563 lines
41 KiB
HTML
563 lines
41 KiB
HTML
<!DOCTYPE html>
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<html class="writer-html5" lang="en" >
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<title>prd command — LAMMPS documentation</title>
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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"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_write.html">dihedral_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dynamical_matrix.html">dynamical_matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fitpod_command.html">fitpod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="geturl.html">geturl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="hyper.html">hyper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kim_commands.html">kim command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="labelmap.html">labelmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mdi.html">mdi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html">min_style spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-cg-command">min_style spin/cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-lbfgs-command">min_style spin/lbfgs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-hftn-command">min_style hftn command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-sd-command">min_style sd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-quickmin-command">min_style quickmin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-fire-command">min_style fire command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-command"><span class="xref std std-doc">min_style spin</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-cg-command"><span class="xref std std-doc">min_style spin/cg</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-lbfgs-command"><span class="xref std std-doc">min_style spin/lbfgs</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb_spin.html">neb/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="plugin.html">plugin command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">prd 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="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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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
|
||
</li>
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</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
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<a href="plugin.html" class="btn btn-neutral float-left" title="plugin command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="print.html" class="btn btn-neutral float-right" title="print 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/>
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||
</div>
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||
<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="prd-command">
|
||
<span id="index-0"></span><h1>prd command<a class="headerlink" href="#prd-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">prd</span><span class="w"> </span><span class="n">N</span><span class="w"> </span><span class="n">t_event</span><span class="w"> </span><span class="n">n_dephase</span><span class="w"> </span><span class="n">t_dephase</span><span class="w"> </span><span class="n">t_correlate</span><span class="w"> </span><span class="n">compute</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">seed</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>N = # of timesteps to run (not including dephasing/quenching)</p></li>
|
||
<li><p>t_event = timestep interval between event checks</p></li>
|
||
<li><p>n_dephase = number of velocity randomizations to perform in each dephase run</p></li>
|
||
<li><p>t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase</p></li>
|
||
<li><p>t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated</p></li>
|
||
<li><p>compute-ID = ID of the compute used for event detection</p></li>
|
||
<li><p>random_seed = random # seed (positive integer)</p></li>
|
||
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>min</em> or <em>temp</em> or <em>vel</em> or <em>time</em></p>
|
||
<pre class="literal-block"><em>min</em> values = etol ftol maxiter maxeval
|
||
etol = stopping tolerance for energy, used in quenching
|
||
ftol = stopping tolerance for force, used in quenching
|
||
maxiter = max iterations of minimize, used in quenching
|
||
maxeval = max number of force/energy evaluations, used in quenching
|
||
<em>temp</em> value = Tdephase
|
||
Tdephase = target temperature for velocity randomization, used in dephasing
|
||
<em>vel</em> values = loop dist
|
||
loop = <em>all</em> or <em>local</em> or <em>geom</em>, used in dephasing
|
||
dist = <em>uniform</em> or <em>gaussian</em>, used in dephasing
|
||
<em>time</em> value = <em>steps</em> or <em>clock</em>
|
||
<em>steps</em> = simulation runs for N timesteps on each replica (default)
|
||
<em>clock</em> = simulation runs for N timesteps across all replicas</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">prd</span><span class="w"> </span><span class="m">5000</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">54982</span>
|
||
<span class="k">prd</span><span class="w"> </span><span class="m">5000</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">54982</span><span class="w"> </span><span class="n">min</span><span class="w"> </span><span class="m">0.1</span><span class="w"> </span><span class="m">0.1</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">200</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Run a parallel replica dynamics (PRD) simulation using multiple
|
||
replicas of a system. One or more replicas can be used. The total
|
||
number of steps <em>N</em> to run can be interpreted in one of two ways; see
|
||
discussion of the <em>time</em> keyword below.</p>
|
||
<p>PRD is described in <a class="reference internal" href="#voter1998"><span class="std std-ref">(Voter1998)</span></a> by Art Voter.
