762 lines
54 KiB
HTML
762 lines
54 KiB
HTML
<!DOCTYPE html>
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<html class="writer-html5" lang="en" >
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<head>
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<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>atom_style command — LAMMPS documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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<link rel="stylesheet" href="_static/css/lammps.css" type="text/css" />
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<link rel="shortcut icon" href="_static/lammps.ico"/>
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<link rel="canonical" href="https://docs.lammps.org/atom_style.html" />
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<script src="_static/js/html5shiv.min.js"></script>
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<![endif]-->
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<script src="_static/jquery.js?v=5d32c60e"></script>
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<script src="_static/js/theme.js"></script>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="next" title="balance command" href="balance.html" />
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<link rel="prev" title="atom_modify command" href="atom_modify.html" />
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</head>
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<body class="wy-body-for-nav">
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<div class="wy-grid-for-nav">
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<div class="wy-side-scroll">
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<div class="wy-side-nav-search" >
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<a href="Manual.html">
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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</a>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<div class="lammps_release">git info: </div>
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</div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<ul>
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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"><a class="reference internal" href="Howto.html">8. Howto discussions</a></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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<ul class="current">
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<li class="toctree-l1 current"><a class="reference internal" href="commands_list.html">Commands</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_write.html">angle_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">atom_style command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#atom-style-attributes">Atom style attributes</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#particle-size-and-mass">Particle size and mass</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#additional-information-about-specific-atom-styles">Additional information about specific atom styles</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</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="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_write.html">dihedral_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dynamical_matrix.html">dynamical_matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fitpod_command.html">fitpod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="geturl.html">geturl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="hyper.html">hyper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kim_commands.html">kim command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="labelmap.html">labelmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mdi.html">mdi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html">min_style spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-cg-command">min_style spin/cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-lbfgs-command">min_style spin/lbfgs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-hftn-command">min_style hftn command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-sd-command">min_style sd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-quickmin-command">min_style quickmin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-fire-command">min_style fire command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-command"><span class="xref std std-doc">min_style spin</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-cg-command"><span class="xref std std-doc">min_style spin/cg</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-lbfgs-command"><span class="xref std std-doc">min_style spin/lbfgs</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb_spin.html">neb/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="plugin.html">plugin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_atoms.html">reset_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper_grem.html">temper/grem command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper_npt.html">temper/npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="third_order.html">third_order command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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</ul>
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</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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</ul>
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</div>
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</div>
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</nav>
