458 lines
33 KiB
HTML
458 lines
33 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_modify 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_modify.html" />
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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="atom_style command" href="atom_style.html" />
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<link rel="prev" title="angle_write command" href="angle_write.html" />
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</head>
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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><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 current"><a class="current reference internal" href="#">atom_modify 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="#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="atom_style.html">atom_style command</a></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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<li class="breadcrumb-item active">atom_modify command</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="atom-modify-command">
|
||
<span id="index-0"></span><h1>atom_modify command<a class="headerlink" href="#atom-modify-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_modify</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
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<li><p>one or more keyword/value pairs may be appended</p></li>
|
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<li><p>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></p>
|
||
<pre class="literal-block"><em>id</em> value = <em>yes</em> or <em>no</em>
|
||
<em>map</em> value = <em>yes</em> or <em>array</em> or <em>hash</em>
|
||
<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
|
||
<em>sort</em> values = Nfreq binsize
|
||
Nfreq = sort atoms spatially every this many time steps
|
||
binsize = bin size for spatial sorting (distance units)</pre>
|
||
</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_modify</span><span class="w"> </span><span class="n">map</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">atom_modify</span><span class="w"> </span><span class="n">map</span><span class="w"> </span><span class="n">hash</span><span class="w"> </span><span class="n">sort</span><span class="w"> </span><span class="m">10000</span><span class="w"> </span><span class="m">2.0</span>
|
||
<span class="k">atom_modify</span><span class="w"> </span><span class="n">first</span><span class="w"> </span><span class="n">colloid</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Modify certain attributes of atoms defined and stored within LAMMPS,
|
||
in addition to what is specified by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>
|
||
command. The <em>id</em> and <em>map</em> keywords must be specified before a
|
||
simulation box is defined; other keywords can be specified any time.</p>
|
||
<p>The <em>id</em> keyword determines whether non-zero atom IDs can be assigned
|
||
to each atom. If the value is <em>yes</em>, which is the default, IDs are
|
||
assigned, whether you use the <a class="reference internal" href="create_atoms.html"><span class="doc">create atoms</span></a> or
|
||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
||
commands to initialize atoms. If the value is <em>no</em> the IDs for all
|
||
atoms are assumed to be 0.</p>
|
||
<p>If atom IDs are used, they must all be positive integers. They should
|
||
also be unique, though LAMMPS does not check for this. Typically they
|
||
should also be consecutively numbered (from 1 to Natoms), though this
|
||
is not required. Molecular <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> are those
|
||
that store bond topology information (styles bond, angle, molecular,
|
||
full). These styles require atom IDs since the IDs are used to encode
|
||
the topology. Some other LAMMPS commands also require the use of atom
|
||
IDs. E.g. some many-body pair styles use them to avoid double
|
||
computation of the I-J interaction between two atoms.</p>
|
||
<p>The only reason not to use atom IDs is if you are running an atomic
|
||
simulation so large that IDs cannot be uniquely assigned. For a
|
||
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
|
||
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
|
||
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
|
||
switch. This is described on the <a class="reference internal" href="Build_settings.html"><span class="doc">Build_settings</span></a>
|
||
doc page. If atom IDs are not used, they must be specified as 0 for
|
||
all atoms, e.g. in a data or restart file.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If a <a class="reference internal" href="Howto_triclinic.html"><span class="doc">triclinic simulation box</span></a> is used,
|
||
atom IDs are required, due to how neighbor lists are built.</p>
|
||
</div>
|
||
<p>The <em>map</em> keyword determines how atoms with specific IDs are found
|
||
when required. For example, the bond (angle, etc) methods need to
|
||
find the local index of an atom with a specific global ID which is a
|
||
bond (angle, etc) partner. LAMMPS performs this operation efficiently
|
||
by creating a “map”, which is either an <em>array</em> or <em>hash</em> table, as
|
||
described below.</p>
|
||
<p>When the <em>map</em> keyword is not specified in your input script, LAMMPS
|
||
only creates a map for <a class="reference internal" href="atom_style.html"><span class="doc">atom_styles</span></a> for molecular
|
||
systems which have permanent bonds (angles, etc). No map is created
|
||
for atomic systems, since it is normally not needed. However some
|
||
LAMMPS commands require a map, even for atomic systems, and will
|
||
generate an error if one does not exist. The <em>map</em> keyword thus
|
||
allows you to force the creation of a map.</p>
|
||
<p>Specifying a value of <em>yes</em> will create either an array-style or
|
||
hash-style map, depending on the size of the system. If no atom ID is
|
||
larger than 1 million, then an array-style map is used, otherwise a
|
||
hash-style map is used. Specifying a value of <em>array</em> or <em>hash</em>
|
||
creates an array-style or hash-style map respectively, regardless of
|
||
the size of the system.</p>
|
||
<p>For an array-style map, each processor stores a lookup table of length
|
||
