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<title>shell command &mdash; LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<li class="toctree-l1 current"><a class="reference internal" href="commands_list.html">Commands</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_write.html">angle_write command</a></li>
<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dihedral_write.html">dihedral_write command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dynamical_matrix.html">dynamical_matrix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fitpod_command.html">fitpod command</a></li>
<li class="toctree-l2"><a class="reference internal" href="geturl.html">geturl command</a></li>
<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="hyper.html">hyper command</a></li>
<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="kim_commands.html">kim command</a></li>
<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
<li class="toctree-l2"><a class="reference internal" href="labelmap.html">labelmap command</a></li>
<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
<li class="toctree-l2"><a class="reference internal" href="mdi.html">mdi command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_spin.html">min_style spin command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-cg-command">min_style spin/cg command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-lbfgs-command">min_style spin/lbfgs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style cg command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-hftn-command">min_style hftn command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-sd-command">min_style sd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-quickmin-command">min_style quickmin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-command"><span class="xref std std-doc">min_style spin</span> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-cg-command"><span class="xref std std-doc">min_style spin/cg</span> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-lbfgs-command"><span class="xref std std-doc">min_style spin/lbfgs</span> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neb_spin.html">neb/spin command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
<li class="toctree-l2"><a class="reference internal" href="plugin.html">plugin command</a></li>
<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
<li class="toctree-l2"><a class="reference internal" href="reset_atoms.html">reset_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">shell command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
<li class="toctree-l2"><a class="reference internal" href="temper_grem.html">temper/grem command</a></li>
<li class="toctree-l2"><a class="reference internal" href="temper_npt.html">temper/npt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="third_order.html">third_order command</a></li>
<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
</ul>
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<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>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="shell-command">
<span id="index-0"></span><h1>shell command<a class="headerlink" href="#shell-command" title="Link to this heading"></a></h1>
<section id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">shell</span><span class="w"> </span><span class="n">command</span><span class="w"> </span><span class="n">args</span>
</pre></div>
</div>
<ul>
<li><p>command = <em>cd</em> or <em>mkdir</em> or <em>mv</em> or <em>rm</em> or <em>rmdir</em> or <em>putenv</em> or arbitrary command</p>
<pre class="literal-block"><em>cd</em> arg = dir
dir = directory to change to
<em>mkdir</em> args = dir1 dir2 ...
dir1,dir2 = one or more directories to create
<em>mv</em> args = old new
old = old filename
new = new filename or destination folder
<em>rm</em> args = [-f] file1 file2 ...
-f = turn off warnings (optional)
file1,file2 = one or more filenames to delete
<em>rmdir</em> args = dir1 dir2 ...
dir1,dir2 = one or more directories to delete
<em>putenv</em> args = var1=value1 var2=value2
var=value = one of more definitions of environment variables
anything else is passed as a command to the shell for direct execution</pre>
</li>
</ul>
</section>
<section id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">shell</span><span class="w"> </span><span class="n">cd</span><span class="w"> </span><span class="n">sub1</span>
<span class="k">shell</span><span class="w"> </span><span class="n">cd</span><span class="w"> </span><span class="n">..</span>
<span class="k">shell</span><span class="w"> </span><span class="n">mkdir</span><span class="w"> </span><span class="n">tmp1</span><span class="w"> </span><span class="n">tmp2</span><span class="o">/</span><span class="n">tmp3</span>
<span class="k">shell</span><span class="w"> </span><span class="n">rmdir</span><span class="w"> </span><span class="n">tmp1</span><span class="w"> </span><span class="n">tmp2</span>
<span class="k">shell</span><span class="w"> </span><span class="n">mv</span><span class="w"> </span><span class="n">log.lammps</span><span class="w"> </span><span class="n">hold</span><span class="o">/</span><span class="n">log.1</span>