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<li class="breadcrumb-item active">atom_style command</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="atom-style-command">
|
||
<span id="index-0"></span><h1>atom_style command<a class="headerlink" href="#atom-style-command" title="Link to this heading"></a></h1>
|
||
<section id="syntax">
|
||
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">atom_style</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">args</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>style = <em>amoeba</em> or <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dielectric</em> or <em>dipole</em> or <em>dpd</em> or <em>edpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>mdpd</em> or <em>molecular</em> or <em>oxdna</em> or <em>peri</em> or <em>smd</em> or <em>sph</em> or <em>sphere</em> or <em>bpm/sphere</em> or <em>spin</em> or <em>tdpd</em> or <em>tri</em> or <em>template</em> or <em>wavepacket</em> or <em>hybrid</em></p>
|
||
<pre class="literal-block">args = none for any style except the following
|
||
<em>body</em> args = bstyle bstyle-args
|
||
bstyle = style of body particles
|
||
bstyle-args = additional arguments specific to the bstyle
|
||
see the <a class="reference internal" href="Howto_body.html"><span class="doc">Howto body</span></a> doc
|
||
page for details
|
||
<em>sphere</em> arg = 0/1 (optional) for static/dynamic particle radii
|
||
<em>bpm/sphere</em> arg = 0/1 (optional) for static/dynamic particle radii
|
||
<em>tdpd</em> arg = Nspecies
|
||
Nspecies = # of chemical species
|
||
<em>template</em> arg = template-ID
|
||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
|
||
<em>hybrid</em> args = list of one or more sub-styles, each with their args</pre>
|
||
</li>
|
||
<li><p>accelerated styles (with same args) = <em>angle/kk</em> or <em>atomic/kk</em> or <em>bond/kk</em> or <em>charge/kk</em> or <em>full/kk</em> or <em>molecular/kk</em> or <em>spin/kk</em></p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">atom_style</span><span class="w"> </span><span class="n">atomic</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">bond</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">full</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">body</span><span class="w"> </span><span class="n">nparticle</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">10</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">hybrid</span><span class="w"> </span><span class="n">charge</span><span class="w"> </span><span class="n">bond</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">hybrid</span><span class="w"> </span><span class="n">charge</span><span class="w"> </span><span class="n">body</span><span class="w"> </span><span class="n">nparticle</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">5</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">spin</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">template</span><span class="w"> </span><span class="n">myMols</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">hybrid</span><span class="w"> </span><span class="n">template</span><span class="w"> </span><span class="n">twomols</span><span class="w"> </span><span class="n">charge</span>
|
||
<span class="k">atom_style</span><span class="w"> </span><span class="n">tdpd</span><span class="w"> </span><span class="m">2</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>The <em>atom_style</em> command selects which per-atom attributes are
|
||
associated with atoms in a LAMMPS simulation and thus stored and
|
||
communicated with those atoms as well as read from and stored in data
|
||
and restart files. Different models (e.g. <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a>) require access to specific per-atom attributes and thus
|
||
require a specific atom style. For example, to compute Coulomb
|
||
interactions, the atom must have a “charge” (aka “q”) attribute.</p>
|
||
<p>A number of distinct atom styles exist that combine attributes. Some
|
||
atom styles are a superset of other atom styles. Further attributes
|
||
may be added to atoms either via using a hybrid style which provides a
|
||
union of the attributes of the sub-styles, or via the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix
|
||
property/atom</span></a> command. The <em>atom_style</em> command
|
||
must be used before a simulation is setup via a <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Many of the atom styles discussed here are only enabled if LAMMPS was
|
||
built with a specific package, as listed below in the Restrictions
|
||
section.</p>
|
||
</div>
|
||
<p>Once a style is selected and the simulation box defined, it cannot be
|
||
changed but only augmented with the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command. So one should select an atom style
|
||
general enough to encompass all attributes required. E.g. with atom
|
||
style <em>bond</em>, it is not possible to define angles and use angle styles.</p>
|
||
<p>It is OK to use a style more general than needed, though it may be
|
||
slightly inefficient because it will allocate and communicate
|
||
additional unused data.</p>
|
||
</section>
|
||
<section id="atom-style-attributes">
|
||
<h2>Atom style attributes<a class="headerlink" href="#atom-style-attributes" title="Link to this heading"></a></h2>
|
||
<p>The atom style <em>atomic</em> has the minimum subset of per-atom attributes
|
||
and is also the default setting. It encompasses the following per-atom
|
||
attributes (name of the vector or array in the <a class="reference internal" href="Classes_atom.html"><span class="doc">Atom class</span></a> is given in parenthesis): atom-ID (tag), type (type),
|
||
position (x), velocities (v), forces (f), image flags (image), group