|
||
Similar to global or local hyperdynamics (HD), PRD is a method for
|
||
performing accelerated dynamics that is suitable for infrequent-event
|
||
systems that obey first-order kinetics. A good overview of
|
||
accelerated dynamics methods (AMD) for such systems in given in this
|
||
review paper <a class="reference internal" href="#voter2002prd"><span class="std std-ref">(Voter2002)</span></a> from Art’s group. To
|
||
quote from the paper: “The dynamical evolution is characterized by
|
||
vibrational excursions within a potential basin, punctuated by
|
||
occasional transitions between basins. The transition probability is
|
||
characterized by p(t) = k*exp(-kt) where k is the rate constant.”</p>
|
||
<p>Both PRD and HD produce a time-accurate trajectory that effectively
|
||
extends the timescale over which a system can be simulated, but they
|
||
do it differently. PRD creates Nr replicas of the system and runs
|
||
dynamics on each independently with a normal unbiased potential until
|
||
an event occurs in one of the replicas. The time between events is
|
||
reduced by a factor of Nr replicas. HD uses a single replica of the
|
||
system and accelerates time by biasing the interaction potential in a
|
||
manner such that each timestep is effectively longer. For both
|
||
methods, per CPU second, more physical time elapses and more events
|
||
occur. See the <a class="reference internal" href="hyper.html"><span class="doc">hyper</span></a> page for more info about HD.</p>
|
||
<p>In PRD, each replica runs on a partition of one or more processors.
|
||
Processor partitions are defined at run-time using the <a class="reference internal" href="Run_options.html"><span class="doc">-partition command-line switch</span></a>. Note that if you have MPI
|
||
installed, you can run a multi-replica simulation with more replicas
|
||
(partitions) than you have physical processors, e.g you can run a
|
||
10-replica simulation on one or two processors. However for PRD, this
|
||
makes little sense, since running a replica on virtual instead of
|
||
physical processors,offers no effective parallel speed-up in searching
|
||
for infrequent events. See the <a class="reference internal" href="Howto_replica.html"><span class="doc">Howto replica</span></a> doc
|
||
page for further discussion.</p>
|
||
<p>When a PRD simulation is performed, it is assumed that each replica is
|
||
running the same model, though LAMMPS does not check for this.
|
||
I.e. the simulation domain, the number of atoms, the interaction
|
||
potentials, etc should be the same for every replica.</p>
|
||
<p>A PRD run has several stages, which are repeated each time an “event”
|
||
occurs in one of the replicas, as explained below. The logic for a
|
||
PRD run is as follows:</p>
|
||
<pre class="literal-block">while (time remains):
|
||
dephase for n_dephase*t_dephase steps
|
||
until (event occurs on some replica):
|
||
run dynamics for t_event steps
|
||
quench
|
||
check for uncorrelated event on any replica
|
||
until (no correlated event occurs):
|
||
run dynamics for t_correlate steps
|
||
quench
|
||
check for correlated event on this replica
|
||
event replica shares state with all replicas</pre>
|
||
<p>Before this loop begins, the state of the system on replica 0 is
|
||
shared with all replicas, so that all replicas begin from the same
|
||
initial state. The first potential energy basin is identified by
|
||
quenching (an energy minimization, see below) the initial state and
|
||
storing the resulting coordinates for reference.</p>
|
||
<p>In the first stage, dephasing is performed by each replica
|
||
independently to eliminate correlations between replicas. This is
|
||
done by choosing a random set of velocities, based on the
|
||
<em>random_seed</em> that is specified, and running <em>t_dephase</em> timesteps of
|
||
dynamics. This is repeated <em>n_dephase</em> times. At each of the
|
||
<em>n_dephase</em> stages, if an event occurs during the <em>t_dephase</em> steps of
|
||
dynamics for a particular replica, the replica repeats the stage until
|
||
no event occurs.</p>
|
||
<p>If the <em>temp</em> keyword is not specified, the target temperature for
|
||
velocity randomization for each replica is the current temperature of
|
||
that replica. Otherwise, it is the specified <em>Tdephase</em> temperature.
|
||
The style of velocity randomization is controlled using the keyword
|
||
<em>vel</em> with arguments that have the same meaning as their counterparts
|
||
in the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command.</p>
|
||
<p>In the second stage, each replica runs dynamics continuously, stopping
|
||
every <em>t_event</em> steps to check if a transition event has occurred.
|
||
This check is performed by quenching the system and comparing the
|
||
resulting atom coordinates to the coordinates from the previous basin.
|
||
The first time through the PRD loop, the “previous basin” is the set
|
||
of quenched coordinates from the initial state of the system.</p>
|
||
<p>A quench is an energy minimization and is performed by whichever
|
||
algorithm has been defined by the <a class="reference internal" href="min_style.html"><span class="doc">min_style</span></a> command.
|
||
Minimization parameters may be set via the
|
||
<a class="reference internal" href="min_modify.html"><span class="doc">min_modify</span></a> command and by the <em>min</em> keyword of the
|
||
PRD command. The latter are the settings that would be used with the
|
||
<a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command. Note that typically, you do not
|
||
need to perform a highly-converged minimization to detect a transition
|
||
event, though you may need to in order to prevent a set of atoms in
|
||
the system from relaxing to a saddle point.</p>
|
||
<p>The event check is performed by a compute with the specified
|
||
<em>compute-ID</em>. Currently there is only one compute that works with the
|
||
PRD command, which is the <a class="reference internal" href="compute_event_displace.html"><span class="doc">compute event/displace</span></a> command. Other
|
||
event-checking computes may be added. <a class="reference internal" href="compute_event_displace.html"><span class="doc">Compute event/displace</span></a> checks whether any atom in
|
||
the compute group has moved further than a specified threshold
|
||
distance. If so, an “event” has occurred.</p>
|
||
<p>In the third stage, the replica on which the event occurred (event
|
||
replica) continues to run dynamics to search for correlated events.
