-substitute 38 56 bto.xsf</code>
<p>This will read the file <code>sto.cfg</code>, replace all strontium atoms (atomic number=38) by barium atoms (atomic number=56), and output the final system into <code>bto.xsf</code>.</p></li>

<li><code class="command">atomsk initial.cfg -sub Fe W final.xyz</code>
<p>This will read <code>initial.cfg</code>, substitute iron (Fe) by tungsten (W) and write the result into <code>final.xyz</code>.</p></li>

<li><code class="command">atomsk initial.lmc -sub 1 Si -sub 2 C final