|
||
membership (mask). Since all atom styles are a superset of atom style
|
||
<em>atomic</em>, they all include these attributes.</p>
|
||
<p>This table lists all the available atom styles, which attributes they
|
||
provide, which <a class="reference internal" href="Packages.html"><span class="doc">package</span></a> is required to use them, and
|
||
what the typical applications are that use them. See the
|
||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, and
|
||
<a class="reference internal" href="set.html"><span class="doc">set</span></a> commands for details on how to set these various
|
||
quantities. More information about many of the styles is provided in
|
||
the Additional Information section below.</p>
|
||
<table class="docutils align-default">
|
||
<colgroup>
|
||
<col style="width: 13.3%" />
|
||
<col style="width: 31.1%" />
|
||
<col style="width: 20.0%" />
|
||
<col style="width: 35.6%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="row-odd"><th class="head"><p>Atom style</p></th>
|
||
<th class="head"><p>Attributes</p></th>
|
||
<th class="head"><p>Required package</p></th>
|
||
<th class="head"><p>Applications</p></th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="row-even"><td><p><em>amoeba</em></p></td>
|
||
<td><p><em>full</em> + “1-5 special neighbor data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-amoeba"><span class="std std-ref">AMOEBA</span></a></p></td>
|
||
<td><p>AMOEBA/HIPPO force fields</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>angle</em></p></td>
|
||
<td><p><em>bond</em> + “angle data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-molecule"><span class="std std-ref">MOLECULE</span></a></p></td>
|
||
<td><p>bead-spring polymers with stiffness</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>atomic</em></p></td>
|
||
<td><p>tag, type, x, v, f, image, mask</p></td>
|
||
<td></td>
|
||
<td><p>atomic liquids, solids, metals</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>body</em></p></td>
|
||
<td><p><em>atomic</em> + radius, rmass, angmom, torque, body</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-body"><span class="std std-ref">BODY</span></a></p></td>
|
||
<td><p>arbitrary bodies, see <a class="reference internal" href="Howto_body.html"><span class="doc">body howto</span></a></p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>bond</em></p></td>
|
||
<td><p><em>atomic</em> + molecule, nspecial, special + “bond data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-molecule"><span class="std std-ref">MOLECULE</span></a></p></td>
|
||
<td><p>bead-spring polymers</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>bpm/sphere</em></p></td>
|
||
<td><p><em>bond</em> + radius, rmass, omega, torque, quat</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-bpm"><span class="std std-ref">BPM</span></a></p></td>
|
||
<td><p>granular bonded particle models, see <a class="reference internal" href="Howto_bpm.html"><span class="doc">BPM howto</span></a></p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>charge</em></p></td>
|
||
<td><p><em>atomic</em> + q</p></td>
|
||
<td></td>
|
||
<td><p>atomic systems with charges</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>dielectric</em></p></td>
|
||
<td><p><em>full</em> + mu, area, ed, em, epsilon, curvature, q_scaled</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-dielectric"><span class="std std-ref">DIELECTRIC</span></a></p></td>
|
||
<td><p>systems with surface polarization</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>dipole</em></p></td>
|
||
<td><p><em>charge</em> + mu</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-dipole"><span class="std std-ref">DIPOLE</span></a></p></td>
|
||
<td><p>atomic systems with charges and point dipoles</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>dpd</em></p></td>
|
||
<td><p><em>atomic</em> + rho + “reactive DPD data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-dpd-react"><span class="std std-ref">DPD-REACT</span></a></p></td>
|
||
<td><p>reactive DPD</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>edpd</em></p></td>
|
||
<td><p><em>atomic</em> + “eDPD data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-dpd-meso"><span class="std std-ref">DPD-MESO</span></a></p></td>
|
||
<td><p>Energy conservative DPD (eDPD)</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>electron</em></p></td>
|
||
<td><p><em>charge</em> + espin, eradius, ervel, erforce</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-eff"><span class="std std-ref">EFF</span></a></p></td>
|
||
<td><p>Electron force field systems</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>ellipsoid</em></p></td>
|
||
<td><p><em>atomic</em> + rmass, angmom, torque, ellipsoid</p></td>
|
||
<td></td>
|
||
<td><p>aspherical particles</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>full</em></p></td>
|
||
<td><p><em>molecular</em> + q</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-molecule"><span class="std std-ref">MOLECULE</span></a></p></td>
|
||
<td><p>molecular force fields</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>line</em></p></td>
|
||
<td><p><em>atomic</em> + molecule, radius, rmass, omega, torque, line</p></td>
|
||
<td></td>
|
||
<td><p>2-d rigid body particles</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>mdpd</em></p></td>
|
||
<td><p><em>atomic</em> + rho, drho, vest</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-dpd-meso"><span class="std std-ref">DPD-MESO</span></a></p></td>
|
||
<td><p>Many-body DPD (mDPD)</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>molecular</em></p></td>
|
||
