891 lines
76 KiB
HTML
891 lines
76 KiB
HTML
<!DOCTYPE html>
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<title>fix hyper/local command — LAMMPS documentation</title>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="next" title="fix imd command" href="fix_imd.html" />
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<div class="lammps_release">git info: </div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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<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"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="fixes.html">Fix Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="fix_accelerate_cos.html">fix accelerate/cos command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_acks2_reaxff.html">fix acks2/reaxff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt.html">fix adapt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt_fep.html">fix adapt/fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_add_heat.html">fix add/heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addforce.html">fix addforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addtorque.html">fix addtorque command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_alchemy.html">fix alchemy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_bitorsion.html">fix amoeba/bitorsion command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_pitorsion.html">fix amoeba/pitorsion command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_append_atoms.html">fix append/atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atc.html">fix atc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atom_swap.html">fix atom/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_atom.html">fix ave/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_chunk.html">fix ave/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate.html">fix ave/correlate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate_long.html">fix ave/correlate/long command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_grid.html">fix ave/grid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html">fix ave/histo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html#fix-ave-histo-weight-command">fix ave/histo/weight command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial.html">fix ave/spatial command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial_sphere.html">fix ave/spatial/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_time.html">fix ave/time command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_aveforce.html">fix aveforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_balance.html">fix balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bocs.html">fix bocs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_break.html">fix bond/break command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html">fix bond/create command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html#fix-bond-create-angle-command">fix bond/create/angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_react.html">fix bond/react command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_swap.html">fix bond/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_box_relax.html">fix box/relax command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html">fix brownian command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-sphere-command">fix brownian/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-asphere-command">fix brownian/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_charge_regulation.html">fix charge/regulation command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_cmap.html">fix cmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_colvars.html">fix colvars command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_controller.html">fix controller command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_damping_cundall.html">fix damping/cundall command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html">fix deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform_pressure.html">fix deform/pressure command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deposit.html">fix deposit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_energy.html">fix dpd/energy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html">fix edpd/source command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html#fix-tdpd-source-command">fix tdpd/source command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drag.html">fix drag command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude.html">fix drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html">fix drude/transform/direct command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html#fix-drude-transform-inverse-command">fix drude/transform/inverse command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dt_reset.html">fix dt/reset command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html">fix efield command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html#fix-efield-tip4p-command">fix efield/tip4p command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ehex.html">fix ehex command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html">fix electrode/conp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html#fix-electrode-conq-command">fix electrode/conq command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html#fix-electrode-thermo-command">fix electrode/thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electron_stopping.html">fix electron/stopping command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electron_stopping.html#fix-electron-stopping-fit-command">fix electron/stopping/fit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_enforce2d.html">fix enforce2d command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_cv.html">fix eos/cv command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table.html">fix eos/table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table_rx.html">fix eos/table/rx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_evaporate.html">fix evaporate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_external.html">fix external command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ffl.html">fix ffl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_filter_corotate.html">fix filter/corotate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_flow_gauss.html">fix flow/gauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_freeze.html">fix freeze command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gcmc.html">fix gcmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gld.html">fix gld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gle.html">fix gle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html">fix gravity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_grem.html">fix grem command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_halt.html">fix halt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_heat.html">fix heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_heat_flow.html">fix heat/flow command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_hyper_global.html">fix hyper/global command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">fix hyper/local 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="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</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="fix_imd.html">fix imd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_indent.html">fix indent command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ipi.html">fix ipi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html">fix langevin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_drude.html">fix langevin/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_eff.html">fix langevin/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_spin.html">fix langevin/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_fluid.html">fix lb/fluid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_momentum.html">fix lb/momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mdi_qm.html">fix mdi/qm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mdi_qmmm.html">fix mdi/qmmm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso_move.html">fix