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711 lines
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<title>kspace_modify command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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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="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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<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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<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"><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 current"><a class="current reference internal" href="#">kspace_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="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>
|
||
</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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<li class="breadcrumb-item active">kspace_modify command</li>
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<a href="kim_commands.html" class="btn btn-neutral float-left" title="kim command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="kspace_style.html" class="btn btn-neutral float-right" title="kspace_style command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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</div>
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<hr/>
|
||
</div>
|
||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||
<div itemprop="articleBody">
|
||
|
||
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="kspace-modify-command">
|
||
<span id="index-0"></span><h1>kspace_modify command<a class="headerlink" href="#kspace-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">kspace_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>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>one or more keyword/value pairs may be listed</p></li>
|
||
<li><p>keyword = <em>collective</em> or <em>compute</em> or <em>cutoff/adjust</em> or <em>diff</em> or <em>disp/auto</em> or <em>fftbench</em> or <em>force/disp/kspace</em> or <em>force/disp/real</em> or <em>force</em> or <em>gewald/disp</em> or <em>gewald</em> or <em>kmax/ewald</em> or <em>mesh</em> or <em>minorder</em> or <em>mix/disp</em> or <em>order/disp</em> or <em>order</em> or <em>overlap</em> or <em>scafacos</em> or <em>slab</em> or <em>splittol</em> or <em>wire</em></p>
|
||
<pre class="literal-block"><em>collective</em> value = <em>yes</em> or <em>no</em>
|
||
<em>compute</em> value = <em>yes</em> or <em>no</em>
|
||
<em>cutoff/adjust</em> value = <em>yes</em> or <em>no</em>
|
||
<em>diff</em> value = <em>ad</em> or <em>ik</em> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
|
||
<em>disp/auto</em> value = yes or no
|
||
<em>fftbench</em> value = <em>yes</em> or <em>no</em>
|
||
<em>force/disp/real</em> value = accuracy (force units)
|
||
<em>force/disp/kspace</em> value = accuracy (force units)
|
||
<em>force</em> value = accuracy (force units)
|
||
<em>gewald</em> value = rinv (1/distance units)
|
||
rinv = G-ewald parameter for Coulombics
|
||
<em>gewald/disp</em> value = rinv (1/distance units)
|
||
rinv = G-ewald parameter for dispersion
|
||
<em>kmax/ewald</em> value = kx ky kz
|
||
kx,ky,kz = number of Ewald sum kspace vectors in each dimension
|
||
<em>mesh</em> value = x y z
|
||
x,y,z = grid size in each dimension for long-range Coulombics
|
||
<em>mesh/disp</em> value = x y z
|
||
x,y,z = grid size in each dimension for 1/r^6 dispersion
|
||
<em>minorder</em> value = M
|
||
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
|
||
<em>mix/disp</em> value = <em>pair</em> or <em>geom</em> or <em>none</em>
|
||
<em>order</em> value = N
|
||
N = extent of Gaussian for PPPM or MSM mapping of charge to grid
|
||
<em>order/disp</em> value = N
|
||
N = extent of Gaussian for PPPM mapping of dispersion term to grid
|
||
<em>overlap</em> = <em>yes</em> or <em>no</em> = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
|
||
<em>pressure/scalar</em> value = <em>yes</em> or <em>no</em>
|
||
<em>scafacos</em> values = option value1 value2 ...
