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LAMMPS Documentation

====================

29 Jan 2016 version

-------------------

Version info:

-------------

The LAMMPS "version" is the date when it was released, such as 1 May

2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a

feature, we release it immediately, and post a notice on `this page of the WWW site <bug_>`_.  Each dated copy of LAMMPS contains all the

features and bug-fixes up to and including that version date. The

version date is printed to the screen and logfile every time you run

LAMMPS. It is also in the file src/version.h and in the LAMMPS

directory name created when you unpack a tarball, and at the top of

the first page of the manual (this page).

* If you browse the HTML doc pages on the LAMMPS WWW site, they always

  describe the most current version of LAMMPS.

* If you browse the HTML doc pages included in your tarball, they

  describe the version you have.

* The `PDF file <Manual.pdf>`_ on the WWW site or in the tarball is updated

  about once per month.  This is because it is large, and we don't want

  it to be part of every patch.

* There is also a `Developer.pdf <Developer.pdf>`_ file in the doc

  directory, which describes the internal structure and algorithms of

  LAMMPS.

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel

Simulator.

LAMMPS is a classical molecular dynamics simulation code designed to

run efficiently on parallel computers.  It was developed at Sandia

National Laboratories, a US Department of Energy facility, with

funding from the DOE.  It is an open-source code, distributed freely

under the terms of the GNU Public License (GPL).

The primary developers of LAMMPS are `Steve Plimpton <sjp_>`_, Aidan

Thompson, and Paul Crozier who can be contacted at

sjplimp,athomps,pscrozi at sandia.gov.  The `LAMMPS WWW Site <lws_>`_ at

http://lammps.sandia.gov has more information about the code and its

uses.

.. _bug: http://lammps.sandia.gov/bug.html

.. _sjp: http://www.sandia.gov/~sjplimp

----------

The LAMMPS documentation is organized into the following sections.  If

you find errors or omissions in this manual or have suggestions for

useful information to add, please send an email to the developers so

we can improve the LAMMPS documentation.

Once you are familiar with LAMMPS, you may want to bookmark :ref:`this page <comm>` at Section_commands.html#comm since

it gives quick access to documentation for all LAMMPS commands.

`PDF file <Manual.pdf>`_ of the entire manual, generated by

`htmldoc <http://freecode.com/projects/htmldoc>`_

.. toctree::

   :maxdepth: 2

   :numbered:

   Section_intro

   Section_start

   Section_commands

   Section_packages

   Section_accelerate

   Section_howto

   Section_example

   Section_perf

   Section_tools

   Section_modify

   Section_python

   Section_errors

   Section_history

Indices and tables

==================

* :ref:`genindex`

* :ref:`search`

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.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm

Example problems

================

The LAMMPS distribution includes an examples sub-directory with

several sample problems.  Each problem is in a sub-directory of its

own.  Most are 2d models so that they run quickly, requiring at most a

couple of minutes to run on a desktop machine.  Each problem has an

input script (in.*) and produces a log file (log.*) and dump file

(dump.*) when it runs.  Some use a data file (data.*) of initial

coordinates as additional input.  A few sample log file outputs on

different machines and different numbers of processors are included in

the directories to compare your answers to.  E.g. a log file like

log.crack.foo.P means it ran on P processors of machine "foo".

For examples that use input data files, many of them were produced by

`Pizza.py <http://pizza.sandia.gov>`_ or setup tools described in the

:doc:`Additional Tools <Section_tools>` section of the LAMMPS

documentation and provided with the LAMMPS distribution.

If you uncomment the :doc:`dump <dump>` command in the input script, a

text dump file will be produced, which can be animated by various

`visualization programs <http://lammps.sandia.gov/viz.html>`_.  It can

also be animated using the xmovie tool described in the :doc:`Additional Tools <Section_tools>` section of the LAMMPS documentation.

If you uncomment the :doc:`dump image <dump>` command in the input

script, and assuming you have built LAMMPS with a JPG library, JPG

snapshot images will be produced when the simulation runs.  They can

be quickly post-processed into a movie using commands described on the

:doc:`dump image <dump_image>` doc page.

Animations of many of these examples can be viewed on the Movies

section of the `LAMMPS WWW Site <lws_>`_.

These are the sample problems in the examples sub-directories:

+-------------+----------------------------------------------------------------------------+

| balance     | dynamic load balancing, 2d system                                          |

+-------------+----------------------------------------------------------------------------+

| body        | body particles, 2d system                                                  |

+-------------+----------------------------------------------------------------------------+

| colloid     | big colloid particles in a small particle solvent, 2d system               |

+-------------+----------------------------------------------------------------------------+

| comb        | models using the COMB potential                                            |

+-------------+----------------------------------------------------------------------------+

| crack       | crack propagation in a 2d solid                                            |

+-------------+----------------------------------------------------------------------------+

| cuda        | use of the USER-CUDA package for GPU acceleration                          |

+-------------+----------------------------------------------------------------------------+

| dipole      | point dipolar particles, 2d system                                         |

+-------------+----------------------------------------------------------------------------+

| dreiding    | methanol via Dreiding FF                                                   |

+-------------+----------------------------------------------------------------------------+

| eim         | NaCl using the EIM potential                                               |

