forked from lijiext/lammps
421 lines
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HTML
421 lines
10 KiB
HTML
<HTML>
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<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="24 Jan 2013 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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<BODY>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H1></H1>
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<CENTER><H3>LAMMPS Documentation
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</H3></CENTER>
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<CENTER><H4>27 Jan 2013 version
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</H4></CENTER>
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<H4>Version info:
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</H4>
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<P>The LAMMPS "version" is the date when it was released, such as 1 May
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2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
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feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
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the WWW site</A>. Each dated copy of LAMMPS contains all the
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features and bug-fixes up to and including that version date. The
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version date is printed to the screen and logfile every time you run
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LAMMPS. It is also in the file src/version.h and in the LAMMPS
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directory name created when you unpack a tarball, and at the top of
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the first page of the manual (this page).
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</P>
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<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
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describe the most current version of LAMMPS.
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<LI>If you browse the HTML doc pages included in your tarball, they
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describe the version you have.
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<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
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about once per month. This is because it is large, and we don't want
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it to be part of every patch.
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<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
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directory, which describes the internal structure and algorithms of
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LAMMPS.
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</UL>
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<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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</P>
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<P>LAMMPS is a classical molecular dynamics simulation code designed to
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run efficiently on parallel computers. It was developed at Sandia
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National Laboratories, a US Department of Energy facility, with
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funding from the DOE. It is an open-source code, distributed freely
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under the terms of the GNU Public License (GPL).
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</P>
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<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
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Thompson, and Paul Crozier who can be contacted at
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sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
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http://lammps.sandia.gov has more information about the code and its
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uses.
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</P>
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<HR>
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<P>The LAMMPS documentation is organized into the following sections. If
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you find errors or omissions in this manual or have suggestions for
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useful information to add, please send an email to the developers so
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we can improve the LAMMPS documentation.
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</P>
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<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
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page</A> at Section_commands.html#comm since
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it gives quick access to documentation for all LAMMPS commands.
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</P>
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<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
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<A HREF = "http://www.easysw.com/htmldoc">htmldoc</A>
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</P>
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<OL><LI><A HREF = "Section_intro.html">Introduction</A>
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<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
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<BR>
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1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
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<BR>
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1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
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<BR>
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1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
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<BR>
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1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
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<BR></UL>
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<LI><A HREF = "Section_start.html">Getting started</A>
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<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
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<BR>
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2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
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<BR>
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2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
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<BR>
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2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
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<BR>
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2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
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<BR>
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2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
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<BR>
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2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
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<BR>
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2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
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<BR>
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2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
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<BR></UL>
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<LI><A HREF = "Section_commands.html">Commands</A>
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<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
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<BR>
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3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
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<BR>
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3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
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<BR>
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3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
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<BR>
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3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
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<BR></UL>
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<LI><A HREF = "Section_packages.html">Packages</A>
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<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
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<BR>
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4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
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<BR></UL>
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<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
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<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
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<BR>
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5.2 <A HREF = "Section_accelerate.html#acc_2">General strategies</A>
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<BR>
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5.3 <A HREF = "Section_accelerate.html#acc_3">Packages with optimized styles</A>
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<BR>
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5.4 <A HREF = "Section_accelerate.html#acc_4">OPT package</A>
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<BR>
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5.5 <A HREF = "Section_accelerate.html#acc_5">USER-OMP package</A>
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<BR>
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5.6 <A HREF = "Section_accelerate.html#acc_6">GPU package</A>
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<BR>
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5.7 <A HREF = "Section_accelerate.html#acc_7">USER-CUDA package</A>
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<BR>
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5.8 <A HREF = "Section_accelerate.html#acc_8">Comparison of GPU and USER-CUDA packages</A>
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<BR></UL>
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<LI><A HREF = "Section_howto.html">How-to discussions</A>
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<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
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<BR>
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6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
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<BR>
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6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
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<BR>
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6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
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<BR>
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6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
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<BR>
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6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
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<BR>
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6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
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<BR>
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6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
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<BR>
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6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
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<BR>
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6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
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<BR>
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6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
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<BR>
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6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
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<BR>
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6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
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<BR>
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6.14 <A HREF = "Section_howto.html#howto_14">Extended spherical and aspherical particles</A>
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<BR>
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6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
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<BR>
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6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
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<BR>
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6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
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<BR>
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6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
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<BR>
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6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
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<BR>
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6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
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<BR>
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6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
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<BR>
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6.22 <A HREF = "Section_howto.html#howto_22">Body particles</A>
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<BR></UL>
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<LI><A HREF = "Section_example.html">Example problems</A>
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<LI><A HREF = "Section_perf.html">Performance & scalability</A>
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<LI><A HREF = "Section_tools.html">Additional tools</A>
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<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
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<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
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<BR>
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10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
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<BR>
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10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
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<BR>
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10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
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<BR>
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10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
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<BR>
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10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
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<BR>
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10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
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<BR>
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10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
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<BR>
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10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
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<BR>
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10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
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<BR>
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10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
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<BR>
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10.12 <A HREF = "Section_modify.html#mod_12">Thermodynamic output options</A>
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<BR>
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10.13 <A HREF = "Section_modify.html#mod_13">Variable options</A>
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<BR>
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10.14 <A HREF = "Section_modify.html#mod_14">Submitting new features for inclusion in LAMMPS</A>
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<BR></UL>
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<LI><A HREF = "Section_python.html">Python interface</A>
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<UL> 11.1 <A HREF = "Section_python.html#py_1">Building LAMMPS as a shared library</A>
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<BR>
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11.2 <A HREF = "Section_python.html#py_2">Installing the Python wrapper into Python</A>
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<BR>
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11.3 <A HREF = "Section_python.html#py_3">Extending Python with MPI to run in parallel</A>
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<BR>
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11.4 <A HREF = "Section_python.html#py_4">Testing the Python-LAMMPS interface</A>
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<BR>
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11.5 <A HREF = "Section_python.html#py_5">Using LAMMPS from Python</A>
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<BR>
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11.6 <A HREF = "Section_python.html#py_6">Example Python scripts that use LAMMPS</A>
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<BR></UL>
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<LI><A HREF = "Section_errors.html">Errors</A>
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<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
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<BR>
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12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
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<BR>
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12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
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<BR></UL>
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<LI><A HREF = "Section_history.html">Future and history</A>
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<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
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<BR>
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13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
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<BR></UL>
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</OL>
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