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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1 current"><a class="reference internal" href="Intro.html">1. Introduction</a><ul class="current">
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<li class="toctree-l2 current"><a class="current reference internal" href="#">1.3. LAMMPS features</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#interatomic-potentials-force-fields">1.3.3. Interatomic potentials (force fields)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.3.5. Ensembles, constraints, and boundary conditions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.3.7. Diagnostics</a></li>
<li class="toctree-l3"><a class="reference internal" href="#output">1.3.8. Output</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="Library.html">1. LAMMPS Library Interfaces</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="lammps-features">
<h1><span class="section-number">1.3. </span>LAMMPS features<a class="headerlink" href="#lammps-features" title="Link to this heading"></a></h1>
<p>LAMMPS is a classical molecular dynamics (MD) code with these general
classes of functionality:</p>
<ol class="arabic simple">
<li><p><a class="reference internal" href="#general"><span class="std std-ref">General features</span></a></p></li>
<li><p><a class="reference internal" href="#particle"><span class="std std-ref">Particle and model types</span></a></p></li>
<li><p><a class="reference internal" href="#ff"><span class="std std-ref">Interatomic potentials (force fields)</span></a></p></li>
<li><p><a class="reference internal" href="#create"><span class="std std-ref">Atom creation</span></a></p></li>
<li><p><a class="reference internal" href="#ensemble"><span class="std std-ref">Ensembles, constraints, and boundary conditions</span></a></p></li>
<li><p><a class="reference internal" href="#integrate"><span class="std std-ref">Integrators</span></a></p></li>
<li><p><a class="reference internal" href="#diag"><span class="std std-ref">Diagnostics</span></a></p></li>
<li><p><a class="reference internal" href="#output"><span class="std std-ref">Output</span></a></p></li>
<li><p><a class="reference internal" href="#replica1"><span class="std std-ref">Multi-replica models</span></a></p></li>
<li><p><a class="reference internal" href="#prepost"><span class="std std-ref">Pre- and post-processing</span></a></p></li>
<li><p><a class="reference internal" href="#special"><span class="std std-ref">Specialized features (beyond MD itself)</span></a></p></li>
</ol>
<hr class="docutils" />
<section id="general-features">
<span id="general"></span><h2><span class="section-number">1.3.1. </span>General features<a class="headerlink" href="#general-features" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p>runs on a single processor or in parallel</p></li>
<li><p>distributed memory message-passing parallelism (MPI)</p></li>
<li><p>shared memory multi-threading parallelism (OpenMP)</p></li>
<li><p>spatial decomposition of simulation domain for MPI parallelism</p></li>
<li><p>particle decomposition inside spatial decomposition for OpenMP and GPU parallelism</p></li>
<li><p>GPLv2 licensed open-source distribution</p></li>
<li><p>highly portable C++-11 (optional packages may require C++17)</p></li>
<li><p>modular code with most functionality in optional packages</p></li>
<li><p>only depends on MPI library for basic parallel functionality, MPI stub for serial compilation</p></li>
<li><p>other libraries are optional and only required for specific packages</p></li>
<li><p>GPU (CUDA, OpenCL, HIP, SYCL), Intel Xeon Phi, and OpenMP support for many code features</p></li>
<li><p>easy to extend with new features and functionality</p></li>
<li><p>runs from an input script</p></li>
<li><p>syntax for defining and using variables and formulas</p></li>
<li><p>syntax for looping over runs and breaking out of loops</p></li>
<li><p>run one or multiple simulations simultaneously (in parallel) from one script</p></li>
<li><p>build as library, invoke LAMMPS through library interface (from C, C++, Fortran) or provided Python wrapper or SWIG based wrappers</p></li>
<li><p>couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both, MDI coupling interface</p></li>
<li><p>call out to Python for computing forces, time integration, or other tasks</p></li>
<li><p>plugin interface for loading external features at runtime</p></li>
<li><p>large integrated collection of tests</p></li>
</ul>
</section>
<section id="particle-and-model-types">
<span id="particle"></span><h2><span class="section-number">1.3.2. </span>Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Link to this heading"></a></h2>
<p>(See <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> command)</p>