|
||
option = <em>tolerance</em>
|
||
value = <em>energy</em> or <em>energy_rel</em> or <em>field</em> or <em>field_rel</em> or <em>potential</em> or <em>potential_rel</em>
|
||
option = <em>fmm_tuning</em>
|
||
value = <em>0</em> or <em>1</em>
|
||
<em>slab</em> value = volfactor or <em>nozforce</em>
|
||
volfactor = ratio of the total extended volume used in the
|
||
2d approximation compared with the volume of the simulation domain
|
||
<em>nozforce</em> turns off kspace forces in the z direction
|
||
<em>splittol</em> value = tol
|
||
tol = relative size of two eigenvalues (see discussion below)
|
||
<em>wire</em> value = volfactor (available with ELECTRODE package)
|
||
volfactor = ratio of the total extended dimension used in the 1d
|
||
approximation compared with the dimension of the simulation domain</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">kspace_modify</span><span class="w"> </span><span class="n">mesh</span><span class="w"> </span><span class="m">24</span><span class="w"> </span><span class="m">24</span><span class="w"> </span><span class="m">30</span><span class="w"> </span><span class="n">order</span><span class="w"> </span><span class="m">6</span>
|
||
<span class="k">kspace_modify</span><span class="w"> </span><span class="n">slab</span><span class="w"> </span><span class="m">3.0</span>
|
||
<span class="k">kspace_modify</span><span class="w"> </span><span class="n">scafacos</span><span class="w"> </span><span class="n">tolerance</span><span class="w"> </span><span class="n">energy</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Set parameters used by the kspace solvers defined by the
|
||
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command. Not all parameters are
|
||
relevant to all kspace styles.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>collective</em> keyword applies only to PPPM. It is set to <em>no</em> by
|
||
default, except on IBM BlueGene machines. If this option is set to
|
||
<em>yes</em>, LAMMPS will use MPI collective operations to remap data for
|
||
3d-FFT operations instead of the default point-to-point communication.
|
||
This is faster on IBM BlueGene machines, and may also be faster on
|
||
other machines if they have an efficient implementation of MPI
|
||
collective operations and adequate hardware.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>compute</em> keyword allows Kspace computations to be turned off,
|
||
even though a <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> is defined. This is
|
||
not useful for running a real simulation, but can be useful for
|
||
debugging purposes or for computing only partial forces that do not
|
||
include the Kspace contribution. You can also do this by simply not
|
||
defining a <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, but a Kspace-compatible
|
||
<a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> requires a kspace style to be defined.
|
||
This keyword gives you that option.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>cutoff/adjust</em> keyword applies only to MSM. If this option is
|
||
turned on, the Coulombic cutoff will be automatically adjusted at the
|
||
beginning of the run to give the desired estimated error. Other
|
||
cutoffs such as LJ will not be affected. If the grid is not set using
|
||
the <em>mesh</em> command, this command will also attempt to use the optimal
|
||
grid that minimizes cost using an estimate given by
|
||
<a class="reference internal" href="#hardy1"><span class="std std-ref">(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
|
||
experimental, and still may not yield the optimal parameters.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>diff</em> keyword specifies the differentiation scheme used by the
|
||
PPPM method to compute forces on particles given electrostatic
|
||
potentials on the PPPM mesh. The <em>ik</em> approach is the default for
|
||
PPPM and is the original formulation used in <a class="reference internal" href="#hockney1"><span class="std std-ref">(Hockney)</span></a>. It
|
||
performs differentiation in Kspace, and uses 3 FFTs to transfer each
|
||
component of the computed fields back to real space for total of 4
|
||
FFTs per timestep.</p>
|
||
<p>The analytic differentiation <em>ad</em> approach uses only 1 FFT to transfer
|
||
information back to real space for a total of 2 FFTs per timestep. It
|
||
then performs analytic differentiation on the single quantity to
|
||
generate the 3 components of the electric field at each grid point.
|
||
This is sometimes referred to as “smoothed” PPPM. This approach
|
||
requires a somewhat larger PPPM mesh to achieve the same accuracy as
|
||
the <em>ik</em> method. Currently, only the <em>ik</em> method (default) can be
|
||
used for a triclinic simulation cell with PPPM. The <em>ad</em> method is
|
||
always used for MSM.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Currently, not all PPPM styles support the <em>ad</em> option. Support
|
||
for those PPPM variants will be added later.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>disp/auto</em> option controls whether the pppm/disp is allowed to
|
||
generate PPPM parameters automatically. If set to <em>no</em>, parameters have
|
||
to be specified using the <em>gewald/disp</em>, <em>mesh/disp</em>,
|
||
<em>force/disp/real</em> or <em>force/disp/kspace</em> keywords, or
|
||
the code will stop with an error message. When this option is set to
|
||
<em>yes</em>, the error message will not appear and the simulation will start.
