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<title>shell command — LAMMPS documentation</title>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<ul>
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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-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>shell command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="shell-command">
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<span id="index-0"></span><h1>shell command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<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>
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</pre></div>
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</div>
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<ul class="simple">
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<li>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</li>
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</ul>
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<pre class="literal-block">
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<em>cd</em> arg = dir
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dir = directory to change to
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<em>mkdir</em> args = dir1 dir2 ...
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dir1,dir2 = one or more directories to create
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<em>mv</em> args = old new
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old = old filename
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new = new filename
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<em>rm</em> args = file1 file2 ...
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file1,file2 = one or more filenames to delete
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<em>rmdir</em> args = dir1 dir2 ...
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dir1,dir2 = one or more directories to delete
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<em>putenv</em> args = var1=value1 var2=value2
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var=value = one of more definitions of environment variables
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anything else is passed as a command to the shell for direct execution
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">shell</span> <span class="n">cd</span> <span class="n">sub1</span>
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<span class="n">shell</span> <span class="n">cd</span> <span class="o">..</span>
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<span class="n">shell</span> <span class="n">mkdir</span> <span class="n">tmp1</span> <span class="n">tmp2</span> <span class="n">tmp3</span>
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<span class="n">shell</span> <span class="n">rmdir</span> <span class="n">tmp1</span>
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<span class="n">shell</span> <span class="n">mv</span> <span class="n">log</span><span class="o">.</span><span class="n">lammps</span> <span class="n">hold</span><span class="o">/</span><span class="n">log</span><span class="o">.</span><span class="mi">1</span>
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<span class="n">shell</span> <span class="n">rm</span> <span class="n">TMP</span><span class="o">/</span><span class="n">file1</span> <span class="n">TMP</span><span class="o">/</span><span class="n">file2</span>
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<span class="n">shell</span> <span class="n">putenv</span> <span class="n">LAMMPS_POTENTIALS</span><span class="o">=../../</span><span class="n">potentials</span>
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<span class="n">shell</span> <span class="n">my_setup</span> <span class="n">file1</span> <span class="mi">10</span> <span class="n">file2</span>
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<span class="n">shell</span> <span class="n">my_post_process</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">out</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Execute a shell command. A few simple file-based shell commands are
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supported directly, in Unix-style syntax. Any command not listed
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above is passed as-is to the C-library system() call, which invokes
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the command in a shell.</p>
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<p>This is means to invoke other commands from your input script. For
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example, you can move files around in preparation for the next section
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of the input script. Or you can run a program that pre-processes data
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for input into LAMMPS. Or you can run a program that post-processes
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LAMMPS output data.</p>
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<p>With the exception of <em>cd</em>, all commands, including ones invoked via a
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system() call, are executed by only a single processor, so that
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files/directories are not being manipulated by multiple processors.</p>
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<p>The <em>cd</em> cmd executes the Unix “cd” command to change the working
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directory. All subsequent LAMMPS commands that read/write files will
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use the new directory. All processors execute this command.</p>
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<p>The <em>mkdir</em> cmd executes the Unix “mkdir” command to create one or
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more directories.</p>
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<p>The <em>mv</em> cmd executes the Unix “mv” command to rename a file and/or
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move it to a new directory.</p>
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<p>The <em>rm</em> cmd executes the Unix “rm” command to remove one or more
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files.</p>
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<p>The <em>rmdir</em> cmd executes the Unix “rmdir” command to remove one or
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more directories. A directory must be empty to be successfully
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removed.</p>
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<p>The <em>putenv</em> cmd defines or updates an environment variable directly.
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Since this command does not pass through the shell, no shell variable
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expansion or globbing is performed, only the usual substitution for
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LAMMPS variables defined with the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command is
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performed. The resulting string is then used literally.</p>
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<p>Any other cmd is passed as-is to the shell along with its arguments as
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one string, invoked by the C-library system() call. For example,
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these lines in your input script:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span>variable n equal 10
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variable foo string file2
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shell my_setup file1 $n ${foo}
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</pre></div>
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</div>
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<p>would be the same as invoking</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">my_setup</span> <span class="n">file1</span> <span class="mi">10</span> <span class="n">file2</span>
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</pre></div>
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</div>
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<p>from a command-line prompt. The executable program “my_setup” is run
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with 3 arguments: file1 10 file2.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>LAMMPS does not detect errors or print warnings when any of these
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commands execute. E.g. if the specified directory does not exist,
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executing the <em>cd</em> command will silently do nothing.</p>
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<p><strong>Related commands:</strong> none</p>
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<p><strong>Default:</strong> none</p>
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