ackland_atom>`
    * :doc:`adf <compute_adf>`

doc/src/Commands_dump.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -12,8 +14,8 @@
       * :doc:`KSpace styles <Commands_kspace>`
       * :doc:`Dump styles <Commands_dump>`
 
-Dump commands
+Dump styles
-=============
+===========
 
 An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
 

doc/src/Commands_fix.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -12,8 +14,8 @@
       * :doc:`KSpace styles <Commands_kspace>`
       * :doc:`Dump styles <Commands_dump>`
 
-Fix commands
+Fix styles
-============
+==========
 
 An alphabetic list of all LAMMPS :doc:`fix <fix>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -21,7 +23,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`accelerate/cos <fix_accelerate_cos>`
    * :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`

doc/src/Commands_input.rst

@@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an
 internal variable, read in a file, or run a simulation.  These actions
 can be grouped into three categories:
 
-a) commands that change a global setting (examples: timestep, newton,
+a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
-   echo, log, thermo, restart),
+   :doc:`echo <echo>`, :doc:`log <log>`, :doc:`thermo <thermo>`, :doc:`restart <restart>`),
 b) commands that add, modify, remove, or replace "styles" that are
-   executed during a "run" (examples: pair_style, fix, compute, dump,
+   executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
-   thermo_style, pair_modify), and
+   :doc:`thermo_style <thermo_style>`, :doc:`pair_modify <pair_modify>`), and
 c) commands that execute a "run" or perform some other computation or
-   operation (examples: print, run, minimize, temper, write_dump, rerun,
+   operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
-   read_data, read_restart)
+   :doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`)
 
 Commands in category a) have default settings, which means you only
 need to use the command if you wish to change the defaults.
@@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply:
     <read_data>` command initializes the system by setting up the
     simulation box and assigning atoms to processors.  If default values
     are not desired, the :doc:`processors <processors>` and
-    :doc:`boundary <boundary>` commands need to be used before read_data
+    :doc:`boundary <boundary>` commands need to be used before ``read_data``
     to tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
@@ -70,6 +70,6 @@ more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
 
 You can use the :ref:`-skiprun <skiprun>` command line flag
-to have LAMMPS skip the execution of any "run", "minimize", or similar
+to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
 commands to check the entire input for correct syntax to avoid crashes
 on typos or syntax errors in long runs.

doc/src/Commands_kspace.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -12,8 +14,8 @@
       * :doc:`KSpace styles <Commands_kspace>`
       * :doc:`Dump styles <Commands_dump>`
 
-KSpace solvers
+KSpace styles
-==============
+=============
 
 All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in

doc/src/Commands_pair.rst

@@ -1,3 +1,5 @@
+.. only:: html
+
    .. table_from_list::
       :columns: 3
    
@@ -12,8 +14,8 @@
       * :doc:`KSpace styles <Commands_kspace>`
       * :doc:`Dump styles <Commands_dump>`
 
-Pair_style potentials
+Pair styles
-======================
+===========
 
 All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -21,7 +23,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 3
 
    * :doc:`none <pair_none>`
    * :doc:`zero <pair_zero>`
@@ -35,10 +37,6 @@ OPT.
    *
    *
    *
-   *
-   *
-   *
-   *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`

doc/src/Commands_parse.rst

@@ -42,8 +42,8 @@ LAMMPS:
    If the $ is followed by text in curly brackets '{}', then the
    variable name is the text inside the curly brackets.  If no curly
    brackets follow the $, then the variable name is the single character
-   immediately following the $.  Thus ${myTemp} and $x refer to variables
+   immediately following the $.  Thus ``${myTemp}`` and ``$x`` refer to variables
-   named "myTemp" and "x", while "$xx" will be interpreted as a variable
+   named "myTemp" and "x", while ``$xx`` will be interpreted as a variable
    named "x" followed by an "x" character.
 
    How the variable is converted to a text string depends on what style
@@ -79,10 +79,10 @@ LAMMPS:
 
    Additionally, the entire "immediate" variable expression may be
    followed by a colon, followed by a C-style format string,
-   e.g. ":%f" or ":%.10g".  The format string must be appropriate for
+   e.g. ``:%f`` or ``:%.10g``.  The format string must be appropriate for
    a double-precision floating-point value.  The format string is used
    to output the result of the variable expression evaluation.  If a
-   format string is not specified, a high-precision "%.20g" is used as
+   format string is not specified, a high-precision ``%.20g`` is used as
    the default format.
 
    This can be useful for formatting print output to a desired precision:
@@ -101,8 +101,8 @@ LAMMPS:
       variable        b2 equal 4
       print           "B2 = ${b$a}"
 
-   Nor can you specify an expression like "$($x-1.0)" for an immediate
+   Nor can you specify an expression like ``$($x-1.0)`` for an immediate
-   variable, but you could use $(v_x-1.0), since the latter is valid
+   variable, but you could use ``$(v_x-1.0)``, since the latter is valid
    syntax for an :doc:`equal-style variable <variable>`.
 
    See the :doc:`variable <variable>` command for more details of how

doc/src/Install.rst

@@ -35,35 +35,35 @@ you **must** build LAMMPS from the source code.
 
 These are the files and subdirectories in the LAMMPS distribution:
 
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| README     | Short description of the LAMMPS package     |
+| ``README``      | Short description of the LAMMPS package     |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| LICENSE    | GNU General Public License (GPL)            |
+| ``LICENSE``     | GNU General Public License (GPL)            |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| SECURITY.md| Security policy for the LAMMPS package      |
+| ``SECURITY.md`` | Security policy for the LAMMPS package      |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| bench      | benchmark inputs                            |
+| ``bench``       | benchmark inputs                            |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| cmake      | CMake build files                           |
+| ``cmake``       | CMake build files                           |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| doc        | documentation and tools to build the manual |
+| ``doc``         | documentation and tools to build the manual |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| examples   | example input files                         |
+| ``examples``    | example input files                         |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| fortran    | Fortran module for LAMMPS library interface |
+| ``fortran``     | Fortran module for LAMMPS library interface |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| lib        | additional provided or external libraries   |
+| ``lib``         | additional provided or external libraries   |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| potentials | selected interatomic potential files        |
+| ``potentials``  | selected interatomic potential files        |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| python     | Python module for LAMMPS library interface  |
+| ``python``      | Python module for LAMMPS library interface  |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| src        | LAMMPS source files                         |
+| ``src``         | LAMMPS source files                         |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| tools      | pre- and post-processing tools              |
+| ``tools``       | pre- and post-processing tools              |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
-| unittest   | source code and inputs for testing LAMMPS   |
+| ``unittest``    | source code and inputs for testing LAMMPS   |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
 
 You will have all of these if you downloaded the LAMMPS source code.
 You will have only some of them if you downloaded executables, as