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Use User's Guide and Programmer's Guide. Normalize header level formatting

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Axel Kohlmeyer
2020-10-12 23:08:41 -04:00
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doc/src/Developer.rst
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LAMMPS Developer Guide
**********************
Information for Developers
==========================
This section describes the internal structure and basic algorithms
of the LAMMPS code. This is a work in progress and additional

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doc/src/Developer_flow.rst
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@ -1,5 +1,5 @@
How a timestep works
====================
--------------------
The first and most fundamental operation within LAMMPS to understand is
how a timestep is structured. Timestepping is performed by calling

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doc/src/Developer_org.rst
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@ -1,5 +1,5 @@
LAMMPS source files
===================
-------------------
The source files of the LAMMPS code are found in two
directories of the distribution: ``src`` and ``lib``.
@ -47,7 +47,7 @@ A small number of C++ classes and utility functions are implemented with
only a ``.h`` file. Examples are the Pointer class or the MathVec functions.
LAMMPS class topology
=====================
---------------------
Though LAMMPS has a lot of source files and classes, its class topology
is relative flat, as outlined in the :ref:`class-topology` figure. Each

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doc/src/Developer_utils.rst
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@ -1,6 +1,6 @@
LAMMPS utility functions
========================
------------------------
The ``utils`` sub-namespace inside the ``LAMMPS_NS`` namespace provides
a collection of convenience functions and utilities that perform common
@ -173,7 +173,7 @@ Customized standard functions
---------------------------
Communication buffer coding with *ubuf*
=========================================
---------------------------------------
LAMMPS uses communication buffers where it collects data from various
class instances and then exchanges the data with neighboring sub-domains.
@ -194,7 +194,7 @@ the communication buffers.
---------------------------
Tokenizer classes
=================
-----------------
The purpose of the tokenizer classes is to simplify the recurring task
of breaking lines of text down into words and/or numbers.
@ -308,7 +308,7 @@ This code example should produce the following output:
----------
File reader classes
====================
-------------------
The purpose of the file reader classes is to simplify the recurring task
of reading and parsing files. They can use the
@ -382,7 +382,7 @@ A file that would be parsed by the reader code fragment looks like this:
----------
Memory pool classes
===================
-------------------
The memory pool classes are used for cases where otherwise many
small memory allocations would be needed and where the data would
@ -446,7 +446,7 @@ its size is registered later with :cpp:func:`vgot()
----------
Eigensolver functions
=====================
---------------------
The ``MathEigen`` sub-namespace of the ``LAMMPS_NS`` namespace contains
functions and classes for eigensolvers. Currently only the

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doc/src/Developer_write.rst
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Writing LAMMPS styles
=====================
---------------------
The :doc:`Modify` section of the manual gives an overview of how LAMMPS can
be extended by writing new classes that derive from existing

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doc/src/Install.rst
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Install LAMMPS
**************
==============
You can download LAMMPS as an executable or as source code.

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doc/src/Install_conda.rst
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Download an executable for Linux or Mac via Conda
=================================================
-------------------------------------------------
Binaries are available for MacOS or Linux via `Conda <conda_>`_.

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doc/src/Install_git.rst
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Download the LAMMPS source with git
===================================
-----------------------------------
All LAMMPS development is coordinated through the "LAMMPS GitHub
site". If you clone the LAMMPS repository onto your local machine, it

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doc/src/Install_linux.rst
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Download an executable for Linux
================================
--------------------------------
Binaries are available for different versions of Linux:
@ -16,7 +16,7 @@ Binaries are available for different versions of Linux:
.. _ubuntu:
Pre-built Ubuntu Linux executables
-----------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS executable suitable for running on the latest
Ubuntu Linux versions, can be downloaded as a Debian package. This
@ -108,7 +108,7 @@ Ubuntu package capability.
.. _fedora:
Pre-built Fedora Linux executables
-----------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS packages for stable releases are available
in the Fedora Linux distribution as of version 28. The packages
@ -162,7 +162,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
.. _epel:
Pre-built EPEL Linux executable
------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS (and KIM) packages for stable releases are available
in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedoraproject.org/wiki/EPEL>`_
@ -182,7 +182,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
.. _opensuse:
Pre-built OpenSuse Linux executable
--------------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS package for stable releases is available
in OpenSuse as of Leap 15.0. You can install the package with:
@ -217,7 +217,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
.. _gentoo:
Gentoo Linux executable
------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS is part of Gentoo's main package tree and can be installed by
typing:
@ -245,7 +245,7 @@ this Gentoo capability.
.. _arch:
Archlinux build-script
---------------------------------
^^^^^^^^^^^^^^^^^^^^^^
LAMMPS is available via Arch's unofficial Arch User repository (AUR).
There are three scripts available, named lammps, lammps-beta and lammps-git.

