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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<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="atom_modify.html">atom_modify command</a></li>
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<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="box.html">box 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>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<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>
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<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="dump.html">dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<div class="section" id="shell-command">
<span id="index-0"></span><h1>shell command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">shell</span> <span class="n">cmd</span> <span class="n">args</span>
</pre></div>
</div>
<ul>
<li><p class="first">cmd = <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
<em>rm</em> args = file1 file2 ...
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>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
shell cd sub1
shell cd ..
shell mkdir tmp1 tmp2 tmp3
shell rmdir tmp1
shell mv log.lammps hold/log.1
shell rm TMP/file1 TMP/file2
shell putenv LAMMPS_POTENTIALS=../../potentials
shell my_setup file1 10 file2
shell my_post_process 100 dump.out
</pre>
</div>
<div class="section" id="description">
<h2>Description</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.</p>
<p>This is means to invoke other commands 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.</p>
<p>The <em>cd</em> cmd executes the Unix &#8220;cd&#8221; command to change the working
directory. All subsequent LAMMPS commands that read/write files will
use the new directory. All processors execute this command.</p>
<p>The <em>mkdir</em> cmd executes the Unix &#8220;mkdir&#8221; command to create one or
more directories.</p>
<p>The <em>mv</em> cmd executes the Unix &#8220;mv&#8221; command to rename a file and/or
move it to a new directory.</p>
<p>The <em>rm</em> cmd executes the Unix &#8220;rm&#8221; command to remove one or more
files.</p>
<p>The <em>rmdir</em> cmd executes the Unix &#8220;rmdir&#8221; command to remove one or
more directories. A directory must be empty to be successfully
removed.</p>
<p>The <em>putenv</em> cmd 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 cmd 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>
<pre class="literal-block">
variable n equal 10
variable foo string file2
shell my_setup file1 $n ${foo}
</pre>
<p>would be the same as invoking</p>
<pre class="literal-block">
% my_setup file1 10 file2
</pre>
<p>from a command-line prompt. The executable program &#8220;my_setup&#8221; is run
with 3 arguments: file1 10 file2.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>LAMMPS does not detect errors or print warnings when any of these
commands execute. E.g. if the specified directory does not exist,
executing the <em>cd</em> command will silently do nothing.</p>
<p><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
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