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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="Commands.html">5. Commands</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="Commands_input.html">5.1. LAMMPS input scripts</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">5.3. Input script structure</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#initialization">5.3.1. Initialization</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_category.html">5.4. Commands by category</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_fix.html">5.6. Fix styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_compute.html">5.7. Compute styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_pair.html">5.8. Pair styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_bond.html#dihedral-styles">5.11. Dihedral styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_bond.html#improper-styles">5.12. Improper styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_kspace.html">5.13. KSpace styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_dump.html">5.14. Dump styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Commands_removed.html">5.15. Removed commands and packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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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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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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<li class="breadcrumb-item"><a href="Commands.html"><span class="section-number">5. </span>Commands</a></li>
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<li class="breadcrumb-item active"><span class="section-number">5.3. </span>Input script structure</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="input-script-structure">
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<h1><span class="section-number">5.3. </span>Input script structure<a class="headerlink" href="#input-script-structure" title="Link to this heading"></a></h1>
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<p>This page describes the structure of a typical LAMMPS input script.
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The examples directory in the LAMMPS distribution contains many sample
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input scripts; it is discussed on the <a class="reference internal" href="Examples.html"><span class="doc">Examples</span></a> doc
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page.</p>
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<p>A LAMMPS input script typically has 4 parts:</p>
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<ol class="arabic simple">
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<li><p><a class="reference internal" href="#init"><span class="std std-ref">Initialization</span></a></p></li>
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<li><p><a class="reference internal" href="#system"><span class="std std-ref">System definition</span></a></p></li>
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<li><p><a class="reference internal" href="#settings"><span class="std std-ref">Simulation settings</span></a></p></li>
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<li><p><a class="reference internal" href="#run"><span class="std std-ref">Run a simulation</span></a></p></li>
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</ol>
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<p>The last 2 parts can be repeated as many times as desired. I.e. run a
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simulation, change some settings, run some more, etc. Each of the 4
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parts is now described in more detail. Remember that almost all
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commands need only be used if a non-default value is desired.</p>
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<section id="initialization">
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<span id="init"></span><h2><span class="section-number">5.3.1. </span>Initialization<a class="headerlink" href="#initialization" title="Link to this heading"></a></h2>
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<p>Set parameters that need to be defined before atoms are created or
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read-in from a file.</p>
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<p>The relevant commands are <a class="reference internal" href="units.html"><span class="doc">units</span></a>,
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<a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a>, <a class="reference internal" href="newton.html"><span class="doc">newton</span></a>,
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<a class="reference internal" href="processors.html"><span class="doc">processors</span></a>, <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>,
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<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>, <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a>.</p>
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<p>If force-field parameters appear in the files that will be read, these
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commands tell LAMMPS what kinds of force fields are being used:
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<a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>, <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>,
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<a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>, <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>,
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<a class="reference internal" href="improper_style.html"><span class="doc">improper_style</span></a>.</p>
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</section>
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<section id="system-definition">
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<span id="system"></span><h2><span class="section-number">5.3.2. </span>System definition<a class="headerlink" href="#system-definition" title="Link to this heading"></a></h2>
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<p>There are 3 ways to define the simulation cell and reserve space for
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force field info and fill it with atoms in LAMMPS. Read them in from
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(1) a data file or (2) a restart file via the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands,
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respectively. These files can also contain molecular topology
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information. Or (3) create a simulation cell and fill it with atoms on
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a lattice (with no molecular topology), using these commands:
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<a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>, <a class="reference internal" href="region.html"><span class="doc">region</span></a>, <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> or
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<a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a>.</p>
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<p>The entire set of atoms can be duplicated to make a larger simulation
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using the <a class="reference internal" href="replicate.html"><span class="doc">replicate</span></a> command.</p>
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</section>
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<section id="simulation-settings">
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<span id="settings"></span><h2><span class="section-number">5.3.3. </span>Simulation settings<a class="headerlink" href="#simulation-settings" title="Link to this heading"></a></h2>
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<p>Once atoms and molecular topology are defined, a variety of settings
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can be specified: force field coefficients, simulation parameters,
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output options, and more.</p>
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<p>Force field coefficients are set by these commands (they can also be
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set in the read-in files): <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>,
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<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>,
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<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>,
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<a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a>,
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<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, <a class="reference internal" href="dielectric.html"><span class="doc">dielectric</span></a>,
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<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>.</p>
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<p>Various simulation parameters are set by these commands:
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<a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a>, <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a>,
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<a class="reference internal" href="group.html"><span class="doc">group</span></a>, <a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a>,
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<a class="reference internal" href="reset_timestep.html"><span class="doc">reset_timestep</span></a>, <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>,
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<a class="reference internal" href="min_style.html"><span class="doc">min_style</span></a>, <a class="reference internal" href="min_modify.html"><span class="doc">min_modify</span></a>.</p>
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<p>Fixes impose a variety of boundary conditions, time integration, and
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diagnostic options. The <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command comes in many flavors.</p>
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<p>Various computations can be specified for execution during a
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simulation using the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>,
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<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a>, and <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>
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commands.</p>
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<p>Output options are set by the <a class="reference internal" href="thermo.html"><span class="doc">thermo</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>,
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and <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> commands.</p>
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</section>
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<section id="run-a-simulation">
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<span id="run"></span><h2><span class="section-number">5.3.4. </span>Run a simulation<a class="headerlink" href="#run-a-simulation" title="Link to this heading"></a></h2>
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<p>A molecular dynamics simulation is run using the <a class="reference internal" href="run.html"><span class="doc">run</span></a>
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command. Energy minimization (molecular statics) is performed using
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the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command. A parallel tempering
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(replica-exchange) simulation can be run using the
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<a class="reference internal" href="temper.html"><span class="doc">temper</span></a> command.</p>
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</section>
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