+-------------+----------------------------------------------------------------------------+

| ellipse     | ellipsoidal particles in spherical solvent, 2d system                      |

+-------------+----------------------------------------------------------------------------+

| flow        | Couette and Poiseuille flow in a 2d channel                                |

+-------------+----------------------------------------------------------------------------+

| friction    | frictional contact of spherical asperities between 2d surfaces             |

+-------------+----------------------------------------------------------------------------+

| gpu         | use of the GPU package for GPU acceleration                                |

+-------------+----------------------------------------------------------------------------+

| hugoniostat | Hugoniostat shock dynamics                                                 |

+-------------+----------------------------------------------------------------------------+

| indent      | spherical indenter into a 2d solid                                         |

+-------------+----------------------------------------------------------------------------+

| intel       | use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor |

+-------------+----------------------------------------------------------------------------+

| kim         | use of potentials in Knowledge Base for Interatomic Models (KIM)           |

+-------------+----------------------------------------------------------------------------+

| line        | line segment particles in 2d rigid bodies                                  |

+-------------+----------------------------------------------------------------------------+

| meam        | MEAM test for SiC and shear (same as shear examples)                       |

+-------------+----------------------------------------------------------------------------+

| melt        | rapid melt of 3d LJ system                                                 |

+-------------+----------------------------------------------------------------------------+

| micelle     | self-assembly of small lipid-like molecules into 2d bilayers               |

+-------------+----------------------------------------------------------------------------+

| min         | energy minimization of 2d LJ melt                                          |

+-------------+----------------------------------------------------------------------------+

| msst        | MSST shock dynamics                                                        |

+-------------+----------------------------------------------------------------------------+

| nb3b        | use of nonbonded 3-body harmonic pair style                                |

+-------------+----------------------------------------------------------------------------+

| neb         | nudged elastic band (NEB) calculation for barrier finding                  |

+-------------+----------------------------------------------------------------------------+

| nemd        | non-equilibrium MD of 2d sheared system                                    |

+-------------+----------------------------------------------------------------------------+

| obstacle    | flow around two voids in a 2d channel                                      |

+-------------+----------------------------------------------------------------------------+

| peptide     | dynamics of a small solvated peptide chain (5-mer)                         |

+-------------+----------------------------------------------------------------------------+

| peri        | Peridynamic model of cylinder impacted by indenter                         |

+-------------+----------------------------------------------------------------------------+

| pour        | pouring of granular particles into a 3d box, then chute flow               |

+-------------+----------------------------------------------------------------------------+

| prd         | parallel replica dynamics of vacancy diffusion in bulk Si                  |

+-------------+----------------------------------------------------------------------------+

| qeq         | use of the QEQ pacakge for charge equilibration                            |

+-------------+----------------------------------------------------------------------------+

| reax        | RDX and TATB models using the ReaxFF                                       |

+-------------+----------------------------------------------------------------------------+

| rigid       | rigid bodies modeled as independent or coupled                             |

+-------------+----------------------------------------------------------------------------+

| shear       | sideways shear applied to 2d solid, with and without a void                |

+-------------+----------------------------------------------------------------------------+

| snap        | NVE dynamics for BCC tantalum crystal using SNAP potential                 |

+-------------+----------------------------------------------------------------------------+

| srd         | stochastic rotation dynamics (SRD) particles as solvent                    |

+-------------+----------------------------------------------------------------------------+

| tad         | temperature-accelerated dynamics of vacancy diffusion in bulk Si           |

+-------------+----------------------------------------------------------------------------+

| tri         | triangular particles in rigid bodies                                       |

+-------------+----------------------------------------------------------------------------+

vashishta: models using the Vashishta potential

Here is how you might run and visualize one of the sample problems:

.. parsed-literal::

   cd indent

   cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir

   lmp_linux -in in.indent            # run the problem

Running the simulation produces the files *dump.indent* and

*log.lammps*.  You can visualize the dump file as follows:

.. parsed-literal::

   ../../tools/xmovie/xmovie -scale dump.indent

If you uncomment the :doc:`dump image <dump_image>` line(s) in the input

script a series of JPG images will be produced by the run.  These can

be viewed individually or turned into a movie or animated by tools

like ImageMagick or QuickTime or various Windows-based tools.  See the

:doc:`dump image <dump_image>` doc page for more details.  E.g. this

Imagemagick command would create a GIF file suitable for viewing in a

browser.

.. parsed-literal::

   % convert -loop 1 *.jpg foo.gif

----------

There is also a COUPLE directory with examples of how to use LAMMPS as

a library, either by itself or in tandem with another code or library.

See the COUPLE/README file to get started.

There is also an ELASTIC directory with an example script for

computing elastic constants at zero temperature, using an Si example.  See

the ELASTIC/in.elastic file for more info.

There is also an ELASTIC_T directory with an example script for

computing elastic constants at finite temperature, using an Si example.  See

the ELASTIC_T/in.elastic file for more info.

There is also a USER directory which contains subdirectories of

user-provided examples for user packages.  See the README files in

those directories for more info.  See the

:doc:`Section_start.html <Section_start>` file for more info about user

packages.

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm