463 lines
35 KiB
HTML
463 lines
35 KiB
HTML
<!DOCTYPE html>
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<title>comm_modify command — LAMMPS documentation</title>
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<link rel="next" title="comm_style command" href="comm_style.html" />
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></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"><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 current"><a class="current reference internal" href="#">comm_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="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">comm_modify command</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="comm-modify-command">
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<span id="index-0"></span><h1>comm_modify command<a class="headerlink" href="#comm-modify-command" title="Link to this heading"></a></h1>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">comm_modify</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
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</pre></div>
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</div>
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<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>mode</em> or <em>cutoff</em> or <em>cutoff/multi</em> or <em>group</em> or <em>reduce/multi</em> or <em>vel</em></p>
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<pre class="literal-block"><em>mode</em> value = <em>single</em>, <em>multi</em>, or <em>multi/old</em> = communicate atoms within a single or multiple distances
|
||
<em>cutoff</em> value = Rcut (distance units) = communicate atoms from this far away
|
||
<em>cutoff/multi</em> collection value
|
||
collection = atom collection or collection range (supports asterisk notation)
|
||
value = Rcut (distance units) = communicate atoms for selected types from this far away
|
||
<em>reduce/multi</em> arg = none = reduce number of communicated ghost atoms for multi style
|
||
<em>cutoff/multi/old</em> type value
|
||
type = atom type or type range (supports asterisk notation)
|
||
value = Rcut (distance units) = communicate atoms for selected types from this far away
|
||
<em>group</em> value = group-ID = only communicate atoms in the group
|
||
<em>vel</em> value = <em>yes</em> or <em>no</em> = do or do not communicate velocity info with ghost atoms</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">comm_modify</span><span class="w"> </span><span class="n">mode</span><span class="w"> </span><span class="n">multi</span><span class="w"> </span><span class="n">reduce</span><span class="o">/</span><span class="n">multi</span>
|
||
<span class="k">comm_modify</span><span class="w"> </span><span class="n">mode</span><span class="w"> </span><span class="n">multi</span><span class="w"> </span><span class="k">group </span><span class="nv nv-Identifier">solvent</span>
|
||
<span class="k">comm_modify</span><span class="w"> </span><span class="n">mode</span><span class="w"> </span><span class="n">multi</span><span class="w"> </span><span class="n">cutoff</span><span class="o">/</span><span class="n">multi</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">10.0</span><span class="w"> </span><span class="n">cutoff</span><span class="o">/</span><span class="n">multi</span><span class="w"> </span><span class="m">2</span><span class="o">*</span><span class="m">4</span><span class="w"> </span><span class="m">15.0</span>
|
||
<span class="k">comm_modify</span><span class="w"> </span><span class="n">vel</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">comm_modify</span><span class="w"> </span><span class="n">mode</span><span class="w"> </span><span class="n">single</span><span class="w"> </span><span class="n">cutoff</span><span class="w"> </span><span class="m">5.0</span><span class="w"> </span><span class="n">vel</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">comm_modify</span><span class="w"> </span><span class="n">cutoff</span><span class="o">/</span><span class="n">multi</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="m">0.0</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>This command sets parameters that affect the inter-processor
|
||
communication of atom information that occurs each timestep as
|
||
coordinates and other properties are exchanged between neighboring
|
||
processors and stored as properties of ghost atoms.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>These options apply to the currently defined comm style. When
|
||
you specify a <a class="reference internal" href="comm_style.html"><span class="doc">comm_style</span></a> or
|
||
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command, all communication settings
|
||
are restored to their default or stored values, including those
|
||
previously reset by a comm_modify command. Thus if your input script
|
||
specifies a comm_style or read_restart command, you should use the
|
||
comm_modify command after it.</p>
|
||
</div>
|
||
<p>The <em>mode</em> keyword determines whether a single or multiple cutoff
|
||
distances are used to determine which atoms to communicate.</p>
|
||
<p>The default mode is <em>single</em> which means each processor acquires
|
||
information for ghost atoms that are within a single distance from its
|
||
subdomain. The distance is by default the maximum of the neighbor
|
||
cutoff across all atom type pairs.</p>
|
||
<p>For many systems this is an efficient algorithm, but for systems with
|
||
widely varying cutoffs for different type pairs, the <em>multi</em> or <em>multi/old</em> mode can
|
||
be faster. In <em>multi</em>, each atom is assigned to a collection which should
|
||
correspond to a set of atoms with similar interaction cutoffs.
