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docs: update commands section

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Richard Berger
2024-08-16 12:50:06 -06:00
parent efc53d6439
commit a625955143
11 changed files with 190 additions and 174 deletions
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34
doc/src/Commands_all.rst
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@ -1,23 +1,27 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :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
commands with many variants, can be more easily accessed via the small
table above.
An alphabetic list of general LAMMPS commands.
.. table_from_list::
:columns: 5

44
doc/src/Commands_bond.rst
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@ -1,21 +1,23 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. only:: html
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _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

40
doc/src/Commands_category.rst
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@ -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

32
doc/src/Commands_compute.rst
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@ -1,19 +1,21 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :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>`

30
doc/src/Commands_dump.rst
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@ -1,19 +1,21 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
Dump styles
===========
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.

32
doc/src/Commands_fix.rst
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@ -1,19 +1,21 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :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>`

16
doc/src/Commands_input.rst
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@ -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,
echo, log, thermo, restart),
a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
: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,
thermo_style, pair_modify), and
executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
: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,
read_data, read_restart)
operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
: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.

30
doc/src/Commands_kspace.rst
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@ -1,19 +1,21 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :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

36
doc/src/Commands_pair.rst
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@ -1,19 +1,21 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :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>`

12
doc/src/Commands_parse.rst
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@ -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 $x refer to variables
named "myTemp" and "x", while "$xx" will be interpreted as a variable
immediately following the $. Thus ``${myTemp}`` and ``$x`` refer to variables
named "myTemp" and "x", while ``$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
variable, but you could use $(v_x-1.0), since the latter is valid
Nor can you specify an expression like ``$($x-1.0)`` for an immediate
variable, but you could use ``$(v_x-1.0)``, since the latter is valid
syntax for an :doc:`equal-style variable <variable>`.
See the :doc:`variable <variable>` command for more details of how

58
doc/src/Install.rst
View File

@ -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 |
+------------+---------------------------------------------+
| LICENSE | GNU General Public License (GPL) |
+------------+---------------------------------------------+
| SECURITY.md| Security policy for the LAMMPS package |
+------------+---------------------------------------------+
| bench | benchmark inputs |
+------------+---------------------------------------------+
| cmake | CMake build files |
+------------+---------------------------------------------+
| doc | documentation and tools to build the manual |
+------------+---------------------------------------------+
| examples | example input files |
+------------+---------------------------------------------+
| fortran | Fortran module for LAMMPS library interface |
+------------+---------------------------------------------+
| lib | additional provided or external libraries |
+------------+---------------------------------------------+
| potentials | selected interatomic potential files |
+------------+---------------------------------------------+
| python | Python module for LAMMPS library interface |
+------------+---------------------------------------------+
| src | LAMMPS source files |
+------------+---------------------------------------------+
| tools | pre- and post-processing tools |
+------------+---------------------------------------------+
| unittest | source code and inputs for testing LAMMPS |
+------------+---------------------------------------------+
+-----------------+---------------------------------------------+
| ``README`` | Short description of the LAMMPS package |
+-----------------+---------------------------------------------+
| ``LICENSE`` | GNU General Public License (GPL) |
+-----------------+---------------------------------------------+
| ``SECURITY.md`` | Security policy for the LAMMPS package |
+-----------------+---------------------------------------------+
| ``bench`` | benchmark inputs |
+-----------------+---------------------------------------------+
| ``cmake`` | CMake build files |
+-----------------+---------------------------------------------+
| ``doc`` | documentation and tools to build the manual |
+-----------------+---------------------------------------------+
| ``examples`` | example input files |
+-----------------+---------------------------------------------+
| ``fortran`` | Fortran module for LAMMPS library interface |
+-----------------+---------------------------------------------+
| ``lib`` | additional provided or external libraries |
+-----------------+---------------------------------------------+
| ``potentials`` | selected interatomic potential files |
+-----------------+---------------------------------------------+
| ``python`` | Python module for LAMMPS library interface |
+-----------------+---------------------------------------------+
| ``src`` | LAMMPS source files |
+-----------------+---------------------------------------------+
| ``tools`` | pre- and post-processing tools |
+-----------------+---------------------------------------------+
| ``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