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doc/src/Install_mac.rst
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Download an executable for Mac
==============================
------------------------------
LAMMPS can be downloaded, built, and configured for OS X on a Mac with
`Homebrew <homebrew_>`_. (Alternatively, see the install instructions for

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doc/src/Install_patch.rst
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Applying patches
================
----------------
It is easy to stay current with the most recent LAMMPS patch releases
if you use git to track the LAMMPS development. Instructions for

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doc/src/Install_tarball.rst
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@ -1,5 +1,5 @@
Download source and documentation as a tarball
==============================================
----------------------------------------------
You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.

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doc/src/Install_windows.rst
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Download an executable for Windows
==================================
----------------------------------
Pre-compiled Windows installers which install LAMMPS executables on a
Windows system can be downloaded from this site:

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doc/src/Intro.rst
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Introduction
************
============
These pages provide a brief introduction to LAMMPS.

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doc/src/Intro_authors.rst
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Authors of LAMMPS
=================
-----------------
The primary LAMMPS developers are at Sandia National Labs and Temple
University:

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doc/src/Intro_citing.rst
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Citing LAMMPS
=============
-------------
Core Algorithms
^^^^^^^^^^^^^^^

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doc/src/Intro_features.rst
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LAMMPS features
===============
---------------
LAMMPS is a classical molecular dynamics (MD) code with these general
classes of functionality:
@ -21,7 +21,7 @@ classes of functionality:
.. _general:
General features
------------------------------
^^^^^^^^^^^^^^^^
* runs on a single processor or in parallel
* distributed-memory message-passing parallelism (MPI)
@ -41,9 +41,9 @@ General features
.. _particle:
Particle and model types
---------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^
(:doc:`atom style <atom_style>` command)
(See :doc:`atom style <atom_style>` command)
* atoms
* coarse-grained particles (e.g. bead-spring polymers)
@ -61,9 +61,9 @@ Particle and model types
.. _ff:
Interatomic potentials (force fields)
----------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
(:doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`,
(See :doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`,
:doc:`angle style <angle_style>`, :doc:`dihedral style <dihedral_style>`,
:doc:`improper style <improper_style>`, :doc:`kspace style <kspace_style>`
commands)
@ -92,9 +92,9 @@ commands)
.. _create:
Atom creation
--------------------------
^^^^^^^^^^^^^
(:doc:`read_data <read_data>`, :doc:`lattice <lattice>`,
(See :doc:`read_data <read_data>`, :doc:`lattice <lattice>`,
:doc:`create_atoms <create_atoms>`, :doc:`delete_atoms <delete_atoms>`,
:doc:`displace_atoms <displace_atoms>`, :doc:`replicate <replicate>` commands)
@ -107,9 +107,9 @@ Atom creation
.. _ensemble:
Ensembles, constraints, and boundary conditions
--------------------------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
(:doc:`fix <fix>` command)
(See :doc:`fix <fix>` command)
* 2d or 3d systems
* orthogonal or non-orthogonal (triclinic symmetry) simulation domains
@ -129,9 +129,9 @@ Ensembles, constraints, and boundary conditions
.. _integrate:
Integrators
---------------------------
^^^^^^^^^^^
(:doc:`run <run>`, :doc:`run_style <run_style>`, :doc:`minimize <minimize>` commands)
(See :doc:`run <run>`, :doc:`run_style <run_style>`, :doc:`minimize <minimize>` commands)
* velocity-Verlet integrator
* Brownian dynamics
@ -143,14 +143,14 @@ Integrators
.. _diag:
Diagnostics
----------------------
^^^^^^^^^^^
* see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
.. _output:
Output
-------------------
^^^^^^
(:doc:`dump <dump>`, :doc:`restart <restart>` commands)
@ -167,7 +167,7 @@ Output
.. _replica1:
Multi-replica models
-----------------------------------
^^^^^^^^^^^^^^^^^^^^
* :doc:`nudged elastic band <neb>`
* :doc:`parallel replica dynamics <prd>`
@ -177,11 +177,11 @@ Multi-replica models
.. _prepost:
Pre- and post-processing
--------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^
* A handful of pre- and post-processing tools are packaged with LAMMPS,
some of which can convert input and output files to/from formats used
by other codes; see the :doc:`Tools <Tools>` doc page.
by other codes; see the :doc:`Tools <Tools>` page.
* Our group has also written and released a separate toolkit called
`Pizza.py <pizza_>`_ which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
@ -194,7 +194,7 @@ Pre- and post-processing
.. _special:
Specialized features
----------------------------------
^^^^^^^^^^^^^^^^^^^^
LAMMPS can be built with optional packages which implement a variety
of additional capabilities. See the :doc:`Optional Packages <Packages>`