|
||
See the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a> command for a detailed description of collections.
|
||
In this case, each atom collection is assigned its own distance
|
||
cutoff for communication purposes, and fewer atoms will be
|
||
communicated. in <em>multi/old</em>, a similar technique is used but atoms
|
||
are grouped by atom type. See the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor multi</span></a> and
|
||
<a class="reference internal" href="neighbor.html"><span class="doc">neighbor multi/old</span></a> commands for
|
||
neighbor list construction options that may also be beneficial for
|
||
simulations of this kind. The <em>multi</em> communication mode is only compatible
|
||
with the <em>multi</em> neighbor style. The <em>multi/old</em> communication mode is comparable
|
||
with both the <em>multi</em> and <em>multi/old</em> neighbor styles.</p>
|
||
<p>The <em>cutoff</em> keyword allows you to extend the ghost cutoff distance
|
||
for communication mode <em>single</em>, which is the distance from the borders
|
||
of a processor’s subdomain at which ghost atoms are acquired from other
|
||
processors. By default the ghost cutoff = neighbor cutoff = pairwise
|
||
force cutoff + neighbor skin. See the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a> command
|
||
for more information about the skin distance. If the specified Rcut is
|
||
greater than the neighbor cutoff, then extra ghost atoms will be acquired.
|
||
If the provided cutoff is smaller, the provided value will be ignored,
|
||
the ghost cutoff is set to the neighbor cutoff and a warning will be
|
||
printed. Specifying a cutoff value of 0.0 will reset any previous value
|
||
to the default. If bonded interactions exist and equilibrium bond length
|
||
information is available, then also a heuristic based on that bond length
|
||
is computed. It is used as communication cutoff, if there is no pair
|
||
style present and no <em>comm_modify cutoff</em> command used. Otherwise a
|
||
warning is printed, if this bond based estimate is larger than the
|
||
communication cutoff used.</p>
|
||
<p>The <em>cutoff/multi</em> option is equivalent to <em>cutoff</em>, but applies to
|
||
communication mode <em>multi</em> instead. Since the communication cutoffs are
|
||
determined per atom collections, a collection specifier is needed and
|
||
cutoff for one or multiple collections can be extended. Also ranges of
|
||
collections using the usual asterisk notation can be given. Collections
|
||
are indexed from 1 to N where N is the total number of collections.
|
||
Note that the arguments for <em>cutoff/multi</em> are parsed right before each
|
||
simulation to account for potential changes in the number of
|
||
collections. Custom cutoffs are preserved between runs but if
|
||
collections are redefined, one may want to re-specify the communication
|
||
cutoffs. For granular pair styles,the default cutoff is set to the sum
|
||
of the current maximum atomic radii for each collection. The
|
||
<em>cutoff/multi/old</em> option is similar to <em>cutoff/multi</em> except it
|
||
operates on atom types as opposed to collections.</p>
|
||
<p>The <em>reduce/multi</em> option applies to <em>multi</em> and sets the communication
|
||
cutoff for a particle equal to the maximum interaction distance between particles
|
||
in the same collection. This reduces the number of
|
||
ghost atoms that need to be communicated. This method is only compatible with the
|
||
<em>multi</em> neighbor style and requires a half neighbor list and Newton on.