|
||
For a typical application, using the automatic parameter generation
|
||
will provide simulations that are either inaccurate or slow. Using this
|
||
option is thus not recommended. For guidelines on how to obtain good
|
||
parameters, see the <a class="reference internal" href="Howto_dispersion.html"><span class="doc">long-range dispersion howto</span></a>
|
||
discussion.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>fftbench</em> keyword applies only to PPPM. It is off by default. If
|
||
this option is turned on, LAMMPS will perform a short FFT benchmark
|
||
computation and report its timings, and will thus finish some seconds
|
||
later than it would if this option were off.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
|
||
accuracy for the real and reciprocal space computations for the dispersion
|
||
part of pppm/disp. As shown in <a class="reference internal" href="#isele-holder1"><span class="std std-ref">(Isele-Holder)</span></a>,
|
||
optimal performance and accuracy in the results is obtained when these
|
||
values are different.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>force</em> keyword overrides the relative accuracy parameter set by
|
||
the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command with an absolute
|
||
accuracy. The accuracy determines the RMS error in per-atom forces
|
||
calculated by the long-range solver and is thus specified in force
|
||
units. A negative value for the accuracy setting means to use the
|
||
relative accuracy parameter. The accuracy setting is used in
|
||
conjunction with the pairwise cutoff to determine the number of
|
||
K-space vectors for style <em>ewald</em>, the FFT grid size for style
|
||
<em>pppm</em>, or the real space grid size for style <em>msm</em>.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>gewald</em> keyword sets the value of the Ewald or PPPM G-ewald
|
||
parameter for charge as <em>rinv</em> in reciprocal distance units. Without
|
||
this setting, LAMMPS chooses the parameter automatically as a function
|
||
of cutoff, precision, grid spacing, etc. This means it can vary from
|
||
one simulation to the next which may not be desirable for matching a
|
||
KSpace solver to a pre-tabulated pairwise potential. This setting can
|
||
also be useful if Ewald or PPPM fails to choose a good grid spacing
|
||
and G-ewald parameter automatically. If the value is set to 0.0,
|
||
LAMMPS will choose the G-ewald parameter automatically. MSM does not
|
||
use the <em>gewald</em> parameter.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>gewald/disp</em> keyword sets the value of the Ewald or PPPM G-ewald
|
||
parameter for dispersion as <em>rinv</em> in reciprocal distance units. It
|
||
has the same meaning as the <em>gewald</em> setting for Coulombics.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>kmax/ewald</em> keyword sets the number of kspace vectors in each
|
||
dimension for kspace style <em>ewald</em>. The three values must be positive
|
||
integers, or else (0,0,0), which unsets the option. When this option
|
||
is not set, the Ewald sum scheme chooses its own kspace vectors,
|
||
consistent with the user-specified accuracy and pairwise cutoff. In
|
||
any case, if kspace style <em>ewald</em> is invoked, the values used are
|
||
printed to the screen and the log file at the start of the run.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>mesh</em> keyword sets the grid size for kspace style <em>pppm</em> or
|
||
<em>msm</em>. In the case of PPPM, this is the FFT mesh, and each dimension
|
||
must be factorizable into powers of 2, 3, and 5. In the case of MSM,
|
||
this is the finest scale real-space mesh, and each dimension must be
|
||
factorizable into powers of 2. When this option is not set, the PPPM
|
||
or MSM solver chooses its own grid size, consistent with the
|
||
user-specified accuracy and pairwise cutoff. Values for x,y,z of
|
||
0,0,0 unset the option.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>mesh/disp</em> keyword sets the grid size for kspace style
|
||
<em>pppm/disp</em>. This is the FFT mesh for long-range dispersion and ach
|
||
dimension must be factorizable into powers of 2, 3, and 5. When this
|
||
option is not set, the PPPM solver chooses its own grid size,
|
||
consistent with the user-specified accuracy and pairwise cutoff.