|
||
This is done by running dynamics for <em>t_correlate</em> steps, quenching
|
||
every <em>t_event</em> steps, and checking if another event has occurred.</p>
|
||
<p>The first time no correlated event occurs, the final state of the
|
||
event replica is shared with all replicas, the new basin reference
|
||
coordinates are updated with the quenched state, and the outer loop
|
||
begins again. While the replica event is searching for correlated
|
||
events, all the other replicas also run dynamics and event checking
|
||
with the same schedule, but the final states are always overwritten by
|
||
the state of the event replica.</p>
|
||
<p>The outer loop of the pseudocode above continues until <em>N</em> steps of
|
||
dynamics have been performed. Note that <em>N</em> only includes the
|
||
dynamics of stages 2 and 3, not the steps taken during dephasing or
|
||
the minimization iterations of quenching. The specified <em>N</em> is
|
||
interpreted in one of two ways, depending on the <em>time</em> keyword. If
|
||
the <em>time</em> value is <em>steps</em>, which is the default, then each replica
|
||
runs for <em>N</em> timesteps. If the <em>time</em> value is <em>clock</em>, then the
|
||
simulation runs until <em>N</em> aggregate timesteps across all replicas have
|
||
elapsed. This aggregate time is the “clock” time defined below, which
|
||
typically advances nearly M times faster than the timestepping on a
|
||
single replica, where M is the number of replicas.</p>
|
||
<hr class="docutils" />
|
||
<p>Four kinds of output can be generated during a PRD run: event
|
||
statistics, thermodynamic output by each replica, dump files, and
|
||
restart files.</p>
|
||
<p>When running with multiple partitions (each of which is a replica in
|
||
this case), the print-out to the screen and master log.lammps file is
|
||
limited to event statistics. Note that if a PRD run is performed on
|
||
only a single replica then the event statistics will be intermixed
|
||
with the usual thermodynamic output discussed below.</p>
|
||
<p>The quantities printed each time an event occurs are the timestep, CPU
|
||
time, clock, event number, a correlation flag, the number of
|
||
coincident events, and the replica number of the chosen event.</p>
|
||
<p>The timestep is the usual LAMMPS timestep, except that time does not
|
||
advance during dephasing or quenches, but only during dynamics. Note
|
||
that are two kinds of dynamics in the PRD loop listed above that
|
||
contribute to this timestepping. The first is when all replicas are
|
||
performing independent dynamics, waiting for an event to occur. The
|
||
second is when correlated events are being searched for, but only one
|
||
replica is running dynamics.</p>
|
||
<p>The CPU time is the total elapsed time on each processor, since the
|
||
start of the PRD run.</p>
|
||
<p>The clock is the same as the timestep except that it advances by M
|
||
steps per timestep during the first kind of dynamics when the M
|
||
replicas are running independently. The clock advances by only 1 step
|
||
per timestep during the second kind of dynamics, when only a single
|
||
replica is checking for a correlated event. Thus “clock” time
|
||
represents the aggregate time (in steps) that has effectively elapsed
|
||
during a PRD simulation on M replicas. If most of the PRD run is
|
||
spent in the second stage of the loop above, searching for infrequent
|
||
events, then the clock will advance nearly M times faster than it
|
||
would if a single replica was running. Note the clock time between
|
||
successive events should be drawn from p(t).</p>
|
||
<p>The event number is a counter that increments with each event, whether
|
||
it is uncorrelated or correlated.</p>
|
||
<p>The correlation flag will be 0 when an uncorrelated event occurs
|
||
during the second stage of the loop listed above, i.e. when all
|
||
replicas are running independently. The correlation flag will be 1
|
||
when a correlated event occurs during the third stage of the loop
|
||
listed above, i.e. when only one replica is running dynamics.</p>
|
||
<p>When more than one replica detects an event at the end of the same
|
||
event check (every <em>t_event</em> steps) during the second stage, then
|
||
one of them is chosen at random. The number of coincident events is
|
||
the number of replicas that detected an event. Normally, this value
|
||
should be 1. If it is often greater than 1, then either the number of
|
||
replicas is too large, or <em>t_event</em> is too large.</p>
|
||
<p>The replica number is the ID of the replica (from 0 to M-1) in which
|
||
the event occurred.</p>
|
||
<hr class="docutils" />
|
||
<p>When running on multiple partitions, LAMMPS produces additional log
|
||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
|
||
the PRD command, these contain the thermodynamic output for each
|
||
replica. You will see short runs and minimizations corresponding to
|
||
the dynamics and quench operations of the loop listed above. The
|
||