|
||
See the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor multi</span></a> command for more information.</p>
|
||
<p>These are simulation scenarios in which it may be useful or even
|
||
necessary to set a ghost cutoff > neighbor cutoff:</p>
|
||
<ul class="simple">
|
||
<li><p>a single polymer chain with bond interactions, but no pairwise interactions</p></li>
|
||
<li><p>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff</p></li>
|
||
<li><p>ghost atoms beyond the pairwise cutoff are needed for some computation</p></li>
|
||
</ul>
|
||
<p>In the first scenario, a pairwise potential is not defined. Thus the
|
||
pairwise neighbor cutoff will be 0.0. But ghost atoms are still
|
||
needed for computing bond, angle, etc interactions between atoms on
|
||
different processors, or when the interaction straddles a periodic
|
||
boundary.</p>
|
||
<p>The appropriate ghost cutoff depends on the <a class="reference internal" href="newton.html"><span class="doc">newton bond</span></a>
|
||
setting. For newton bond <em>off</em>, the distance needs to be the furthest
|
||
distance between any two atoms in the bond, angle, etc. E.g. the
|
||
distance between 1-4 atoms in a dihedral. For newton bond <em>on</em>, the
|
||
distance between the central atom in the bond, angle, etc and any
|
||
other atom is sufficient. E.g. the distance between 2-4 atoms in a
|
||
dihedral.</p>
|
||
<p>In the second scenario, a pairwise potential is defined, but its
|
||
neighbor cutoff is not sufficiently long enough to enable bond, angle,
|
||
etc terms to be computed. As in the previous scenario, an appropriate
|
||
ghost cutoff should be set.</p>
|
||
<p>In the last scenario, a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> or <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or
|
||
<a class="reference internal" href="pair_style.html"><span class="doc">pairwise potential</span></a> needs to calculate with ghost
|
||
atoms beyond the normal pairwise cutoff for some computation it
|
||
performs (e.g. locate neighbors of ghost atoms in a manybody pair
|
||
potential). Setting the ghost cutoff appropriately can ensure it will
|
||
find the needed atoms.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>In these scenarios, if you do not set the ghost cutoff long
|
||
enough, and if there is only one processor in a periodic dimension
|
||
(e.g. you are running in serial), then LAMMPS may “find” the atom it
|
||
is looking for (e.g. the partner atom in a bond), that is on the far
|
||
side of the simulation box, across a periodic boundary. This will
|
||
typically lead to bad dynamics (i.e. the bond length is now the
|
||
simulation box length). To detect if this is happening, see the
|
||
<a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify cluster</span></a> command.</p>
|
||
</div>
|
||
<p>The <em>group</em> keyword will limit communication to atoms in the specified
|
||
group. This can be useful for models where no ghost atoms are needed
|
||
for some kinds of particles. All atoms (not just those in the
|
||
specified group) will still migrate to new processors as they move.
|
||
The group specified with this option must also be specified via the
|
||
<a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify first</span></a> command.</p>
|
||
<p>The <em>vel</em> keyword enables velocity information to be communicated with
|
||
ghost particles. Depending on the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>,
|
||
velocity info includes the translational velocity, angular velocity,
|
||
and angular momentum of a particle. If the <em>vel</em> option is set to
|
||
<em>yes</em>, then ghost atoms store these quantities; if <em>no</em> then they do
|
||
not. The <em>yes</em> setting is needed by some pair styles which require
|
||
the velocity state of both the I and J particles to compute a pairwise
|
||
I,J interaction, as well as by some compute and fix commands.</p>
|
||
<p>Note that if the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command is being used
|
||
with its “remap v” option enabled, then the velocities for ghost atoms
|
||
(in the fix deform group) mirrored across a periodic boundary will
|
||
also include components due to any velocity shift that occurs across
|
||
that boundary (e.g. due to dilation or shear).</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>Communication mode <em>multi</em> is currently only available for
|
||
<a class="reference internal" href="comm_style.html"><span class="doc">comm_style</span></a> <em>brick</em>.</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="comm_style.html"><span class="doc">comm_style</span></a>, <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The option defaults are mode = single, group = all, cutoff = 0.0, vel =
|
||
no. The cutoff default of 0.0 means that ghost cutoff = neighbor
|
||
cutoff = pairwise force cutoff + neighbor skin.</p>
|
||
</section>
|
||
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