|
||
Values for x,y,z of 0,0,0 unset the option.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>minorder</em> keyword allows LAMMPS to reduce the <em>order</em> setting if
|
||
necessary to keep the communication of ghost grid point limited to
|
||
exchanges between nearest-neighbor processors. See the discussion of
|
||
the <em>overlap</em> keyword for details. If the <em>overlap</em> keyword is set to
|
||
<em>yes</em>, which is the default, this is never needed. If it set to <em>no</em>
|
||
and overlap occurs, then LAMMPS will reduce the order setting, one
|
||
step at a time, until the ghost grid overlap only extends to nearest
|
||
neighbor processors. The <em>minorder</em> keyword limits how small the
|
||
<em>order</em> setting can become. The minimum allowed value for PPPM is 2,
|
||
which is the default. If <em>minorder</em> is set to the same value as
|
||
<em>order</em> then no reduction is allowed, and LAMMPS will generate an
|
||
error if the grid communication is non-nearest-neighbor and <em>overlap</em>
|
||
is set to <em>no</em>. The <em>minorder</em> keyword is not currently supported in
|
||
MSM.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>mix/disp</em> keyword selects the mixing rule for the dispersion
|
||
coefficients. With <em>pair</em>, the dispersion coefficients of unlike
|
||
types are computed as indicated with <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>.
|
||
With <em>geom</em>, geometric mixing is enforced on the dispersion
|
||
coefficients in the kspace coefficients. When using the arithmetic
|
||
mixing rule, this will speed-up the simulations but introduces some
|
||
error in the force computations, as shown in <a class="reference internal" href="#wennberg"><span class="std std-ref">(Wennberg)</span></a>.
|
||
With <em>none</em>, it is assumed that no mixing rule is
|
||
applicable. Splitting of the dispersion coefficients will be performed
|
||
as described in <a class="reference internal" href="#isele-holder1"><span class="std std-ref">(Isele-Holder)</span></a>.</p>
|
||
<p>This splitting can be influenced with the <em>splittol</em> keywords. Only
|
||
the eigenvalues that are larger than tol compared to the largest
|
||
eigenvalues are included. Using this keywords the original matrix of
|
||
dispersion coefficients is approximated. This leads to faster
|
||
computations, but the accuracy in the reciprocal space computations of
|
||
the dispersion part is decreased.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>order</em> keyword determines how many grid spacings an atom’s charge
|
||
extends when it is mapped to the grid in kspace style <em>pppm</em> or <em>msm</em>.
|
||
The default for this parameter is 5 for PPPM and 8 for MSM, which
|
||
means each charge spans 5 or 8 grid cells in each dimension,
|
||
respectively. For the LAMMPS implementation of MSM, the order can
|
||
range from 4 to 10 and must be even. For PPPM, the minimum allowed
|
||
setting is 2 and the maximum allowed setting is 7. The larger the
|
||
value of this parameter, the smaller that LAMMPS will set the grid
|
||
size, to achieve the requested accuracy. Conversely, the smaller the
|
||
order value, the larger the grid size will be. Note that there is an
|
||
inherent trade-off involved: a small grid will lower the cost of FFTs
|
||
or MSM direct sum, but a larger order parameter will increase the cost
|
||
of interpolating charge/fields to/from the grid.</p>
|
||
<p>The PPPM order parameter may be reset by LAMMPS when it sets up the
|
||
FFT grid if the implied grid stencil extends beyond the grid cells
|
||
owned by neighboring processors. Typically this will only occur when
|
||
small problems are run on large numbers of processors. A warning will
|
||
be generated indicating the order parameter is being reduced to allow
|
||
LAMMPS to run the problem. Automatic adjustment of the order parameter
|
||
is not supported in MSM.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>order/disp</em> keyword determines how many grid spacings an atom’s
|
||
dispersion term extends when it is mapped to the grid in kspace style
|
||
<em>pppm/disp</em>. It has the same meaning as the <em>order</em> setting for
|
||
