427 lines
32 KiB
HTML
427 lines
32 KiB
HTML
<!DOCTYPE html>
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<title>temper command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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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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<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"><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 current"><a class="current reference internal" href="#">temper 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="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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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="temper-command">
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<span id="index-0"></span><h1>temper command<a class="headerlink" href="#temper-command" title="Link to this heading"></a></h1>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">temper</span><span class="w"> </span><span class="n">N</span><span class="w"> </span><span class="n">M</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="n">fix</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">seed1</span><span class="w"> </span><span class="n">seed2</span><span class="w"> </span><span class="n">index</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li><p>N = total # of timesteps to run</p></li>
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<li><p>M = attempt a tempering swap every this many steps</p></li>
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<li><p>temp = initial temperature for this ensemble</p></li>
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<li><p>fix-ID = ID of the fix that will control temperature during the run</p></li>
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<li><p>seed1 = random # seed used to decide on adjacent temperature to partner with</p></li>
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<li><p>seed2 = random # seed for Boltzmann factor in Metropolis swap</p></li>
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<li><p>index = which temperature (0 to N-1) I am simulating (optional)</p></li>
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</ul>
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</section>
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<section id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">temper</span><span class="w"> </span><span class="m">100000</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="nv">$t</span><span class="w"> </span><span class="n">tempfix</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">58728</span>
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<span class="k">temper</span><span class="w"> </span><span class="m">40000</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="nv">$t</span><span class="w"> </span><span class="n">tempfix</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">32285</span><span class="w"> </span><span class="nv">$w</span>
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</pre></div>
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</div>
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</section>
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<section id="description">
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<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
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<p>Run a parallel tempering or replica exchange simulation using multiple
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||
replicas (ensembles) of a system. Two or more replicas must be used.</p>
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<p>Each replica runs on a partition of one or more processors. Processor
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||
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)
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||
than you have physical processors, e.g you can run a 10-replica
|
||
simulation on one or two processors. You will simply not get the
|
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performance speed-up you would see with one or more physical
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||
processors per replica. See the <a class="reference internal" href="Howto_replica.html"><span class="doc">Howto replica</span></a>
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||
doc page for further discussion.</p>
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<p>Each replica’s temperature is controlled at a different value by a fix
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with <em>fix-ID</em> that controls temperature. Most thermostat fix styles
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||
(with and without included time integration) are supported. The command
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will print an error message and abort, if the chosen fix is unsupported.
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The desired temperature is specified by <em>temp</em>, which is typically a
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variable previously set in the input script, so that each partition is
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assigned a different temperature. See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>
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command for more details. For example:</p>
|
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">t</span><span class="w"> </span><span class="n">world</span><span class="w"> </span><span class="m">300.0</span><span class="w"> </span><span class="m">310.0</span><span class="w"> </span><span class="m">320.0</span><span class="w"> </span><span class="m">330.0</span>
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<span class="k">fix </span><span class="nv nv-Identifier">myfix</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">nvt</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="nv">$t</span><span class="w"> </span><span class="nv">$t</span><span class="w"> </span><span class="m">100.0</span>
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<span class="k">temper</span><span class="w"> </span><span class="m">100000</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="nv">$t</span><span class="w"> </span><span class="n">myfix</span><span class="w"> </span><span class="m">3847</span><span class="w"> </span><span class="m">58382</span>
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</pre></div>
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</div>
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<p>would define 4 temperatures, and assign one of them to the thermostat
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used by each replica, and to the temper command.</p>
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<p>As the tempering simulation runs for <em>N</em> timesteps, a temperature swap
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between adjacent ensembles will be attempted every <em>M</em> timesteps. If
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<em>seed1</em> is 0, then the swap attempts will alternate between odd and
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even pairings. If <em>seed1</em> is non-zero then it is used as a seed in a
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random number generator to randomly choose an odd or even pairing each
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time. Each attempted swap of temperatures is either accepted or
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rejected based on a Boltzmann-weighted Metropolis criterion which uses
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<em>seed2</em> in the random number generator.</p>
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<p>As a tempering run proceeds, multiple log files and screen output
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files are created, one per replica. By default these files are named
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log.lammps.M and screen.M where M is the replica number from 0 to N-1,
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with N = # of replicas. See the <a class="reference internal" href="Run_options.html"><span class="doc">-log and -screen command-line swiches</span></a> for info on how to change these names.</p>
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<p>The main screen and log file (log.lammps) will list information about
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which temperature is assigned to each replica at each thermodynamic
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output timestep. E.g. for a simulation with 16 replicas:</p>
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<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>Running on 16 partitions of processors
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Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
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0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
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500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
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1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
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1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
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2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
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2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
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||
...
|
||
</pre></div>
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</div>
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<p>The column headings T0 to TN-1 mean which temperature is currently
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assigned to the replica 0 to N-1. Thus the columns represent replicas
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||
and the value in each column is its temperature (also numbered 0 to
|
||
N-1). For example, a 0 in the fourth column (column T3, step 2500) means
|
||
that the fourth replica is assigned temperature 0, i.e. the lowest
|
||
temperature. You can verify this time sequence of temperature
|
||
assignments for the Nth replica by comparing the Nth column of screen
|
||
output to the thermodynamic data in the corresponding log.lammps.N or
|
||
screen.N files as time proceeds.</p>
|
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<p>You can have each replica create its own dump file in the following
|
||
manner:</p>
|
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">rep</span><span class="w"> </span><span class="n">world</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">6</span><span class="w"> </span><span class="m">7</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="n">dump.temper.</span><span class="nv">${rep}</span>
|
||
</pre></div>
|
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</div>
|
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<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Each replica’s dump file will contain a continuous trajectory
|
||
for its atoms where the temperature varies over time as swaps take
|
||
place involving that replica. If you want a series of dump files,
|
||
each with snapshots (from all replicas) that are all at a single
|
||
temperature, then you will need to post-process the dump files using
|
||
the information from the log.lammps file. E.g. you could produce one
|
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dump file with snapshots at 300K (from all replicas), another with
|
||
snapshots at 310K, etc. Note that these new dump files will not
|
||
contain “continuous trajectories” for individual atoms, because two
|
||
successive snapshots (in time) may be from different replicas. The
|
||
reorder_remd_traj python script can do the reordering for you
|
||
(and additionally also calculated configurational log-weights of
|
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trajectory snapshots in the canonical ensemble). The script can be found
|
||
in the tools/replica directory while instructions on how to use it is
|
||
available in doc/Tools (in brief) and as a README file in tools/replica
|
||
(in detail).</p>
|
||
</div>
|
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<p>The last argument <em>index</em> in the temper command is optional and is
|
||
used when restarting a tempering run from a set of restart files (one
|
||
for each replica) which had previously swapped to new temperatures.
|
||
The <em>index</em> value (from 0 to N-1, where N is the # of replicas)
|
||
identifies which temperature the replica was simulating on the
|
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timestep the restart files were written. Obviously, this argument
|
||
must be a variable so that each partition has the correct value. Set
|
||
the variable to the <em>N</em> values listed in the log file for the previous
|
||
run for the replica temperatures at that timestep. For example if the
|
||
log file listed the following for a simulation with 5 replicas:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>500000 2 4 0 1 3
|
||
</pre></div>
|
||
</div>
|
||
<p>then a setting of</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">w</span><span class="w"> </span><span class="n">world</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">3</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>would be used to restart the run with a tempering command like the
|
||
example above with $w as the last argument.</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>
|
||
</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="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="neb.html"><span class="doc">neb</span></a></p>
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</section>
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<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
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<p>none</p>
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