240 lines
16 KiB
HTML
240 lines
16 KiB
HTML
<!DOCTYPE html>
|
||
<html class="writer-html5" lang="en" >
|
||
<head>
|
||
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
|
||
|
||
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
|
||
<title>4.1. Basics of running LAMMPS — LAMMPS documentation</title>
|
||
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/sphinx-design.min.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/css/lammps.css" type="text/css" />
|
||
<link rel="shortcut icon" href="_static/lammps.ico"/>
|
||
<link rel="canonical" href="https://docs.lammps.org/Run_basics.html" />
|
||
<!--[if lt IE 9]>
|
||
<script src="_static/js/html5shiv.min.js"></script>
|
||
<![endif]-->
|
||
|
||
<script src="_static/jquery.js?v=5d32c60e"></script>
|
||
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
|
||
<script src="_static/documentation_options.js?v=5929fcd5"></script>
|
||
<script src="_static/doctools.js?v=9bcbadda"></script>
|
||
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
|
||
<script src="_static/design-tabs.js?v=f930bc37"></script>
|
||
<script async="async" src="_static/mathjax/es5/tex-mml-chtml.js?v=cadf963e"></script>
|
||
<script src="_static/js/theme.js"></script>
|
||
<link rel="index" title="Index" href="genindex.html" />
|
||
<link rel="search" title="Search" href="search.html" />
|
||
<link rel="next" title="4.2. Command-line options" href="Run_options.html" />
|
||
<link rel="prev" title="4. Run LAMMPS" href="Run_head.html" />
|
||
</head>
|
||
|
||
<body class="wy-body-for-nav">
|
||
<div class="wy-grid-for-nav">
|
||
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
|
||
<div class="wy-side-scroll">
|
||
<div class="wy-side-nav-search" >
|
||
|
||
|
||
|
||
<a href="Manual.html">
|
||
|
||
<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
|
||
</a>
|
||
<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
|
||
<div class="lammps_release">git info: </div>
|
||
<div role="search">
|
||
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
|
||
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
|
||
<input type="hidden" name="check_keywords" value="yes" />
|
||
<input type="hidden" name="area" value="default" />
|
||
</form>
|
||
</div>
|
||
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
|
||
<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
|
||
<ul class="current">
|
||
<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
|
||
<li class="toctree-l1 current"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a><ul class="current">
|
||
<li class="toctree-l2 current"><a class="current reference internal" href="#">4.1. Basics of running LAMMPS</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="Run_options.html">4.2. Command-line options</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="Run_output.html">4.3. Screen and logfile output</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="Run_windows.html">4.4. Running LAMMPS on Windows</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
|
||
</ul>
|
||
<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
|
||
<ul>
|
||
<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
|
||
</ul>
|
||
<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
|
||
<ul>
|
||
<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
</div>
|
||
</nav>
|
||
|
||
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
|
||
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
|
||
<a href="Manual.html">LAMMPS</a>
|
||
</nav>
|
||
|
||
<div class="wy-nav-content">
|
||
<div class="rst-content style-external-links">
|
||
<div role="navigation" aria-label="Page navigation">
|
||
<ul class="wy-breadcrumbs">
|
||
<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
|
||
<li class="breadcrumb-item"><a href="Run_head.html"><span class="section-number">4. </span>Run LAMMPS</a></li>
|
||
<li class="breadcrumb-item active"><span class="section-number">4.1. </span>Basics of running LAMMPS</li>
|
||
<li class="wy-breadcrumbs-aside">
|
||
<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
|
||
</li>
|
||
</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
|
||
<a href="Run_head.html" class="btn btn-neutral float-left" title="4. Run LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="Run_options.html" class="btn btn-neutral float-right" title="4.2. Command-line options" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
<hr/>
|
||
</div>
|
||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||
<div itemprop="articleBody">
|
||
|
||
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="basics-of-running-lammps">
|
||
<h1><span class="section-number">4.1. </span>Basics of running LAMMPS<a class="headerlink" href="#basics-of-running-lammps" title="Link to this heading"></a></h1>
|
||
<p>LAMMPS is run from the command-line, reading commands from a file via
|
||
the <code class="docutils literal notranslate"><span class="pre">-in</span></code> command-line flag, or from standard input. Using the <code class="docutils literal notranslate"><span class="pre">-in</span>
|
||
<span class="pre">in.file</span></code> variant is recommended (see note below). The name of the
|
||
LAMMPS executable is either <code class="docutils literal notranslate"><span class="pre">lmp</span></code> or <code class="docutils literal notranslate"><span class="pre">lmp_<machine></span></code> with
|
||
<cite><machine></cite> being the machine string used when compiling LAMMPS. This
|
||
is required when compiling LAMMPS with the traditional build system
|
||
(e.g. with <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">mpi</span></code>), but optional when using CMake to configure and
|
||
build LAMMPS:</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>lmp_serial<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.file
|
||
lmp_serial<span class="w"> </span><<span class="w"> </span><span class="k">in</span>.file
|
||
lmp<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.file
|
||
lmp<span class="w"> </span><<span class="w"> </span><span class="k">in</span>.file
|
||
/path/to/lammps/src/lmp_serial<span class="w"> </span>-i<span class="w"> </span><span class="k">in</span>.file
|
||
mpirun<span class="w"> </span>-np<span class="w"> </span><span class="m">4</span><span class="w"> </span>lmp_mpi<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.file
|
||