Coulombics.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>overlap</em> keyword can be used in conjunction with the <em>minorder</em>
|
||
keyword with the PPPM styles to adjust the amount of communication
|
||
that occurs when values on the FFT grid are exchanged between
|
||
processors. This communication is distinct from the communication
|
||
inherent in the parallel FFTs themselves, and is required because
|
||
processors interpolate charge and field values using grid point values
|
||
owned by neighboring processors (i.e. ghost point communication). If
|
||
the <em>overlap</em> keyword is set to <em>yes</em> then this communication is
|
||
allowed to extend beyond nearest-neighbor processors, e.g. when using
|
||
lots of processors on a small problem. If it is set to <em>no</em> then the
|
||
communication will be limited to nearest-neighbor processors and the
|
||
<em>order</em> setting will be reduced if necessary, as explained by the
|
||
<em>minorder</em> keyword discussion. The <em>overlap</em> keyword is always set to
|
||
<em>yes</em> in MSM.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>pressure/scalar</em> keyword applies only to MSM. If this option is
|
||
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
|
||
be computed, which can be used, for example, to run an isotropic barostat.
|
||
Computing the full pressure tensor with MSM is expensive, and this option
|
||
provides a faster alternative. The scalar pressure is computed using a
|
||
relationship between the Coulombic energy and pressure <a class="reference internal" href="#hummer"><span class="std std-ref">(Hummer)</span></a>
|
||
instead of using the virial equation. This option cannot be used to access
|
||
individual components of the pressure tensor, to compute per-atom virial,
|
||
or with suffix kspace/pair styles of MSM, like OMP or GPU.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>scafacos</em> keyword is used for settings that are passed to the
|
||
ScaFaCoS library when using <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style scafacos</span></a>.</p>
|
||
<p>The <em>tolerance</em> option affects how the <em>accuracy</em> specified with the
|
||
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command is interpreted by ScaFaCoS.
|
||
The following values may be used:</p>
|
||
<ul class="simple">
|
||
<li><p>energy = absolute accuracy in total Coulombic energy</p></li>
|
||
<li><p>energy_rel = relative accuracy in total Coulombic energy</p></li>
|
||
<li><p>potential = absolute accuracy in total Coulombic potential</p></li>
|
||
<li><p>potential_rel = relative accuracy in total Coulombic potential</p></li>
|
||
<li><p>field = absolute accuracy in electric field</p></li>
|
||
<li><p>field_rel = relative accuracy in electric field</p></li>
|
||
</ul>
|
||
<p>The values with suffix _rel indicate the tolerance is a relative
|
||
tolerance; the other values impose an absolute tolerance on the given
|
||
quantity. Absolute tolerance in this case means, that for a given
|
||
quantity q and a given absolute tolerance of t_a the result should
|
||
be between q-t_a and q+t_a. For a relative tolerance t_r the relative
|
||
error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r.
|
||
As a consequence of this, the tolerance type should be checked, when
|
||
performing computations with a high absolute field / energy. E.g.
|
||
if the total energy in the system is 1000000.0 an absolute tolerance
|
||
of 1e-3 would mean that the result has to be between 999999.999 and
|
||
1000000.001, which would be equivalent to a relative tolerance of
|
||
1e-9.</p>
|
||
<p>The energy and energy_rel values, set a tolerance based on the total
|
||
Coulombic energy of the system. The potential and potential_rel set a
|
||
tolerance based on the per-atom Coulombic energy. The field and
|
||
field_rel tolerance types set a tolerance based on the electric field
|
||
values computed by ScaFaCoS. Since per-atom forces are derived from
|
||
the per-atom electric field, this effectively sets a tolerance on the
|
||
forces, similar to other LAMMPS KSpace styles, as explained on the
|
||
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> doc page.</p>
|
||
<p>Note that not all ScaFaCoS solvers support all tolerance types.