meso/move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mol_swap.html">fix mol/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html">fix momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html#fix-momentum-chunk-command">fix momentum/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_move.html">fix move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html">fix mvv/dpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-edpd-command">fix mvv/edpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-tdpd-command">fix mvv/tdpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb_spin.html">fix neb/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html">fix nvt/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html#fix-npt-uef-command">fix npt/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nonaffine_displacement.html">fix nonaffine/displacement command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_cauchy.html">fix npt/cauchy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html">fix npt/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_numdiff.html">fix numdiff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_numdiff_virial.html">fix numdiff/virial command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_awpmd.html">fix nve/awpmd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_body.html">fix nve/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_bpm_sphere.html">fix nve/bpm/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_dot.html">fix nve/dot command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_dotc_langevin.html">fix nve/dotc/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_eff.html">fix nve/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_limit.html">fix nve/limit command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_line.html">fix nve/line command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_manifold_rattle.html">fix nve/manifold/rattle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_noforce.html">fix nve/noforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html">fix nve/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_spin.html">fix nve/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_tri.html">fix nve/tri command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvk.html">fix nvk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html">fix nvt/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_body.html">fix nvt/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html">fix nvt/sllod command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod_eff.html">fix nvt/sllod/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html">fix nvt/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_oneway.html">fix oneway command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_orient.html">fix orient/fcc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_orient_eco.html">fix orient/eco command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pafi.html">fix pafi command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pair.html">fix pair command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_phonon.html">fix phonon command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html">fix pimd/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html#fix-pimd-nvt-command">fix pimd/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimdb.html">fix pimdb/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimdb.html#fix-pimdb-nvt-command">fix pimdb/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_planeforce.html">fix planeforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_plumed.html">fix plumed command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html">fix polarize/bem/gmres command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html#fix-polarize-bem-icc-command">fix polarize/bem/icc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html#fix-polarize-functional-command">fix polarize/functional command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pour.html">fix pour command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_precession_spin.html">fix precession/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_press_berendsen.html">fix press/berendsen command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_press_langevin.html">fix press/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_print.html">fix print command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_propel_self.html">fix propel/self command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_property_atom.html">fix property/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_python_invoke.html">fix python/invoke command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_python_move.html">fix python/move command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qbmsst.html">fix qbmsst command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html">fix qeq/point command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-shielded-command">fix qeq/shielded command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-slater-command">fix qeq/slater command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-ctip-command">fix qeq/ctip command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-dynamic-command">fix qeq/dynamic command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-fire-command">fix qeq/fire command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html">fix qeq/comb command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reaxff.html">fix qeq/reaxff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qmmm.html">fix qmmm command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qtb.html">fix qtb command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qtpie_reaxff.html">fix qtpie/reaxff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_reaxff_bonds.html">fix reaxff/bonds command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_reaxff_species.html">fix reaxff/species command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_recenter.html">fix recenter command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_restrain.html">fix restrain command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo.html">fix rheo command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_oxidation.html">fix rheo/oxidation command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_pressure.html">fix rheo/pressure command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_thermal.html">fix rheo/thermal command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_viscosity.html">fix rheo/viscosity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rhok.html">fix rhok command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html">fix rigid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-command">fix rigid/nve command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-command">fix rigid/npt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-command">fix rigid/nph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-small-command">fix rigid/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-small-command">fix rigid/nph/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid_meso.html">fix rigid/meso command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rx.html">fix rx command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_saed_vtk.html">fix saed/vtk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html">fix setforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html#fix-setforce-spin-command">fix setforce/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sgcmc.html">fix sgcmc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_shake.html">fix shake command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_shake.html#fix-rattle-command">fix rattle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_shardlow.html">fix shardlow command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd.html">fix smd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_adjust_dt.html">fix smd/adjust_dt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_tlsph.html">fix smd/integrate_tlsph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_ulsph.html">fix smd/integrate_ulsph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_move_triangulated_surface.html">fix smd/move_tri_surf command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_setvel.html">fix smd/setvel command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_wall_surface.html">fix smd/wall_surface command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sph.html">fix sph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sph_stationary.html">fix sph/stationary command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring.html">fix spring command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring_chunk.html">fix spring/chunk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring_rg.html">fix spring/rg command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring_self.html">fix spring/self command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_srd.html">fix srd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_store_force.html">fix store/force command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_store_state.html">fix store/state command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_berendsen.html">fix temp/berendsen command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html">fix temp/csvr command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html#fix-temp-csld-command">fix temp/csld command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale.html">fix temp/rescale command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tgnh_drude.html">fix tgnvt/drude command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tgnh_drude.html#fix-tgnpt-drude-command">fix tgnpt/drude command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-grid-command">fix ttm/grid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_viscosity.html">fix viscosity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_viscous.html">fix viscous command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_viscous_sphere.html">fix viscous/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lepton-command">fix wall/lepton command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-morse-command">fix wall/morse command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-table-command">fix wall/table command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polygon.html">fix wall/body/polygon command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polyhedron.html">fix wall/body/polyhedron command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_ees.html">fix wall/ees command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_ees.html#fix-wall-region-ees-command">fix wall/region/ees command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_flow.html">fix wall/flow command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran_region.html">fix wall/gran/region command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_piston.html">fix wall/piston command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect_stochastic.html">fix wall/reflect/stochastic command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_widom.html">fix widom command</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
</div>
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</nav>
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
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<li class="breadcrumb-item"><a href="fixes.html">Fix Styles</a></li>
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<li class="breadcrumb-item active">fix hyper/local command</li>
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<li class="wy-breadcrumbs-aside">
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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</li>
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</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
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<a href="fix_hyper_global.html" class="btn btn-neutral float-left" title="fix hyper/global command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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||
<a href="fix_imd.html" class="btn btn-neutral float-right" title="fix imd command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
<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="fix-hyper-local-command">
|
||
<span id="index-0"></span><h1>fix hyper/local command<a class="headerlink" href="#fix-hyper-local-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">fix </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">hyper</span><span class="o">/</span><span class="n">local</span><span class="w"> </span><span class="n">cutbond</span><span class="w"> </span><span class="n">qfactor</span><span class="w"> </span><span class="n">Vmax</span><span class="w"> </span><span class="n">Tequil</span><span class="w"> </span><span class="n">Dcut</span><span class="w"> </span><span class="n">alpha</span><span class="w"> </span><span class="n">Btarget</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p></li>
|
||
<li><p>hyper/local = style name of this fix command</p></li>
|
||
<li><p>cutbond = max distance at which a pair of atoms is considered bonded (distance units)</p></li>
|
||
<li><p>qfactor = max strain at which bias potential goes to 0.0 (unitless)</p></li>
|
||
<li><p>Vmax = estimated height of bias potential (energy units)</p></li>
|
||
<li><p>Tequil = equilibration temperature (temperature units)</p></li>
|
||
<li><p>Dcut = minimum distance between boosted bonds (distance units)</p></li>
|
||
<li><p>alpha = boostostat relaxation time (time units)</p></li>
|
||
<li><p>Btarget = desired time boost factor (unitless)</p></li>
|
||
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>bound</em> or <em>reset</em> or <em>check/ghost</em> or <em>check/bias</em></p>
|
||
<pre class="literal-block"><em>bound</em> value = Bfrac
|
||
Bfrac = -1 or a value >= 0.0
|
||
<em>reset</em> value = Rfreq
|
||
Rfreq = -1 or 0 or timestep value > 0
|
||
<em>check/ghost</em> values = none
|
||
<em>check/bias</em> values = Nevery error/warn/ignore</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">fix </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">hyper</span><span class="o">/</span><span class="n">local</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="m">0.3</span><span class="w"> </span><span class="m">0.8</span><span class="w"> </span><span class="m">300.0</span>
|
||
<span class="k">fix </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">hyper</span><span class="o">/</span><span class="n">local</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="m">0.3</span><span class="w"> </span><span class="m">0.8</span><span class="w"> </span><span class="m">300.0</span><span class="w"> </span><span class="n">bound</span><span class="w"> </span><span class="m">0.1</span><span class="w"> </span><span class="n">reset</span><span class="w"> </span><span class="m">0</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>This fix is meant to be used with the <a class="reference internal" href="hyper.html"><span class="doc">hyper</span></a> command to
|
||
perform a bond-boost local hyperdynamics (LHD) simulation. The role
|
||
of this fix is to a select multiple pairs of atoms in the system at
|
||
each timestep to add a local bias potential to, which will alter the
|
||
dynamics of the system in a manner that effectively accelerates time.
|
||
This is in contrast to the <a class="reference internal" href="fix_hyper_global.html"><span class="doc">fix hyper/global</span></a>
|
||
command, which can be user to perform a global hyperdynamics (GHD)
|
||
simulation, by adding a global bias potential to a single pair of
|
||
atoms at each timestep. GHD can time accelerate a small simulation
|
||
with up to a few 100 atoms. For larger systems, LHD is needed to
|
||
achieve good time acceleration.</p>
|
||
<p>For a system that undergoes rare transition events, where one or more
|
||
atoms move over an energy barrier to a new potential energy basin, the
|
||
effect of the bias potential is to induce more rapid transitions.
|
||
This can lead to a dramatic speed-up in the rate at which events
|
||
occurs, without altering their relative frequencies, thus leading to
|
||
an overall increase in the elapsed real time of the simulation as
|
||
compared to running for the same number of timesteps with normal MD.