mpiexec<span class="w"> </span>-np<span class="w"> </span><span class="m">4</span><span class="w"> </span>lmp<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.file
|
||
mpirun<span class="w"> </span>-np<span class="w"> </span><span class="m">8</span><span class="w"> </span>/path/to/lammps/src/lmp_mpi<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.file
|
||
mpiexec<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>/usr/local/bin/lmp<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.file
|
||
</pre></div>
|
||
</div>
|
||
<p>You normally run the LAMMPS command in the directory where your input
|
||
script is located. That is also where output files are produced by
|
||
default, unless you provide specific other paths in your input script or
|
||
on the command-line. As in some of the examples above, the LAMMPS
|
||
executable itself can be placed elsewhere.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>The redirection operator “<” will not always work when running in
|
||
parallel with <code class="docutils literal notranslate"><span class="pre">mpirun</span></code> or <code class="docutils literal notranslate"><span class="pre">mpiexec</span></code>; for those systems the -in
|
||
form is required.</p>
|
||
</div>
|
||
<p>As LAMMPS runs it prints info to the screen and a logfile named
|
||
<code class="docutils literal notranslate"><span class="pre">log.lammps</span></code>. More info about output is given on the <a class="reference internal" href="Run_output.html"><span class="doc">screen and
|
||
logfile output</span></a> page.</p>
|
||
<p>If LAMMPS encounters errors in the input script or while running a
|
||
simulation it will print an ERROR message and stop or a WARNING
|
||
message and continue. See the <a class="reference internal" href="Errors.html"><span class="doc">Common Problems</span></a> page for a
|
||
discussion of the various kinds of errors LAMMPS can or can’t detect,
|
||
a list of all ERROR and WARNING messages, and what to do about them.</p>
|
||
<hr class="docutils" />
|
||
<p>LAMMPS can run the same problem on any number of processors, including a
|
||
single processor. In theory you should get identical answers on any
|
||
number of processors and on any machine. In practice, numerical
|
||
round-off due to using floating-point math can cause slight differences
|
||
and an eventual divergence of molecular dynamics trajectories. See the
|
||
<a class="reference internal" href="Errors_common.html"><span class="doc">Errors common</span></a> page for discussion of this.</p>
|
||
<p>LAMMPS can run as large a problem as will fit in the physical memory of
|
||
one or more processors. If you run out of memory, you must run on more
|
||
processors or define a smaller problem. The amount of memory needed and
|
||
how well it can be distributed across processors may vary based
|
||
on the models and settings and commands used.</p>
|
||
<p>If you run LAMMPS in parallel via mpirun, you should be aware of the
|
||
<a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command, which controls how MPI tasks are
|
||
mapped to the simulation box, as well as mpirun options that control how
|
||
MPI tasks are assigned to physical cores of the node(s) of the machine
|
||
you are running on. These settings can improve performance, though the
|
||
defaults are often adequate.</p>
|
||
<p>For example, it is often important to bind MPI tasks (processes) to
|
||
physical cores (processor affinity), so that the operating system does
|
||
not migrate them during a simulation. If this is not the default
|
||
behavior on your machine, the mpirun option <code class="docutils literal notranslate"><span class="pre">--bind-to</span> <span class="pre">core</span></code> (OpenMPI)
|
||
or <code class="docutils literal notranslate"><span class="pre">-bind-to</span> <span class="pre">core</span></code> (MPICH) can be used.</p>
|
||
<p>If the LAMMPS command(s) you are using support multi-threading, you
|
||
can set the number of threads per MPI task via the environment
|
||
variable <code class="docutils literal notranslate"><span class="pre">OMP_NUM_THREADS</span></code>, before you launch LAMMPS:</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">OMP_NUM_THREADS</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="c1"># bash</span>
|
||
setenv<span class="w"> </span>OMP_NUM_THREADS<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="c1"># csh or tcsh</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>This can also be done via the <a class="reference internal" href="package.html"><span class="doc">package</span></a> command or via
|
||
the <a class="reference internal" href="Run_options.html"><span class="doc">-pk command-line switch</span></a> which invokes the
|
||
package command. See the <a class="reference internal" href="package.html"><span class="doc">package</span></a> command or
|
||
<a class="reference internal" href="Speed.html"><span class="doc">Speed</span></a> doc pages for more details about which accelerator
|
||
packages and which commands support multi-threading.</p>
|
||
<hr class="docutils" />
|
||
<p>You can experiment with running LAMMPS using any of the input scripts
|
||
provided in the examples or bench directory. Input scripts are named
|
||
<code class="docutils literal notranslate"><span class="pre">in.*</span></code> and sample outputs are named <code class="docutils literal notranslate"><span class="pre">log.*.P</span></code> where P is the number of
|
||
processors it was run on.</p>
|
||
<p>Some of the examples or benchmarks require LAMMPS to be built with
|
||
optional packages.</p>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="Run_head.html" class="btn btn-neutral float-left" title="4. Run LAMMPS" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="Run_options.html" class="btn btn-neutral float-right" title="4.2. Command-line options" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
|
||
<hr/>
|
||
|
||
<div role="contentinfo">
|
||
<p>© Copyright 2003-2025 Sandia Corporation.</p>
|
||
</div>
|
||
|
||
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
|
||
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
|
||
provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
||
|
||
|
||
</footer>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</div>
|
||
<script>
|
||
jQuery(function () {
|
||
SphinxRtdTheme.Navigation.enable(false);
|
||
});
|
||
</script>
|
||
|
||
</body>
|
||
</html> |