|
||
These are the allowed values for each method:</p>
|
||
<ul class="simple">
|
||
<li><p>fmm = energy and energy_rel</p></li>
|
||
<li><p>p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)</p></li>
|
||
<li><p>p3m = field</p></li>
|
||
<li><p>ewald = field</p></li>
|
||
<li><p>direct = has no tolerance tuning</p></li>
|
||
</ul>
|
||
<p>If the tolerance type is not changed, the default values for the
|
||
tolerance type are the first values in the above list, e.g. energy
|
||
is the default tolerance type for the fmm solver.</p>
|
||
<p>The <em>fmm_tuning</em> option is only relevant when using the FMM method.
|
||
It activates (value=1) or deactivates (value=0) an internal tuning
|
||
mechanism for the FMM solver. The tuning operation runs sequentially
|
||
and can be very time-consuming. Usually it is not needed for systems
|
||
with a homogeneous charge distribution. The default for this option is
|
||
therefore <em>0</em>. The FMM internal tuning is performed once, when the
|
||
solver is set up.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>slab</em> keyword allows an Ewald or PPPM solver to be used for a
|
||
systems that are periodic in x,y but non-periodic in z - a
|
||
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> setting of “boundary p p f”. This is done
|
||
by treating the system as if it were periodic in z, but inserting
|
||
empty volume between atom slabs and removing dipole inter-slab
|
||
interactions so that slab-slab interactions are effectively turned
|
||
off. The volfactor value sets the ratio of the extended dimension in
|
||
z divided by the actual dimension in z. It must be a value >= 1.0. A
|
||
value of 1.0 (the default) means the slab approximation is not used.</p>
|
||
<p>The recommended value for volfactor is 3.0. A larger value is
|
||
inefficient; a smaller value introduces unwanted slab-slab
|
||
interactions. The use of fixed boundaries in z means that the user
|
||
must prevent particle migration beyond the initial z-bounds, typically
|
||
by providing a wall-style fix. The methodology behind the <em>slab</em>
|
||
option is explained in the paper by <a class="reference internal" href="#yeh"><span class="std std-ref">(Yeh)</span></a>. The <em>slab</em>
|
||
option is also extended to non-neutral systems <a class="reference internal" href="#ballenegger"><span class="std std-ref">(Ballenegger)</span></a>.</p>
|
||
<p>An alternative slab option can be invoked with the <em>nozforce</em> keyword
|
||
in lieu of the volfactor. This turns off all kspace forces in the z
|
||
direction. The <em>nozforce</em> option is not supported by MSM. For MSM,
|
||
any combination of periodic, non-periodic, or shrink-wrapped
|
||
boundaries can be set using <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> (the slab
|
||
approximation in not needed). The <em>slab</em> keyword is not currently
|
||
supported by Ewald or PPPM when using a triclinic simulation cell. The
|
||
slab correction has also been extended to point dipole interactions
|
||
<a class="reference internal" href="#klapp"><span class="std std-ref">(Klapp)</span></a> in <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>
|
||
<em>ewald/disp</em>, <em>ewald/dipole</em>, and <em>pppm/dipole</em>.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you wish to apply an electric field in the Z-direction, in
|
||
conjunction with the <em>slab</em> keyword, you should do it by adding
|
||
explicit charged particles to the +/- Z surfaces. If you do it via
|
||
the <a class="reference internal" href="fix_efield.html"><span class="doc">fix efield</span></a> command, it will not give the correct
|
||
dielectric constant due to the Yeh/Berkowitz <a class="reference internal" href="#yeh"><span class="std std-ref">(Yeh)</span></a> correction
|
||
not being compatible with how <a class="reference internal" href="fix_efield.html"><span class="doc">fix efield</span></a> works.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