<ul class="simple">
<li><p>atoms</p></li>
<li><p>coarse-grained particles (e.g. bead-spring polymers)</p></li>
<li><p>united-atom polymers or organic molecules</p></li>
<li><p>all-atom polymers, organic molecules, proteins, DNA</p></li>
<li><p>metals</p></li>
<li><p>metal oxides</p></li>
<li><p>granular materials</p></li>
<li><p>coarse-grained mesoscale models</p></li>
<li><p>finite-size spherical and ellipsoidal particles</p></li>
<li><p>finite-size line segment (2d) and triangle (3d) particles</p></li>
<li><p>finite-size rounded polygons (2d) and polyhedra (3d) particles</p></li>
<li><p>point dipole particles</p></li>
<li><p>particles with magnetic spin</p></li>
<li><p>rigid collections of n particles</p></li>
<li><p>hybrid combinations of these</p></li>
</ul>
</section>
<section id="interatomic-potentials-force-fields">
<span id="ff"></span><h2><span class="section-number">1.3.3. </span>Interatomic potentials (force fields)<a class="headerlink" href="#interatomic-potentials-force-fields" title="Link to this heading"></a></h2>
<p>(See <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>,
<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>,
<a class="reference internal" href="improper_style.html"><span class="doc">improper style</span></a>, <a class="reference internal" href="kspace_style.html"><span class="doc">kspace style</span></a>
commands)</p>
<ul class="simple">
<li><p>pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted</p></li>
<li><p>charged pairwise potentials: Coulombic, point-dipole</p></li>
<li><p>many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta</p></li>
<li><p>machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP</p></li>
<li><p>interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP</p></li>
<li><p>long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS</p></li>
<li><p>polarization models: <a class="reference internal" href="fix_qeq.html"><span class="doc">QEq</span></a>, <a class="reference internal" href="Howto_coreshell.html"><span class="doc">core/shell model</span></a>, <a class="reference internal" href="Howto_drude.html"><span class="doc">Drude dipole model</span></a></p></li>
<li><p>charge equilibration (QEq via dynamic, point, shielded, Slater methods)</p></li>
<li><p>coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO, oxDNA / oxRNA, SPICA</p></li>
<li><p>mesoscopic potentials: granular, Peridynamics, SPH, mesoscopic tubular potential (MESONT)</p></li>
<li><p>semi-empirical potentials: multi-ion generalized pseudopotential theory (MGPT), second moment tight binding + QEq (SMTB-Q)</p></li>
<li><p>electron force field (eFF, AWPMD)</p></li>
<li><p>bond potentials: harmonic, FENE, Morse, nonlinear, Class II (COMPASS), quartic (breakable), tabulated, scripted</p></li>
<li><p>angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, Class II (COMPASS), tabulated, scripted</p></li>
<li><p>dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, Class II (COMPASS), OPLS, tabulated, scripted</p></li>
<li><p>improper potentials: harmonic, cvff, umbrella, Class II (COMPASS), tabulated</p></li>
<li><p>polymer potentials: all-atom, united-atom, bead-spring, breakable</p></li>
<li><p>water potentials: TIP3P, TIP4P, SPC, SPC/E and variants</p></li>
<li><p>interlayer potentials for graphene and analogues, hetero-junctions</p></li>
<li><p>metal-organic framework potentials (QuickFF, MO-FF)</p></li>
<li><p>implicit solvent potentials: hydrodynamic lubrication, Debye</p></li>
<li><p>force-field compatibility with CHARMM, AMBER, DREIDING, OPLS, GROMACS, Class II (COMPASS), UFF, ClayFF, DREIDING, AMOEBA, INTERFACE</p></li>
<li><p>access to the <a class="reference external" href="https://openkim.org">OpenKIM Repository</a> of potentials via the <a class="reference internal" href="kim_commands.html"><span class="doc">kim command</span></a></p></li>
<li><p>hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation</p></li>
<li><p>overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor</p></li>
</ul>
</section>
<section id="atom-creation">
<span id="create"></span><h2><span class="section-number">1.3.4. </span>Atom creation<a class="headerlink" href="#atom-creation" title="Link to this heading"></a></h2>
<p>(See <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>,
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a>,
<a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a>, <a class="reference internal" href="replicate.html"><span class="doc">replicate</span></a> commands)</p>
<ul class="simple">
<li><p>read in atom coordinates from files</p></li>
<li><p>create atoms on one or more lattices (e.g. grain boundaries)</p></li>
<li><p>delete geometric or logical groups of atoms (e.g. voids)</p></li>