N, where N is the largest atom ID in the system. This is a fast,
|
||
simple method for many simulations, but requires too much memory for
|
||
large simulations. For a hash-style map, a hash table is created on
|
||
each processor, which finds an atom ID in constant time (independent
|
||
of the global number of atom IDs). It can be slightly slower than the
|
||
<em>array</em> map, but its memory cost is proportional to the number of
|
||
atoms owned by a processor, i.e. N/P when N is the total number of
|
||
atoms in the system and P is the number of processors.</p>
|
||
<p>The <em>first</em> keyword allows a <a class="reference internal" href="group.html"><span class="doc">group</span></a> to be specified
|
||
whose atoms will be maintained as the first atoms in each processor’s
|
||
list of owned atoms. This in only useful when the specified group is
|
||
a small fraction of all the atoms, and there are other operations
|
||
LAMMPS is performing that will be sped-up significantly by being able
|
||
to loop over the smaller set of atoms. Otherwise the reordering
|
||
required by this option will be a net slow-down. The
|
||
<a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify include</span></a> and <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify group</span></a> commands are two examples of commands that require this
|
||
setting to work efficiently. Several <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, most notably
|
||
time integration fixes like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, also take
|
||
advantage of this setting if the group they operate on is the group
|
||
specified by this command. Note that specifying “all” as the group-ID
|
||
effectively turns off the <em>first</em> option.</p>
|
||
<p>It is OK to use the <em>first</em> keyword with a group that has not yet been
|
||
defined, e.g. to use the atom_modify first command at the beginning of
|
||
your input script. LAMMPS does not use the group until a simulation
|
||
is run.</p>
|
||
<p>The <em>sort</em> keyword turns on a spatial sorting or reordering of atoms
|
||
within each processor’s subdomain every <em>Nfreq</em> timesteps. If
|
||
<em>Nfreq</em> is set to 0, then sorting is turned off. Sorting can improve
|
||
cache performance and thus speed-up a LAMMPS simulation, as discussed
|
||
in a paper by <a class="reference internal" href="#meloni"><span class="std std-ref">(Meloni)</span></a>. Its efficacy depends on the problem
|
||
size (atoms/processor), how quickly the system becomes disordered, and
|
||
various other factors. As a general rule, sorting is typically more
|
||
effective at speeding up simulations of liquids as opposed to solids.
|
||
In tests we have done, the speed-up can range from zero to 3-4x.</p>
|
||
<p>Reordering is performed every <em>Nfreq</em> timesteps during a dynamics run
|
||
or iterations during a minimization. More precisely, reordering
|
||
occurs at the first reneighboring that occurs after the target
|
||
timestep. The reordering is performed locally by each processor,
|
||
using bins of the specified <em>binsize</em>. If <em>binsize</em> is set to 0.0,
|
||
then a binsize equal to half the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a> cutoff
|
||
distance (force cutoff plus skin distance) is used, which is a
|
||
reasonable value. After the atoms have been binned, they are
|
||
reordered so that atoms in the same bin are adjacent to each other in
|
||
the processor’s 1d list of atoms.</p>
|
||
<p>The goal of this procedure is for atoms to put atoms close to each
|
||
other in the processor’s one-dimensional list of atoms that are also
|
||
near to each other spatially. This can improve cache performance when
|
||
pairwise interactions and neighbor lists are computed. Note that if
|
||
bins are too small, there will be few atoms/bin. Likewise if bins are
|
||
too large, there will be many atoms/bin. In both cases, the goal of
|
||
cache locality will be undermined.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Running a simulation with sorting on versus off should not change
|
||
the simulation results in a statistical sense. However, a
|
||
different ordering will induce round-off differences, which will
|
||
lead to diverging trajectories over time when comparing two
|
||
simulations. Various commands, particularly those which use random
|
||
numbers (e.g. <a class="reference internal" href="velocity.html"><span class="doc">velocity create</span></a>, and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix
|
||
langevin</span></a>), may generate (statistically identical)
|
||
results which depend on the order in which atoms are processed.
|
||
The order of atoms in a <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> file will also typically
|
||
change if sorting is enabled.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When running simple pair-wise potentials like Lennard Jones on GPUs
|
||
with the KOKKOS package, using a larger binsize (e.g. 2x larger than
|
||
default) and a more frequent reordering than default (e.g. every 100
|
||
time steps) may improve performance.</p>
|
||
</div>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>The <em>first</em> and <em>sort</em> options cannot be used together. Since sorting
|
||
is on by default, it will be turned off if the <em>first</em> keyword is
|
||
used with a group-ID that is not “all”.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p>none</p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>By default, <em>id</em> is yes. By default, atomic systems (no bond topology
|
||
info) do not use a map. For molecular systems (with bond topology
|
||
info), the default is to use a map of either <em>array</em> or <em>hash</em> style
|
||
depending on the size of the system, as explained above for the <em>map
|
||
yes</em> keyword/value option. By default, a <em>first</em> group is not
|
||
defined. By default, sorting is enabled with a frequency of 1000 and
|
||
a binsize of 0.0, which means the neighbor cutoff will be used to set
|
||
the bin size. If no neighbor cutoff is defined, sorting will be turned
|
||
off.</p>
|
||
<hr class="docutils" />
|
||
<p id="meloni"><strong>(Meloni)</strong> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).</p>
|
||
</section>
|
||
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|
||
|
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