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doc/src/Intro_nonfeatures.rst
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LAMMPS non-features
===================
-------------------
LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of

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doc/src/Intro_opensource.rst
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@ -1,5 +1,5 @@
LAMMPS open-source license
==========================
--------------------------
LAMMPS is a freely-available open-source code, distributed under the
terms of the `GNU Public License <gnu_>`_, which means you can use or

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doc/src/Intro_overview.rst
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@ -1,5 +1,5 @@
Overview of LAMMPS
==================
------------------
LAMMPS is a classical molecular dynamics (MD) code that models
ensembles of particles in a liquid, solid, or gaseous state. It can

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doc/src/Intro_website.rst
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Additional website links
========================
------------------------
The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some other useful resources

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doc/src/Manual.rst
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@ -1,3 +1,4 @@
######################################
LAMMPS version |version| Documentation
######################################
@ -12,10 +13,11 @@ funding for LAMMPS has come from the US Department of Energy (DOE).
LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the code.
It includes links to an on-line version of this manual, a `mailing list <https://lammps.sandia.gov/mail.html>`_ where users can post
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
all LAMMPS development is coordinated.
The `LAMMPS website <lws_>`_ has a variety of information about the
code. It includes links to an on-line version of this manual, a
`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
where all LAMMPS development is coordinated.
----------
@ -23,8 +25,8 @@ The content for this manual is part of the LAMMPS distribution. You can
build a local copy of the Manual as HTML pages or a PDF file, by
following the steps on the :doc:`Build_manual` page. The manual is
organized in two parts:
1) the :ref:`User documentation <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer documentation <programmer_documentation>`
1) the :ref:`User's Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer's Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS.
@ -38,14 +40,16 @@ programming languages and how to modify and extend LAMMPS.
----------
User Documentation
******************
************
User's Guide
************
.. _user_documentation:
.. toctree::
:maxdepth: 2
:numbered: 3
:caption: User Documentation
:caption: User's Guide
:name: userdoc
:includehidden:
@ -61,14 +65,16 @@ User Documentation
Tools
Errors
Programmer Documentation
************************
******************
Programmer's Guide
******************
.. _programmer_documentation:
.. toctree::
:maxdepth: 2
:numbered: 3
:caption: Programmer Documentation
:caption: Programmer's Guide
:name: progdoc
:includehidden:
@ -93,6 +99,7 @@ Programmer Documentation
fix_modify_atc_commands
Bibliography
******************
Indices and tables
******************

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doc/src/Manual_version.rst
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What does a LAMMPS version mean
===============================
-------------------------------
The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a

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doc/utils/sphinx-config/_static/css/lammps.css
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@ -27,11 +27,11 @@ hr {
margin-bottom: 12px !important;
}
#user-documentation.section h2 {
#user-s-guide.section h2 {
display: none;
}
#programmer-documentation.section h2 {
#programmer-s-guide.section h2 {
display: none;
}