<li><p>replicate existing atoms multiple times</p></li>
<li><p>displace atoms</p></li>
</ul>
</section>
<section id="ensembles-constraints-and-boundary-conditions">
<span id="ensemble"></span><h2><span class="section-number">1.3.5. </span>Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Link to this heading"></a></h2>
<p>(See <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command)</p>
<ul class="simple">
<li><p>2d or 3d systems</p></li>
<li><p>orthogonal or non-orthogonal (triclinic symmetry) simulation domains</p></li>
<li><p>constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators</p></li>
<li><p>thermostatting options for groups and geometric regions of atoms</p></li>
<li><p>pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions</p></li>
<li><p>simulation box deformation (tensile and shear)</p></li>
<li><p>harmonic (umbrella) constraint forces</p></li>
<li><p>rigid body constraints</p></li>
<li><p>SHAKE / RATTLE bond and angle constraints</p></li>
<li><p>motion constraints to manifold surfaces</p></li>
<li><p>Monte Carlo bond breaking, formation, swapping, template based reaction modeling</p></li>
<li><p>atom/molecule insertion and deletion</p></li>
<li><p>walls of various kinds, static and moving</p></li>
<li><p>non-equilibrium molecular dynamics (NEMD)</p></li>
<li><p>variety of additional boundary conditions and constraints</p></li>
</ul>
</section>
<section id="integrators">
<span id="integrate"></span><h2><span class="section-number">1.3.6. </span>Integrators<a class="headerlink" href="#integrators" title="Link to this heading"></a></h2>
<p>(See <a class="reference internal" href="run.html"><span class="doc">run</span></a>, <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>, <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> commands)</p>
<ul class="simple">
<li><p>velocity-Verlet integrator</p></li>
<li><p>Brownian dynamics</p></li>
<li><p>rigid body integration</p></li>
<li><p>energy minimization via conjugate gradient, steepest descent relaxation, or damped dynamics (FIRE, Quickmin)</p></li>
<li><p>rRESPA hierarchical timestepping</p></li>
<li><p>fixed or adaptive time step</p></li>
<li><p>rerun command for post-processing of dump files</p></li>
</ul>
</section>
<section id="diagnostics">
<span id="diag"></span><h2><span class="section-number">1.3.7. </span>Diagnostics<a class="headerlink" href="#diagnostics" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p>see various flavors of the <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> and <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> commands</p></li>
<li><p>introspection command for system, simulation, and compile time settings and configurations</p></li>
</ul>
</section>
<section id="output">
<span id="id1"></span><h2><span class="section-number">1.3.8. </span>Output<a class="headerlink" href="#output" title="Link to this heading"></a></h2>
<p>(<a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> commands)</p>
<ul class="simple">
<li><p>log file of thermodynamic info</p></li>
<li><p>text dump files of atom coordinates, velocities, other per-atom quantities</p></li>
<li><p>dump output on fixed and variable intervals, based timestep or simulated time</p></li>
<li><p>binary restart files</p></li>
<li><p>parallel I/O of dump and restart files</p></li>
<li><p>per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc.)</p></li>
<li><p>user-defined system-wide (log file) or per-atom (dump file) calculations</p></li>
<li><p>custom partitioning (chunks) for binning, and static or dynamic grouping of atoms for analysis</p></li>
<li><p>spatial, time, and per-chunk averaging of per-atom quantities</p></li>
<li><p>time averaging and histogramming of system-wide quantities</p></li>
<li><p>atom snapshots in native, XYZ, XTC, DCD, CFG, NetCDF, HDF5, ADIOS2, YAML formats</p></li>
<li><p>on-the-fly compression of output and decompression of read in files</p></li>
</ul>
</section>
<section id="multi-replica-models">
<span id="replica1"></span><h2><span class="section-number">1.3.9. </span>Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="neb.html"><span class="doc">nudged elastic band</span></a></p></li>
<li><p><a class="reference internal" href="hyper.html"><span class="doc">hyperdynamics</span></a></p></li>
<li><p><a class="reference internal" href="prd.html"><span class="doc">parallel replica dynamics</span></a></p></li>
<li><p><a class="reference internal" href="tad.html"><span class="doc">temperature accelerated dynamics</span></a></p></li>
<li><p><a class="reference internal" href="temper.html"><span class="doc">parallel tempering</span></a></p></li>