<span class="k">shell</span><span class="w"> </span><span class="n">rm</span><span class="w"> </span><span class="n">TMP</span><span class="o">/</span><span class="n">file1</span><span class="w"> </span><span class="n">TMP</span><span class="o">/</span><span class="n">file2</span>
<span class="k">shell</span><span class="w"> </span><span class="n">putenv</span><span class="w"> </span><span class="n">LAMMPS_POTENTIALS</span><span class="o">=</span><span class="n">..</span><span class="o">/</span><span class="n">..</span><span class="o">/</span><span class="n">potentials</span>
<span class="k">shell</span><span class="w"> </span><span class="n">my_setup</span><span class="w"> </span><span class="n">file1</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">file2</span>
<span class="k">shell</span><span class="w"> </span><span class="n">my_post_process</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.out</span>
</pre></div>
</div>
</section>
<section id="description">
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
<p>Execute a shell command. A few simple file-based shell commands are
supported directly, in Unix-style syntax. Any command not listed
above is passed as-is to the C-library system() call, which invokes
the command in a shell. To use the external executable instead of
the built-in version one needs to use a full path, for example
<em>/bin/rm</em> instead of <em>rm</em>. The built-in commands will also work
on operating systems, that do not - by default - provide the
corresponding external executables (like <em>mkdir</em> on Windows).</p>
<p>This command provides a ways to invoke custom commands or executables
from your input script. For example, you can move files around in
preparation for the next section of the input script. Or you can run a
program that pre-processes data for input into LAMMPS. Or you can run a
program that post-processes LAMMPS output data.</p>
<p>With the exception of <em>cd</em>, all commands, including ones invoked via a
system() call, are executed by only a single processor, so that
files/directories are not being manipulated by multiple processors
concurrently which may result in unexpected errors or corrupted files.</p>
<p>The <em>cd</em> command changes the current working directory similar to
the <code class="docutils literal notranslate"><span class="pre">cd</span></code> command. All subsequent LAMMPS commands that read/write files
will use the new directory. All processors execute this command.</p>
<p>The <em>mkdir</em> command creates directories similar to the Unix <code class="docutils literal notranslate"><span class="pre">mkdir</span> <span class="pre">-p</span></code>
command. That is, it will attempt to create the entire path of
subdirectories if they do not exist yet.</p>
<p>The <em>mv</em> command renames a file and/or moves it to a new directory.
It cannot rename files across filesystem boundaries or between drives.</p>
<p>The <em>rm</em> command deletes file similar to the Unix <code class="docutils literal notranslate"><span class="pre">rm</span></code> command.</p>
<p>The <em>rmdir</em> command deletes directories similar to Unix <code class="docutils literal notranslate"><span class="pre">rmdir</span></code> command.
If a directory is not empty, its contents are also removed recursively
similar to the Unix <code class="docutils literal notranslate"><span class="pre">rm</span> <span class="pre">-r</span></code> command.</p>
<p>The <em>putenv</em> command defines or updates an environment variable directly.
Since this command does not pass through the shell, no shell variable
expansion or globbing is performed, only the usual substitution for
LAMMPS variables defined with the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command is
performed. The resulting string is then used literally.</p>
<p>Any other command is passed as-is to the shell along with its arguments as
one string, invoked by the C-library system() call. For example,
these lines in your input script:</p>
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">n</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">10</span>
<span class="k">variable </span><span class="nv nv-Identifier">foo</span><span class="w"> </span><span class="n">string</span><span class="w"> </span><span class="n">file2</span>
<span class="k">shell</span><span class="w"> </span><span class="n">my_setup</span><span class="w"> </span><span class="n">file1</span><span class="w"> </span><span class="nv">$n</span><span class="w"> </span><span class="nv">${foo}</span>
</pre></div>
</div>
<p>would be the same as invoking</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>my_setup<span class="w"> </span>file1<span class="w"> </span><span class="m">10</span><span class="w"> </span>file2
</pre></div>
</div>
<p>from a command-line prompt. The executable program “my_setup” is run
with 3 arguments: file1 10 file2.</p>
</section>
<section id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
<p>LAMMPS will do a best effort to detect errors and print suitable
warnings, but due to the nature of delegating commands to the C-library
system() call, this is not always reliable.</p>
</section>
<section id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
<p>none</p>
</section>
<section id="default">
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
<p>none</p>
</section>
</section>
</div>
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