|
||
accuracy for the real and reciprocal space computations for the dispersion
|
||
part of pppm/disp. As shown in <a class="reference internal" href="#isele-holder1"><span class="std std-ref">(Isele-Holder)</span></a>,
|
||
optimal performance and accuracy in the results is obtained when these
|
||
values are different.</p>
|
||
<p>The <em>disp/auto</em> option controls whether the pppm/disp is allowed to
|
||
generate PPPM parameters automatically. If set to <em>no</em>, parameters
|
||
have to be specified using the <em>gewald/disp</em>, <em>mesh/disp</em>,
|
||
<em>force/disp/real</em> or <em>force/disp/kspace</em> keywords, or the code will
|
||
stop with an error message. When this option is set to <em>yes</em>, the
|
||
error message will not appear and the simulation will start. For a
|
||
typical application, using the automatic parameter generation will
|
||
provide simulations that are either inaccurate or slow. Using this
|
||
option is thus not recommended. For guidelines on how to obtain good
|
||
parameters, see the <a class="reference internal" href="Howto_dispersion.html"><span class="doc">Howto dispersion</span></a> doc page.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>none</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="kspace_style.html"><span class="doc">kspace_style</span></a>, <a class="reference internal" href="boundary.html"><span class="doc">boundary</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 as follows:</p>
|
||
<ul class="simple">
|
||
<li><p>compute = yes</p></li>
|
||
<li><p>cutoff/adjust = yes (MSM)</p></li>
|
||
<li><p>diff = ik (PPPM)</p></li>
|
||
<li><p>disp/auto = no</p></li>
|
||
<li><p>fftbench = no (PPPM)</p></li>
|
||
<li><p>force = -1.0</p></li>
|
||
<li><p>force/disp/kspace = -1.0</p></li>
|
||
<li><p>force/disp/real = -1.0</p></li>
|
||
<li><p>gewald = gewald/disp = 0.0</p></li>
|
||
<li><p>mesh = mesh/disp = 0 0 0</p></li>
|
||
<li><p>minorder = 2</p></li>
|
||
<li><p>mix/disp = pair</p></li>
|
||
<li><p>order = 10 (MSM)</p></li>
|
||
<li><p>order = order/disp = 5 (PPPM)</p></li>
|
||
<li><p>order = order/disp = 7 (PPPM/intel)</p></li>
|
||
<li><p>overlap = yes</p></li>
|
||
<li><p>pressure/scalar = yes (MSM)</p></li>
|
||
<li><p>slab = 1.0</p></li>
|
||
<li><p>split = 0</p></li>
|
||
<li><p>tol = 1.0e-6</p></li>
|
||
</ul>
|
||
<p>For scafacos settings, the scafacos tolerance option depends on the
|
||
method chosen, as documented above. The scafacos fmm_tuning default
|
||
= 0.</p>
|
||
<hr class="docutils" />
|
||
<p id="hockney1"><strong>(Hockney)</strong> Hockney and Eastwood, Computer Simulation Using Particles,
|
||
Adam Hilger, NY (1989).</p>
|
||
<p id="yeh"><strong>(Yeh)</strong> Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).</p>
|
||
<p id="ballenegger"><strong>(Ballenegger)</strong> Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
|
||
(2009).</p>
|
||
<p id="klapp"><strong>(Klapp)</strong> Klapp, Schoen, J Chem Phys, 117, 8050 (2002).</p>
|
||
<p id="hardy1"><strong>(Hardy)</strong> David Hardy thesis: Multilevel Summation for the Fast
|
||
Evaluation of Forces for the Simulation of Biomolecules, University of
|
||
Illinois at Urbana-Champaign, (2006).</p>
|
||
<p id="hummer"><strong>(Hummer)</strong> Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)</p>
|
||
<p id="isele-holder1"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
|
||
Chem Theory Comput, 9, 5412 (2013).</p>
|
||
<p id="wennberg"><strong>(Wennberg)</strong> Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
|
||
9, 3527 (2013).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
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<a href="kim_commands.html" class="btn btn-neutral float-left" title="kim command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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