<li><p>path-integral MD: <a class="reference internal" href="fix_pimd.html"><span class="doc">first variant</span></a>, <a class="reference internal" href="fix_ipi.html"><span class="doc">second variant</span></a></p></li>
<li><p>multi-walker collective variables with <a class="reference internal" href="fix_colvars.html"><span class="doc">Colvars</span></a> and <a class="reference internal" href="fix_plumed.html"><span class="doc">Plumed</span></a></p></li>
</ul>
</section>
<section id="pre-and-post-processing">
<span id="prepost"></span><h2><span class="section-number">1.3.10. </span>Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p>A handful of pre- and post-processing tools are packaged with LAMMPS,
some of which can convert input and output files to/from formats used
by other codes; see the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> page.</p></li>
<li><p>Our group has also written and released a separate toolkit called
<a class="reference external" href="https://lammps.github.io/pizza">Pizza.py</a> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in <a class="reference external" href="https://www.python.org">Python</a> and is available for download from <a class="reference external" href="https://lammps.github.io/pizza">the Pizza.py WWW site</a>.</p></li>
</ul>
</section>
<section id="specialized-features">
<span id="special"></span><h2><span class="section-number">1.3.11. </span>Specialized features<a class="headerlink" href="#specialized-features" title="Link to this heading"></a></h2>
<p>LAMMPS can be built with optional packages which implement a variety of
additional capabilities. See the <a class="reference internal" href="Packages.html"><span class="doc">Optional Packages</span></a>
page for details.</p>
<p>These are LAMMPS capabilities which you may not think of as typical
classical MD options:</p>
<ul class="simple">
<li><p><a class="reference internal" href="balance.html"><span class="doc">static</span></a> and <a class="reference internal" href="fix_balance.html"><span class="doc">dynamic load-balancing</span></a>, optional with recursive bisectioning decomposition</p></li>
<li><p><a class="reference internal" href="Howto_body.html"><span class="doc">generalized aspherical particles</span></a></p></li>
<li><p><a class="reference internal" href="fix_srd.html"><span class="doc">stochastic rotation dynamics (SRD)</span></a></p></li>
<li><p><a class="reference internal" href="fix_imd.html"><span class="doc">real-time visualization and interactive MD</span></a>, <a class="reference internal" href="dump_image.html"><span class="doc">built-in renderer for images and movies</span></a></p></li>
<li><p>calculate <a class="reference internal" href="compute_xrd.html"><span class="doc">virtual diffraction patterns</span></a></p></li>
<li><p>calculate <a class="reference internal" href="fix_phonon.html"><span class="doc">finite temperature phonon dispersion</span></a> and the <a class="reference internal" href="dynamical_matrix.html"><span class="doc">dynamical matrix of minimized structures</span></a></p></li>
<li><p><a class="reference internal" href="fix_atc.html"><span class="doc">atom-to-continuum coupling</span></a> with finite elements</p></li>
<li><p>coupled rigid body integration via the <a class="reference internal" href="fix_poems.html"><span class="doc">POEMS</span></a> library</p></li>
<li><p><a class="reference internal" href="fix_qmmm.html"><span class="doc">QM/MM coupling</span></a></p></li>
<li><p>Monte Carlo via <a class="reference internal" href="fix_gcmc.html"><span class="doc">GCMC</span></a> and <a class="reference internal" href="fix_tfmc.html"><span class="doc">tfMC</span></a> and <a class="reference internal" href="fix_atom_swap.html"><span class="doc">atom swapping</span></a></p></li>
<li><p><a class="reference internal" href="fix_ipi.html"><span class="doc">path-integral molecular dynamics (PIMD)</span></a> and <a class="reference internal" href="fix_pimd.html"><span class="doc">this as well</span></a></p></li>
<li><p><a class="reference internal" href="pair_dsmc.html"><span class="doc">Direct Simulation Monte Carlo</span></a> for low-density fluids</p></li>
<li><p><a class="reference internal" href="pair_peri.html"><span class="doc">Peridynamics modeling</span></a></p></li>
<li><p><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">Lattice Boltzmann fluid</span></a></p></li>
<li><p><a class="reference internal" href="fix_tmd.html"><span class="doc">targeted</span></a> and <a class="reference internal" href="fix_smd.html"><span class="doc">steered</span></a> molecular dynamics</p></li>
<li><p><a class="reference internal" href="fix_ttm.html"><span class="doc">two-temperature electron model</span></a></p></li>
</ul>
</section>
</section>
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