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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"><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"><a class="reference internal" href="Commands.html">5. Commands</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 current"><a class="current reference internal" href="#">8. Howto discussions</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#general-howto">8.1. General howto</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Howto_restart.html">8.1.1. Restart a simulation</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_viz.html">8.1.2. Visualize LAMMPS snapshots</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_multiple.html">8.1.3. Run multiple simulations from one input script</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_replica.html">8.1.4. Multi-replica simulations</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_library.html">8.1.5. Library interface to LAMMPS</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_couple.html">8.1.6. Coupling LAMMPS to other codes</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_mdi.html">8.1.7. Using LAMMPS with the MDI library for code coupling</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_broken_bonds.html">8.1.8. Broken Bonds</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#settings-howto">8.2. Settings howto</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Howto_2d.html">8.2.1. 2d simulations</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_type_labels.html">8.2.2. Type labels</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_triclinic.html">8.2.3. Triclinic (non-orthogonal) simulation boxes</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_thermostat.html">8.2.4. Thermostats</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_barostat.html">8.2.5. Barostats</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_walls.html">8.2.6. Walls</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_nemd.html">8.2.7. NEMD simulations</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_dispersion.html">8.2.8. Long-range dispersion settings</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#analysis-howto">8.3. Analysis howto</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Howto_output.html">8.3.1. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_chunk.html">8.3.2. Use chunks to calculate system properties</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_grid.html">8.3.3. Using distributed grids</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_temperature.html">8.3.4. Calculate temperature</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_elastic.html">8.3.5. Calculate elastic constants</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_kappa.html">8.3.6. Calculate thermal conductivity</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_viscosity.html">8.3.7. Calculate viscosity</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_diffusion.html">8.3.8. Calculate diffusion coefficients</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_structured_data.html">8.3.9. Output structured data from LAMMPS</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#force-fields-howto">8.4. Force fields howto</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Howto_bioFF.html">8.4.1. CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_amoeba.html">8.4.2. AMOEBA and HIPPO force fields</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_tip3p.html">8.4.3. TIP3P water model</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_tip4p.html">8.4.4. TIP4P water model</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_tip5p.html">8.4.5. TIP5P water model</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_spc.html">8.4.6. SPC water model</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#packages-howto">8.5. Packages howto</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Howto_spherical.html">8.5.1. Finite-size spherical and aspherical particles</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_granular.html">8.5.2. Granular models</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_body.html">8.5.3. Body particles</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_bpm.html">8.5.4. Bonded particle models</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_polarizable.html">8.5.5. Polarizable models</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_coreshell.html">8.5.6. Adiabatic core/shell model</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_drude.html">8.5.7. Drude induced dipoles</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_drude2.html">8.5.8. Tutorial for Thermalized Drude oscillators in LAMMPS</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_peri.html">8.5.9. Peridynamics with LAMMPS</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_manifold.html">8.5.10. Manifolds (surfaces)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_rheo.html">8.5.11. Reproducing hydrodynamics and elastic objects (RHEO)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_spins.html">8.5.12. Magnetic spins</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#tutorials-howto">8.6. Tutorials howto</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Howto_cmake.html">8.6.1. Using CMake with LAMMPS</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_github.html">8.6.2. LAMMPS GitHub tutorial</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_lammps_gui.html">8.6.3. Using LAMMPS-GUI</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_moltemplate.html">8.6.4. Moltemplate Tutorial</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_pylammps.html">8.6.5. PyLammps Tutorial</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_wsl.html">8.6.6. Using LAMMPS on Windows 10 with WSL</a></li>
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</ul>
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</li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</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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</ul>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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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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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
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<li class="breadcrumb-item active"><span class="section-number">8. </span>Howto discussions</li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="howto-discussions">
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<h1><span class="section-number">8. </span>Howto discussions<a class="headerlink" href="#howto-discussions" title="Link to this heading"></a></h1>
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<p>These doc pages describe how to perform various tasks with LAMMPS,
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both for users and developers. The
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<a class="reference external" href="https://www.lammps.org/glossary.html">glossary</a> website page also lists MD
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terminology, with links to corresponding LAMMPS manual pages. The
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example input scripts included in the <code class="docutils literal notranslate"><span class="pre">examples</span></code> directory of the LAMMPS
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source code distribution and highlighted on the <a class="reference internal" href="Examples.html"><span class="doc">Example scripts</span></a> page
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also show how to set up and run various kinds of simulations.</p>
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<section id="general-howto">
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<h2><span class="section-number">8.1. </span>General howto<a class="headerlink" href="#general-howto" title="Link to this heading"></a></h2>