|
||
See the <a class="reference internal" href="hyper.html"><span class="doc">hyper</span></a> page for a more general discussion of
|
||
hyperdynamics and citations that explain both GHD and LHD.</p>
|
||
<p>The equations and logic used by this fix and described here to perform
|
||
LHD follow the description given in <a class="reference internal" href="#voter2013lhd"><span class="std std-ref">(Voter2013)</span></a>. The
|
||
bond-boost form of a bias potential for HD is due to Miron and
|
||
Fichthorn as described in <a class="reference internal" href="#mironlhd"><span class="std std-ref">(Miron)</span></a>.</p>
|
||
<p>To understand this description, you should first read the description
|
||
of the GHD algorithm on the <a class="reference internal" href="fix_hyper_global.html"><span class="doc">fix hyper/global</span></a>
|
||
doc page. This description of LHD builds on the GHD description.</p>
|
||
<p>The definition of bonds and <span class="math notranslate nohighlight">\(E_{ij}\)</span> are the same for GHD and LHD.
|
||
The formulas for <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> and <span class="math notranslate nohighlight">\(F^{max}_{ij}\)</span> are also
|
||
the same except for a prefactor <span class="math notranslate nohighlight">\(C_{ij}\)</span>, explained below.</p>
|
||
<p>The bias energy <span class="math notranslate nohighlight">\(V_{ij}\)</span> applied to a bond <em>ij</em> with maximum strain is</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[V^{max}_{ij} = C_{ij} \cdot V^{max} \cdot \left(1 - \left(\frac{E_{ij}}{q}\right)^2\right) \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise}\]</div>
|
||
<p>The derivative of <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> with respect to the position of
|
||
each atom in the <em>ij</em> bond gives a bias force <span class="math notranslate nohighlight">\(F^{max}_{ij}\)</span> acting
|
||
on the bond as</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[F^{max}_{ij} = - \frac{dV^{max}_{ij}}{dE_{ij}} = 2 C_{ij} V^{max} \frac{E_{ij}}{qfactor^2} \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise}\]</div>
|
||
<p>which can be decomposed into an equal and opposite force acting on
|
||
only the two atoms <em>i</em> and <em>j</em> in the <em>ij</em> bond.</p>
|
||
<p>The key difference is that in GHD a bias energy and force is added (on
|
||
a particular timestep) to only one bond (pair of atoms) in the system,
|
||
which is the bond with maximum strain <span class="math notranslate nohighlight">\(E^{max}\)</span>.</p>
|
||
<p>In LHD, a bias energy and force can be added to multiple bonds
|
||
separated by the specified <em>Dcut</em> distance or more. A bond <em>ij</em> is
|
||
biased if it is the maximum strain bond within its local
|
||
“neighborhood”, which is defined as the bond <em>ij</em> plus any neighbor
|
||
bonds within a distance <em>Dcut</em> from <em>ij</em>. The “distance” between bond
|
||
<em>ij</em> and bond <em>kl</em> is the minimum distance between any of the <em>ik</em>, <em>il</em>,
|
||
<em>jk</em>, and <em>jl</em> pairs of atoms.</p>
|
||
<p>For a large system, multiple bonds will typically meet this
|
||
requirement, and thus a bias potential <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> will be
|
||
applied to many bonds on the same timestep.</p>
|
||
<p>In LHD, all bonds store a <span class="math notranslate nohighlight">\(C_{ij}\)</span> prefactor which appears in
|
||
the <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> and <span class="math notranslate nohighlight">\(F^{max}_{ij}equations above. Note
|
||
that the :math:`C_{ij}\)</span> factor scales the strength of the bias energy
|
||
and forces whenever bond <em>ij</em> is the maximum strain bond in its neighborhood.</p>
|
||
<p><span class="math notranslate nohighlight">\(C_{ij}\)</span> is initialized to 1.0 when a bond between the <em>ij</em> atoms
|
||
