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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 This section describes the internal structure and basic algorithms
of the LAMMPS code. This is a work in progress and additional 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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How a timestep works How a timestep works
==================== --------------------
The first and most fundamental operation within LAMMPS to understand is The first and most fundamental operation within LAMMPS to understand is
how a timestep is structured. Timestepping is performed by calling how a timestep is structured. Timestepping is performed by calling

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doc/src/Developer_org.rst
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LAMMPS source files LAMMPS source files
=================== -------------------
The source files of the LAMMPS code are found in two The source files of the LAMMPS code are found in two
directories of the distribution: ``src`` and ``lib``. 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. only a ``.h`` file. Examples are the Pointer class or the MathVec functions.
LAMMPS class topology LAMMPS class topology
===================== ---------------------
Though LAMMPS has a lot of source files and classes, its 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 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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LAMMPS utility functions LAMMPS utility functions
======================== ------------------------
The ``utils`` sub-namespace inside the ``LAMMPS_NS`` namespace provides The ``utils`` sub-namespace inside the ``LAMMPS_NS`` namespace provides
a collection of convenience functions and utilities that perform common a collection of convenience functions and utilities that perform common
@ -173,7 +173,7 @@ Customized standard functions
--------------------------- ---------------------------
Communication buffer coding with *ubuf* Communication buffer coding with *ubuf*
========================================= ---------------------------------------
LAMMPS uses communication buffers where it collects data from various LAMMPS uses communication buffers where it collects data from various
class instances and then exchanges the data with neighboring sub-domains. class instances and then exchanges the data with neighboring sub-domains.
@ -194,7 +194,7 @@ the communication buffers.
--------------------------- ---------------------------
Tokenizer classes Tokenizer classes
================= -----------------
The purpose of the tokenizer classes is to simplify the recurring task The purpose of the tokenizer classes is to simplify the recurring task
of breaking lines of text down into words and/or numbers. 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 File reader classes
==================== -------------------
The purpose of the file reader classes is to simplify the recurring task The purpose of the file reader classes is to simplify the recurring task
of reading and parsing files. They can use the 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 Memory pool classes
=================== -------------------
The memory pool classes are used for cases where otherwise many The memory pool classes are used for cases where otherwise many
small memory allocations would be needed and where the data would 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 Eigensolver functions
===================== ---------------------
The ``MathEigen`` sub-namespace of the ``LAMMPS_NS`` namespace contains The ``MathEigen`` sub-namespace of the ``LAMMPS_NS`` namespace contains
functions and classes for eigensolvers. Currently only the functions and classes for eigensolvers. Currently only the

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

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doc/src/Install.rst
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Install LAMMPS Install LAMMPS
************** ==============
You can download LAMMPS as an executable or as source code. 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 Download an executable for Linux or Mac via Conda
================================================= -------------------------------------------------
Binaries are available for MacOS or Linux via `Conda <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 Download the LAMMPS source with git
=================================== -----------------------------------
All LAMMPS development is coordinated through the "LAMMPS GitHub All LAMMPS development is coordinated through the "LAMMPS GitHub
site". If you clone the LAMMPS repository onto your local machine, it 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 Download an executable for Linux
================================ --------------------------------
Binaries are available for different versions of Linux: Binaries are available for different versions of Linux:
@ -16,7 +16,7 @@ Binaries are available for different versions of Linux:
.. _ubuntu: .. _ubuntu:
Pre-built Ubuntu Linux executables Pre-built Ubuntu Linux executables
----------------------------------------------- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS executable suitable for running on the latest A pre-built LAMMPS executable suitable for running on the latest
Ubuntu Linux versions, can be downloaded as a Debian package. This Ubuntu Linux versions, can be downloaded as a Debian package. This
@ -108,7 +108,7 @@ Ubuntu package capability.
.. _fedora: .. _fedora:
Pre-built Fedora Linux executables Pre-built Fedora Linux executables
----------------------------------------------- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS packages for stable releases are available Pre-built LAMMPS packages for stable releases are available
in the Fedora Linux distribution as of version 28. The packages 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: .. _epel:
Pre-built EPEL Linux executable Pre-built EPEL Linux executable
------------------------------------------ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS (and KIM) packages for stable releases are available 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>`_ 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: .. _opensuse:
Pre-built OpenSuse Linux executable Pre-built OpenSuse Linux executable
-------------------------------------------------- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS package for stable releases is available A pre-built LAMMPS package for stable releases is available
in OpenSuse as of Leap 15.0. You can install the package with: 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:
Gentoo Linux executable Gentoo Linux executable
------------------------------------ ^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS is part of Gentoo's main package tree and can be installed by LAMMPS is part of Gentoo's main package tree and can be installed by
typing: typing:
@ -245,7 +245,7 @@ this Gentoo capability.
.. _arch: .. _arch:
Archlinux build-script Archlinux build-script
--------------------------------- ^^^^^^^^^^^^^^^^^^^^^^
LAMMPS is available via Arch's unofficial Arch User repository (AUR). LAMMPS is available via Arch's unofficial Arch User repository (AUR).
There are three scripts available, named lammps, lammps-beta and lammps-git. 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 Download an executable for Mac
============================== ------------------------------
LAMMPS can be downloaded, built, and configured for OS X on a Mac with LAMMPS can be downloaded, built, and configured for OS X on a Mac with
`Homebrew <homebrew_>`_. (Alternatively, see the install instructions for `Homebrew <homebrew_>`_. (Alternatively, see the install instructions for