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<div class="toctree-wrapper compound" id="id1">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Howto_restart.html">8.1.1. Restart a simulation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_viz.html">8.1.2. Visualize LAMMPS snapshots</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_multiple.html">8.1.3. Run multiple simulations from one input script</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_replica.html">8.1.4. Multi-replica simulations</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_library.html">8.1.5. Library interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_couple.html">8.1.6. Coupling LAMMPS to other codes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_mdi.html">8.1.7. Using LAMMPS with the MDI library for code coupling</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_broken_bonds.html">8.1.8. Broken Bonds</a></li>
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</ul>
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</div>
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</section>
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<section id="settings-howto">
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<h2><span class="section-number">8.2. </span>Settings howto<a class="headerlink" href="#settings-howto" title="Link to this heading"></a></h2>
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<div class="toctree-wrapper compound" id="id2">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Howto_2d.html">8.2.1. 2d simulations</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_type_labels.html">8.2.2. Type labels</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_triclinic.html">8.2.3. Triclinic (non-orthogonal) simulation boxes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_thermostat.html">8.2.4. Thermostats</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_barostat.html">8.2.5. Barostats</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_walls.html">8.2.6. Walls</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_nemd.html">8.2.7. NEMD simulations</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_dispersion.html">8.2.8. Long-range dispersion settings</a></li>
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</ul>
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</div>
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</section>
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<section id="analysis-howto">
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<h2><span class="section-number">8.3. </span>Analysis howto<a class="headerlink" href="#analysis-howto" title="Link to this heading"></a></h2>
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<div class="toctree-wrapper compound" id="id3">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Howto_output.html">8.3.1. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_chunk.html">8.3.2. Use chunks to calculate system properties</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_grid.html">8.3.3. Using distributed grids</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_temperature.html">8.3.4. Calculate temperature</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_elastic.html">8.3.5. Calculate elastic constants</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_kappa.html">8.3.6. Calculate thermal conductivity</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_viscosity.html">8.3.7. Calculate viscosity</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_diffusion.html">8.3.8. Calculate diffusion coefficients</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_structured_data.html">8.3.9. Output structured data from LAMMPS</a></li>
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</ul>
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</div>
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</section>
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<section id="force-fields-howto">
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<h2><span class="section-number">8.4. </span>Force fields howto<a class="headerlink" href="#force-fields-howto" title="Link to this heading"></a></h2>
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<div class="toctree-wrapper compound" id="force-howto">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Howto_bioFF.html">8.4.1. CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_amoeba.html">8.4.2. AMOEBA and HIPPO force fields</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_tip3p.html">8.4.3. TIP3P water model</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_tip4p.html">8.4.4. TIP4P water model</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_tip5p.html">8.4.5. TIP5P water model</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_spc.html">8.4.6. SPC water model</a></li>
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</ul>
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</div>
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</section>
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<section id="packages-howto">
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<h2><span class="section-number">8.5. </span>Packages howto<a class="headerlink" href="#packages-howto" title="Link to this heading"></a></h2>
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<div class="toctree-wrapper compound" id="id4">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Howto_spherical.html">8.5.1. Finite-size spherical and aspherical particles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_granular.html">8.5.2. Granular models</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_body.html">8.5.3. Body particles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_bpm.html">8.5.4. Bonded particle models</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_polarizable.html">8.5.5. Polarizable models</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_coreshell.html">8.5.6. Adiabatic core/shell model</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_drude.html">8.5.7. Drude induced dipoles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_drude2.html">8.5.8. Tutorial for Thermalized Drude oscillators in LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_peri.html">8.5.9. Peridynamics with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_manifold.html">8.5.10. Manifolds (surfaces)</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_rheo.html">8.5.11. Reproducing hydrodynamics and elastic objects (RHEO)</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_spins.html">8.5.12. Magnetic spins</a></li>
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</ul>
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</div>
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</section>
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<section id="tutorials-howto">
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<h2><span class="section-number">8.6. </span>Tutorials howto<a class="headerlink" href="#tutorials-howto" title="Link to this heading"></a></h2>
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<div class="toctree-wrapper compound" id="tutorials">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Howto_cmake.html">8.6.1. Using CMake with LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Howto_github.html">8.6.2. LAMMPS GitHub tutorial</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_lammps_gui.html">8.6.3. Using LAMMPS-GUI</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_moltemplate.html">8.6.4. Moltemplate Tutorial</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_pylammps.html">8.6.5. PyLammps Tutorial</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto_wsl.html">8.6.6. Using LAMMPS on Windows 10 with WSL</a></li>
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</ul>
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</div>
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