<td><p><em>angle</em> + “dihedral and improper data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-molecule"><span class="std std-ref">MOLECULE</span></a></p></td>
|
||
<td><p>apolar and uncharged molecules</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>oxdna</em></p></td>
|
||
<td><p><em>atomic</em> + id5p</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-cg-dna"><span class="std std-ref">CG-DNA</span></a></p></td>
|
||
<td><p>coarse-grained DNA and RNA models</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>peri</em></p></td>
|
||
<td><p><em>atomic</em> + rmass, vfrac, s0, x0</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-peri"><span class="std std-ref">PERI</span></a></p></td>
|
||
<td><p>mesoscopic Peridynamics models</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>smd</em></p></td>
|
||
<td><p><em>atomic</em> + molecule, radius, rmass + “smd data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-machdyn"><span class="std std-ref">MACHDYN</span></a></p></td>
|
||
<td><p>Smooth Mach Dynamics models</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>rheo</em></p></td>
|
||
<td><p><em>atomic</em> + rho, status</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-rheo"><span class="std std-ref">RHEO</span></a></p></td>
|
||
<td><p>solid and fluid RHEO particles</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>rheo/thermal</em></p></td>
|
||
<td><p><em>atomic</em> + rho, status, energy, temperature</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-rheo"><span class="std std-ref">RHEO</span></a></p></td>
|
||
<td><p>RHEO particles with temperature</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>sph</em></p></td>
|
||
<td><p><em>atomic</em> + “sph data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-sph"><span class="std std-ref">SPH</span></a></p></td>
|
||
<td><p>Smoothed particle hydrodynamics models</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>sphere</em></p></td>
|
||
<td><p><em>atomic</em> + radius, rmass, omega, torque</p></td>
|
||
<td></td>
|
||
<td><p>finite size spherical particles, e.g. granular models</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>spin</em></p></td>
|
||
<td><p><em>atomic</em> + “magnetic moment data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-spin"><span class="std std-ref">SPIN</span></a></p></td>
|
||
<td><p>magnetic particles</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>tdpd</em></p></td>
|
||
<td><p><em>atomic</em> + cc, cc_flux, vest</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-dpd-meso"><span class="std std-ref">DPD-MESO</span></a></p></td>
|
||
<td><p>Transport DPD (tDPD)</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>template</em></p></td>
|
||
<td><p><em>atomic</em> + molecule, molindex, molatom</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-molecule"><span class="std std-ref">MOLECULE</span></a></p></td>
|
||
<td><p>molecular systems where attributes are taken from <a class="reference internal" href="molecule.html"><span class="doc">molecule files</span></a></p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><em>tri</em></p></td>
|
||
<td><p><em>sphere</em> + molecule, angmom, tri</p></td>
|
||
<td></td>
|
||
<td><p>3-d triangulated rigid body LJ particles</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><em>wavepacket</em></p></td>
|
||
<td><p><em>charge</em> + “wavepacket data”</p></td>
|
||
<td><p><a class="reference internal" href="Packages_details.html#pkg-awpmd"><span class="std std-ref">AWPMD</span></a></p></td>
|
||
<td><p>Antisymmetrized wave packet MD</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>It is possible to add some attributes, such as a molecule ID and
|
||
charge, to atom styles that do not have them built in using the
|
||
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command. This command
|
||
also allows new custom-named attributes consisting of extra integer
|
||
or floating-point values or vectors to be added to atoms. See the
|
||
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> page for examples of
|
||
cases where this is useful and details on how to initialize,
|
||
access, and output these custom values.</p>
|
||
</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="particle-size-and-mass">
|
||
<h2>Particle size and mass<a class="headerlink" href="#particle-size-and-mass" title="Link to this heading"></a></h2>
|
||
<p>All of the atom styles define point particles unless they (1) define
|
||
finite-size spherical particles via the <em>radius</em> attribute, or (2)
|
||
define finite-size aspherical particles (e.g. the <em>body</em>, <em>ellipsoid</em>,
|
||
<em>line</em>, and <em>tri</em> styles). Most of these styles can also be used with
|
||
mixtures of point and finite-size particles.</p>
|
||
<p>Note that the <em>radius</em> property may need to be provided as a
|
||
<em>diameter</em> (e.g. in <a class="reference internal" href="molecule.html"><span class="doc">molecule files</span></a> or <a class="reference internal" href="read_data.html"><span class="doc">data
|
||
files</span></a>). See the <a class="reference internal" href="Howto_spherical.html"><span class="doc">Howto spherical</span></a>
|
||
page for an overview of using finite-size spherical and aspherical
|
||
particle models with LAMMPS.</p>
|
||
<p>Unless an atom style defines the per-atom <em>rmass</em> attribute, particle
|
||
masses are defined on a per-type basis, using the <a class="reference internal" href="mass.html"><span class="doc">mass</span></a>
|
||
command. This means each particle’s mass is indexed by its atom
|
||
<em>type</em>.</p>
|
||
<p>A few styles define the per-atom <em>rmass</em> attribute which can also be
|
||
added using the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command.