is first defined. The specified <em>Btarget</em> factor is then used to adjust the
|
||
<span class="math notranslate nohighlight">\(C_{ij}\)</span> prefactors for each bond every timestep in the following manner.</p>
|
||
<p>An instantaneous boost factor <span class="math notranslate nohighlight">\(B_{ij}\)</span> is computed each timestep
|
||
for each bond, as</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[B_{ij} = e^{\beta V^{max}_{kl}}\]</div>
|
||
<p>where <span class="math notranslate nohighlight">\(V^{max}_{kl}\)</span> is the bias energy of the maxstrain bond <em>kl</em>
|
||
within bond <em>ij</em>‘s neighborhood, <span class="math notranslate nohighlight">\(\beta = \frac{1}{kT_{equil}}\)</span>,
|
||
and <span class="math notranslate nohighlight">\(T_{equil}\)</span> is the temperature of the system and an argument
|
||
to this fix.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>To run an LHD simulation, the input script must also use the
|
||
<a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command to thermostat the atoms at
|
||
the same <span class="math notranslate nohighlight">\(T_{equil}\)</span> as specified by this fix, so that the
|
||
system is running constant-temperature (NVT) dynamics. LAMMPS does
|
||
not check that this is done.</p>
|
||
</div>
|
||
<p>Note that if <em>ij</em>== <em>kl</em>, then bond <em>ij</em> is a biased bond on that
|
||
timestep, otherwise it is not. But regardless, the boost factor
|
||
<span class="math notranslate nohighlight">\(B_{ij}\)</span> can be thought of an estimate of time boost currently
|
||
being applied within a local region centered on bond <em>ij</em>. For LHD,
|
||
we want this to be the specified <em>Btarget</em> value everywhere in the
|
||
simulation domain.</p>
|
||
<p>To accomplish this, if <span class="math notranslate nohighlight">\(B_{ij} < B_{target}\)</span>, the <span class="math notranslate nohighlight">\(C_{ij}\)</span>
|
||
prefactor for bond <em>ij</em> is incremented on the current timestep by an
|
||
amount proportional to the inverse of the specified <span class="math notranslate nohighlight">\(\alpha\)</span> and
|
||
the difference (<span class="math notranslate nohighlight">\(B_{ij} - B_{target}\)</span>). Conversely if
|
||
<span class="math notranslate nohighlight">\(B_{ij} > B_{target}\)</span>, <span class="math notranslate nohighlight">\(C_{ij}\)</span> is decremented by the same
|
||
amount. This procedure is termed “boostostatting” in <a class="reference internal" href="#voter2013lhd"><span class="std std-ref">(Voter2013)</span></a>. It drives all of the individual <span class="math notranslate nohighlight">\(C_{ij}\)</span> to
|
||
values such that when <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> is applied as a bias to bond
|
||
<em>ij</em>, the resulting boost factor <span class="math notranslate nohighlight">\(B_{ij}\)</span> will be close to
|
||
<span class="math notranslate nohighlight">\(B_{target}\)</span> on average. Thus the LHD time acceleration factor
|
||
for the overall system is effectively <em>Btarget</em>.</p>
|
||
<p>Note that in LHD, the boost factor <span class="math notranslate nohighlight">\(B_{target}\)</span> is specified by the user.
|
||
This is in contrast to global hyperdynamics (GHD) where the boost
|
||
factor varies each timestep and is computed as a function of <span class="math notranslate nohighlight">\(V_{max}\)</span>,
|
||
<span class="math notranslate nohighlight">\(E_{max}\)</span>, and <span class="math notranslate nohighlight">\(T_{equil}\)</span>; see the
|
||
<a class="reference internal" href="fix_hyper_global.html"><span class="doc">fix hyper/global</span></a> page for details.</p>
|
||
<hr class="docutils" />
|
||
<p>Here is additional information on the input parameters for LHD.</p>
|
||
<p>Note that the <em>cutbond</em>, <em>qfactor</em>, and <em>Tequil</em> arguments have the
|
||
same meaning as for GHD. The <em>Vmax</em> argument is slightly different.