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

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

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

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

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

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

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

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doc/src/Intro_opensource.rst
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LAMMPS open-source license LAMMPS open-source license
========================== --------------------------
LAMMPS is a freely-available open-source code, distributed under the LAMMPS is a freely-available open-source code, distributed under the
terms of the `GNU Public License <gnu_>`_, which means you can use or 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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Overview of LAMMPS Overview of LAMMPS
================== ------------------
LAMMPS is a classical molecular dynamics (MD) code that models LAMMPS is a classical molecular dynamics (MD) code that models
ensembles of particles in a liquid, solid, or gaseous state. It can 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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@ -1,5 +1,5 @@
Additional website links Additional website links
======================== ------------------------
The `LAMMPS website <lws_>`_ has a variety of additional info about The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some other useful resources 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 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 LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL). the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the code. The `LAMMPS website <lws_>`_ has a variety of information about the
It includes links to an on-line version of this manual, a `mailing list <https://lammps.sandia.gov/mail.html>`_ where users can post code. It includes links to an on-line version of this manual, a
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where `mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
all LAMMPS development is coordinated. 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 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 following the steps on the :doc:`Build_manual` page. The manual is
organized in two parts: organized in two parts:
1) the :ref:`User documentation <user_documentation>` for how to install 1) the :ref:`User's Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer documentation <programmer_documentation>` and use LAMMPS and 2) the :ref:`Programmer's Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS. 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: .. _user_documentation:
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: 3 :numbered: 3
:caption: User Documentation :caption: User's Guide
:name: userdoc :name: userdoc
:includehidden: :includehidden:
@ -61,14 +65,16 @@ User Documentation
Tools Tools
Errors Errors
Programmer Documentation
************************ ******************
Programmer's Guide
******************
.. _programmer_documentation: .. _programmer_documentation:
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: 3 :numbered: 3
:caption: Programmer Documentation :caption: Programmer's Guide
:name: progdoc :name: progdoc
:includehidden: :includehidden:
@ -93,6 +99,7 @@ Programmer Documentation
fix_modify_atc_commands fix_modify_atc_commands
Bibliography Bibliography
******************
Indices and tables Indices and tables
****************** ******************

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doc/src/Manual_version.rst
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What does a LAMMPS version mean What does a LAMMPS version mean
=============================== -------------------------------
The LAMMPS "version" is the date when it was released, such as 1 May 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 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; margin-bottom: 12px !important;
} }
#user-documentation.section h2 { #user-s-guide.section h2 {
display: none; display: none;
} }
#programmer-documentation.section h2 { #programmer-s-guide.section h2 {
display: none; display: none;
} }