|
||
In this case each particle stores its own mass. Atom styles that have
|
||
a per-atom rmass may define it indirectly through setting particle
|
||
diameter and density on a per-particle basis. If both per-type mass
|
||
and per-atom <em>rmass</em> are defined (e.g. in a hybrid style), the
|
||
per-atom mass will take precedence in any operation which which works
|
||
with both flavors of mass.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="additional-information-about-specific-atom-styles">
|
||
<h2>Additional information about specific atom styles<a class="headerlink" href="#additional-information-about-specific-atom-styles" title="Link to this heading"></a></h2>
|
||
<p>For the <em>body</em> style, the particles are arbitrary bodies with internal
|
||
attributes defined by the “style” of the bodies, which is specified by
|
||
the <em>bstyle</em> argument. Body particles can represent complex entities,
|
||
such as surface meshes of discrete points, collections of
|
||
sub-particles, deformable objects, etc.</p>
|
||
<p>The <a class="reference internal" href="Howto_body.html"><span class="doc">Howto body</span></a> page describes the body styles
|
||
LAMMPS currently supports, and provides more details as to the kind of
|
||
body particles they represent. For all styles, each body particle
|
||
stores moments of inertia and a quaternion 4-vector, so that its
|
||
orientation and position can be time integrated due to forces and
|
||
torques.</p>
|
||
<p>Note that there may be additional arguments required along with the
|
||
<em>bstyle</em> specification, in the atom_style body command. These
|
||
arguments are described on the <a class="reference internal" href="Howto_body.html"><span class="doc">Howto body</span></a> doc page.</p>
|
||
<p>For the <em>dielectric</em> style, each particle can be either a physical
|
||
particle (e.g. an ion), or an interface particle representing a
|
||
boundary element between two regions of different dielectric
|
||
constant. For interface particles, in addition to the properties
|
||
associated with atom_style full, each particle also should be assigned
|
||
a unit dipole vector (mu) representing the direction of the induced
|
||
dipole moment at each interface particle, an area (area/patch), the
|
||
difference and mean of the dielectric constants of two sides of the
|
||
interface along the direction of the normal vector (ed and em), the
|
||
local dielectric constant at the boundary element (epsilon), and a
|
||
mean local curvature (curv). Physical particles must be assigned
|
||
these values, as well, but only their local dielectric constants will
|
||
be used; see documentation for associated <a class="reference internal" href="pair_dielectric.html"><span class="doc">pair styles</span></a> and <a class="reference internal" href="fix_polarize.html"><span class="doc">fixes</span></a>. The distinction
|
||
between the physical and interface particles is only meaningful when
|
||
<a class="reference internal" href="fix_polarize.html"><span class="doc">fix polarize</span></a> commands are applied to the
|
||
interface particles. This style is part of the DIELECTRIC package.</p>
|
||
<p>For the <em>dipole</em> style, a point dipole vector mu is defined for each
|
||
point particle. Note that if you wish the particles to be finite-size
|
||
spheres as in a Stockmayer potential for a dipolar fluid, so that the
|
||
particles can rotate due to dipole-dipole interactions, then you need
|
||
to use the command <cite>atom_style hybrid sphere dipole</cite>, which will
|
||
assign both a diameter and dipole moment to each particle. This also
|
||
requires using an integrator with a “/sphere” suffix like <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix
|
||
nve/sphere</span></a> or <a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">fix nvt/sphere</span></a>
|
||
and the “update dipole” or “update dlm” parameters to the fix
|
||
commands.</p>
|
||
<p>The <em>dpd</em> style is for reactive dissipative particle dynamics (DPD)
|
||
particles. Note that it is part of the DPD-REACT package, and is not
|
||
required for use with the <a class="reference internal" href="pair_dpd.html"><span class="doc">pair_style dpd or dpd/stat</span></a>
|
||
commands, which only require the attributes from atom_style <em>atomic</em>.