timestep will be reset appropriately depending on whether the
|
||
operation advances time or not.</p>
|
||
<p>After the PRD command completes, timing statistics for the PRD run are
|
||
printed in each replica’s log file, giving a breakdown of how much CPU
|
||
time was spent in each stage (dephasing, dynamics, quenching, etc).</p>
|
||
<hr class="docutils" />
|
||
<p>Any <a class="reference internal" href="dump.html"><span class="doc">dump files</span></a> defined in the input script, will be
|
||
written to during a PRD run at timesteps corresponding to both
|
||
uncorrelated and correlated events. This means the requested dump
|
||
frequency in the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command is ignored. There will be
|
||
one dump file (per dump command) created for all partitions.</p>
|
||
<p>The atom coordinates of the dump snapshot are those of the minimum
|
||
energy configuration resulting from quenching following a transition
|
||
event. The timesteps written into the dump files correspond to the
|
||
timestep at which the event occurred and NOT the clock. A dump
|
||
snapshot corresponding to the initial minimum state used for event
|
||
detection is written to the dump file at the beginning of each PRD
|
||
run.</p>
|
||
<hr class="docutils" />
|
||
<p>If the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> command is used, a single restart file
|
||
for all the partitions is generated, which allows a PRD run to be
|
||
continued by a new input script in the usual manner.</p>
|
||
<p>The restart file is generated at the end of the loop listed above. If
|
||
no correlated events are found, this means it contains a snapshot of
|
||
the system at time T + <em>t_correlate</em>, where T is the time at which the
|
||
uncorrelated event occurred. If correlated events were found, then it
|
||
contains a snapshot of the system at time T + <em>t_correlate</em>, where T
|
||
is the time of the last correlated event.</p>
|
||
<p>The restart frequency specified in the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> command
|
||
is interpreted differently when performing a PRD run. It does not
|
||
mean the timestep interval between restart files. Instead it means an
|
||
event interval for uncorrelated events. Thus a frequency of 1 means
|
||
write a restart file every time an uncorrelated event occurs. A
|
||
frequency of 10 means write a restart file every 10th uncorrelated
|
||
event.</p>
|
||
<p>When an input script reads a restart file from a previous PRD run, the
|
||
new script can be run on a different number of replicas or processors.
|
||
However, it is assumed that <em>t_correlate</em> in the new PRD command is
|
||
the same as it was previously. If not, the calculation of the “clock”
|
||
value for the first event in the new run will be slightly off.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This command can only be used if LAMMPS was built with the REPLICA
|
||
package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> doc
|
||
page for more info.</p>
|
||
<p>The <em>N</em> and <em>t_correlate</em> settings must be integer multiples of
|
||
<em>t_event</em>.</p>
|
||
<p>Runs restarted from restart file written during a PRD run will not
|
||
produce identical results due to changes in the random numbers used
|
||
for dephasing.</p>
|
||
<p>This command cannot be used when any fixes are defined that keep track
|
||
of elapsed time to perform time-dependent operations. Examples
|
||
include the “ave” fixes such as <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>.
|
||
Also <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> and <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>.</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="compute_event_displace.html"><span class="doc">compute event/displace</span></a>,
|
||
<a class="reference internal" href="min_modify.html"><span class="doc">min_modify</span></a>, <a class="reference internal" href="min_style.html"><span class="doc">min_style</span></a>,
|
||
<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>, <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a>,
|
||
<a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a>, <a class="reference internal" href="temper.html"><span class="doc">temper</span></a>, <a class="reference internal" href="neb.html"><span class="doc">neb</span></a>,
|
||
<a class="reference internal" href="tad.html"><span class="doc">tad</span></a>, <a class="reference internal" href="hyper.html"><span class="doc">hyper</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 min = 0.1 0.1 40 50, no temp setting, vel =
|
||
geom gaussian, and time = steps.</p>
|
||
<hr class="docutils" />
|
||
<p id="voter1998"><strong>(Voter1998)</strong> Voter, Phys Rev B, 57, 13985 (1998).</p>
|
||
<p id="voter2002prd"><strong>(Voter2002)</strong> Voter, Montalenti, Germann, Annual Review of Materials
|
||
Research 32, 321 (2002).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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