|
||
Atom_style <em>dpd</em> extends DPD particle properties with internal
|
||
temperature (dpdTheta), internal conductive energy (uCond), internal
|
||
mechanical energy (uMech), and internal chemical energy (uChem).</p>
|
||
<p>The <em>edpd</em> style is for energy-conserving dissipative particle
|
||
dynamics (eDPD) particles which store a temperature (edpd_temp), and
|
||
heat capacity (edpd_cv).</p>
|
||
<p>For the <em>electron</em> style, the particles representing electrons are 3d
|
||
Gaussians with a specified position and bandwidth or uncertainty in
|
||
position, which is represented by the eradius = electron size.</p>
|
||
<p>For the <em>ellipsoid</em> style, particles can be ellipsoids which each
|
||
stores a shape vector with the 3 diameters of the ellipsoid and a
|
||
quaternion 4-vector with its orientation. Each particle stores a flag
|
||
in the ellipsoid vector which indicates whether it is an ellipsoid (1)
|
||
or a point particle (0).</p>
|
||
<p>For the <em>line</em> style, particles can be are idealized line segments
|
||
which store a per-particle mass and length and orientation (i.e. the
|
||
end points of the line segment). Each particle stores a flag in the
|
||
line vector which indicates whether it is a line segment (1) or a
|
||
point particle (0).</p>
|
||
<p>The <em>mdpd</em> style is for many-body dissipative particle dynamics (mDPD)
|
||
particles which store a density (rho) for considering density-dependent
|
||
many-body interactions.</p>
|
||
<p>The <em>oxdna</em> style is for coarse-grained nucleotides and stores the
|
||
3’-to-5’ polarity of the nucleotide strand, which is set through
|
||
the bond topology in the data file. The first (second) atom in a
|
||
bond definition is understood to point towards the 3’-end (5’-end)
|
||
of the strand.</p>
|
||
<p>For the <em>peri</em> style, the particles are spherical and each stores a
|
||
per-particle mass and volume.</p>
|
||
<p>The <em>smd</em> style is for Smooth Particle Mach dynamics. Both fluids and
|
||
solids can be modeled. Particles store the mass and volume of an
|
||
integration point, a kernel diameter used for calculating the field
|
||
variables (e.g. stress and deformation) and a contact radius for
|
||
calculating repulsive forces which prevent individual physical bodies
|
||
from penetrating each other.</p>
|
||
<p>The <em>sph</em> style is for smoothed particle hydrodynamics (SPH) particles
|
||
which store a density (rho), energy (esph), and heat capacity (cv).</p>
|
||
<p>For the <em>spin</em> style, a magnetic spin is associated with each atom.
|
||
Those spins have a norm (their magnetic moment) and a direction.</p>
|
||
<p>The <em>tdpd</em> style is for transport dissipative particle dynamics (tDPD)
|
||
particles which store a set of chemical concentration. An integer
|
||
“cc_species” is required to specify the number of chemical species
|
||
involved in a tDPD system.</p>
|
||
<p>The <em>wavepacket</em> style is similar to the <em>electron</em> style, but the
|
||
electrons may consist of several Gaussian wave packets, summed up with
|
||
coefficients cs= (cs_re,cs_im). Each of the wave packets is treated
|
||
as a separate particle in LAMMPS, wave packets belonging to the same
|
||
electron must have identical <em>etag</em> values.</p>
|
||
<p>The <em>sphere</em> and <em>bpm/sphere</em> styles allow particles to be either point
|
||
particles or finite-size particles. If the <em>radius</em> attribute is >
|
||
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
|
||
is a point particle. Note that by using the <em>disc</em> keyword with the
|
||
<a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a>, <a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">fix nvt/sphere</span></a>, <a class="reference internal" href="fix_nph_sphere.html"><span class="doc">fix nph/sphere</span></a>, <a class="reference internal" href="fix_npt_sphere.html"><span class="doc">fix
|
||
npt/sphere</span></a> commands for the <em>sphere</em> style, spheres
|
||
can be effectively treated as 2d discs for a 2d simulation if desired.
|
||
See also the <a class="reference internal" href="set.html"><span class="doc">set density/disc</span></a> command. These styles also
|
||
take an optional 0 or 1 argument. A value of 0 means the radius of
|
||
each sphere is constant for the duration of the simulation (this is
|
||
the default). A value of 1 means the radii may vary dynamically
|
||
during the simulation, e.g. due to use of the <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> command.</p>
|
||
<p>The <em>template</em> style allows molecular topology (bonds,angles,etc) to be
|
||
defined via a molecule template using the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a>
|
||
command. The template stores one or more molecules with a single copy
|
||
of the topology info (bonds,angles,etc) of each. Individual atoms only
|
||
store a template index and template atom to identify which molecule and
|
||
which atom-within-the-molecule they represent. Using the <em>template</em>
|
||
style instead of the <em>bond</em>, <em>angle</em>, <em>molecular</em> styles can save memory
|
||
for systems comprised of a large number of small molecules, all of a
|
||
single type (or small number of types). See the paper by Grime and
|
||
Voth, in <a class="reference internal" href="#grime"><span class="std std-ref">(Grime)</span></a>, for examples of how this can be
|
||
advantageous for large-scale coarse-grained systems. The
|
||
<code class="docutils literal notranslate"><span class="pre">examples/template</span></code> directory has a few demo inputs and examples
|
||
showing the use of the <em>template</em> atom style versus <em>molecular</em>.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When using the <em>template</em> style with a <a class="reference internal" href="molecule.html"><span class="doc">molecule template</span></a> that contains multiple molecules, you should ensure the
|
||
atom types, bond types, angle_types, etc in all the molecules are
|
||
consistent. E.g. if one molecule represents H2O and another CO2,
|
||
then you probably do not want each molecule file to define two atom
|
||
types and a single bond type, because they will conflict with each
|
||
other when a mixture system of H2O and CO2 molecules is defined,
|
||
e.g. by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. Rather the H2O
|
||
molecule should define atom types 1 and 2, and bond type 1. And
|
||
the CO2 molecule should define atom types 3 and 4 (or atom types 3
|
||
and 2 if a single oxygen type is desired), and bond type 2.</p>
|
||
</div>
|
||
<p>For the <em>tri</em> style, particles can be planar triangles which each
|
||
stores a per-particle mass and size and orientation (i.e. the corner
|
||
points of the triangle). Each particle stores a flag in the tri
|
||
vector which indicates whether it is a triangle (1) or a point
|
||
particle (0).</p>
|
||
<hr class="docutils" />
|
||
<p>Typically, simulations require only a single (non-hybrid) atom style.
|
||
If some atoms in the simulation do not have all the properties defined
|
||
by a particular style, use the simplest style that defines all the
|
||
needed properties by any atom. For example, if some atoms in a
|
||
simulation are charged, but others are not, use the <em>charge</em> style.
|
||
If some atoms have bonds, but others do not, use the <em>bond</em> style.</p>
|
||
<p>The only scenario where the <em>hybrid</em> style is needed is if there is no
|
||
single style which defines all needed properties of all atoms. For
|
||
example, as mentioned above, if you want dipolar particles which will
|
||
rotate due to torque, you need to use “atom_style hybrid sphere
|
||
dipole”. When a hybrid style is used, atoms store and communicate the
|
||
union of all quantities implied by the individual styles.</p>
|
||
<p>When using the <em>hybrid</em> style, you cannot combine the <em>template</em> style
|
||
with another molecular style that stores bond, angle, etc info on a
|
||
per-atom basis.</p>
|
||
<p>LAMMPS can be extended with new atom styles as well as new body styles;
|
||
see the corresponding manual page on <a class="reference internal" href="Modify_atom.html"><span class="doc">modifying & extending LAMMPS</span></a>.</p>
|
||
<hr class="docutils" />
|
||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||
functionally the same as the corresponding style without the suffix.
|
||
They have been optimized to run faster, depending on your available
|
||
hardware, as discussed on the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a>
|
||
page. The accelerated styles take the same arguments and should
|
||
produce the same results, except for round-off and precision issues.</p>
|
||
<p>These accelerated styles are part of the GPU, INTEL, KOKKOS,
|
||
OPENMP, and OPT packages, respectively. They are only enabled if
|
||
LAMMPS was built with those packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
<p>You can specify the accelerated styles explicitly in your input script
|
||
by including their suffix, or you can use the <a class="reference internal" href="Run_options.html"><span class="doc">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can use the
|
||
<a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||
<p>See the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a> page for more
|
||
instructions on how to use the accelerated styles effectively.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This command cannot be used after the simulation box is defined by a
|
||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.</p>
|
||
<p>Many of the styles listed above are only enabled if LAMMPS was built
|
||
with a specific package, as listed below. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info. The table above lists which package
|
||
is required for individual atom styles.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>,
|
||
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a>, <a class="reference internal" href="set.html"><span class="doc">set</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The default atom style is <em>atomic</em>. If atom_style <em>sphere</em> or
|
||
<em>bpm/sphere</em> is used, its default argument is 0.</p>
|
||
<hr class="docutils" />
|
||
<p id="grime"><strong>(Grime)</strong> Grime and Voth, to appear in J Chem Theory & Computation
|
||
(2014).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="atom_modify.html" class="btn btn-neutral float-left" title="atom_modify command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="balance.html" class="btn btn-neutral float-right" title="balance command" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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</div>
|
||
|
||
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