|
||
The <em>Dcut</em>, <em>alpha</em>, and <em>Btarget</em> parameters are unique to LHD.</p>
|
||
<p>The <em>cutbond</em> argument is the cutoff distance for defining bonds
|
||
between pairs of nearby atoms. A pair of I,J atoms in their
|
||
equilibrium, minimum-energy configuration, which are separated by a
|
||
distance <span class="math notranslate nohighlight">\(R_{ij} < cutbond\)</span>, are flagged as a bonded pair. Setting
|
||
<em>cubond</em> to be ~25% larger than the nearest-neighbor distance in a
|
||
crystalline lattice is a typical choice for solids, so that bonds
|
||
exist only between nearest neighbor pairs.</p>
|
||
<p>The <em>qfactor</em> argument is the limiting strain at which the bias
|
||
potential goes to 0.0. It is dimensionless, so a value of 0.3 means a
|
||
bond distance can be up to 30% larger or 30% smaller than the
|
||
equilibrium (quenched) <span class="math notranslate nohighlight">\(R^0_{ij}\)</span> distance and the two atoms in the bond
|
||
could still experience a non-zero bias force.</p>
|
||
<p>If <em>qfactor</em> is set too large, then transitions from one energy basin
|
||
to another are affected because the bias potential is non-zero at the
|
||
transition state (e.g. saddle point). If <em>qfactor</em> is set too small
|
||
than little boost can be achieved because the <span class="math notranslate nohighlight">\(E_{ij}\)</span> strain of
|
||
some bond in
|
||
the system will (nearly) always exceed <em>qfactor</em>. A value of 0.3 for
|
||
<em>qfactor</em> is typically a reasonable value.</p>
|
||
<p>The <em>Vmax</em> argument is a fixed prefactor on the bias potential. There
|
||
is a also a dynamic prefactor <span class="math notranslate nohighlight">\(C_{ij}\)</span>, driven by the choice of
|
||
<em>Btarget</em> as discussed above. The product of these should be a value less than
|
||
the smallest barrier height for an event to occur. Otherwise the
|
||
applied bias potential may be large enough (when added to the
|
||
interatomic potential) to produce a local energy basin with a maxima
|
||
in the center. This can produce artificial energy minima in the same
|
||
basin that trap an atom. Or if <span class="math notranslate nohighlight">\(C_{ij} \cdot V^{max}\)</span> is even
|
||
larger, it may
|
||
induce an atom(s) to rapidly transition to another energy basin. Both
|
||
cases are “bad dynamics” which violate the assumptions of LHD that
|
||
guarantee an accelerated time-accurate trajectory of the system.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>It may seem that <span class="math notranslate nohighlight">\(V^{max}\)</span> can be set to any value, and
|
||
<span class="math notranslate nohighlight">\(C_{ij}\)</span> will compensate to reduce the overall prefactor
|
||
if necessary. However the <span class="math notranslate nohighlight">\(C_{ij}\)</span> are initialized to 1.0
|
||
and the boostostatting procedure typically operates slowly enough
|
||
that there can be a time period of bad dynamics if <span class="math notranslate nohighlight">\(V^{max}\)</span>
|
||
is set too large. A better strategy is to set <span class="math notranslate nohighlight">\(V^{max}\)</span> to the
|
||
slightly smaller than the lowest barrier height for an event (the same
|
||
as for GHD), so that the <span class="math notranslate nohighlight">\(C_{ij}\)</span> remain near unity.</p>
|
||
</div>
|
||
<p>The <em>Tequil</em> argument is the temperature at which the system is
|
||
simulated; see the comment above about the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> thermostatting. It is also part of the beta term in the
|
||
exponential factor that determines how much boost is achieved as a
|
||
function of the bias potential. See the discussion of the <em>Btarget</em>
|
||
argument below.</p>
|
||
<p>As discussed above, the <em>Dcut</em> argument is the distance required
|
||
between two locally maxstrain bonds for them to both be selected as
|
||
biased bonds on the same timestep. Computationally, the larger <em>Dcut</em>
|
||
is, the more work (computation and communication) must be done each
|
||
timestep within the LHD algorithm. And the fewer bonds can be
|
||
simultaneously biased, which may mean the specified <em>Btarget</em> time
|
||
acceleration cannot be achieved.</p>
|
||
<p>Physically <em>Dcut</em> should be a long enough distance that biasing two
|
||
pairs of atoms that close together will not influence the dynamics of
|
||
each pair. E.g. something like 2x the cutoff of the interatomic
|
||
potential. In practice a <em>Dcut</em> value of ~10 Angstroms seems to work
|
||
well for many solid-state systems.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>You should ensure that ghost atom communication is performed for
|
||
a distance of at least <em>Dcut</em> + <em>cutevent</em> = the distance one or more
|
||
atoms move (between quenched states) to be considered an “event”. It
|
||
is an argument to the “compute event/displace” command used to detect
|
||
events. By default the ghost communication distance is set by the
|
||
pair_style cutoff, which will typically be < <em>Dcut</em>. The <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify cutoff</span></a> command should be used to override the ghost
|
||
cutoff explicitly, e.g.</p>
|
||
</div>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">comm_modify</span><span class="w"> </span><span class="n">cutoff</span><span class="w"> </span><span class="m">12.0</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Note that this fix does not know the <em>cutevent</em> parameter, but uses
|
||
half the <em>cutbond</em> parameter as an estimate to warn if the ghost
|
||
cutoff is not long enough.</p>
|
||
<p>As described above the <em>alpha</em> argument is a prefactor in the
|
||
boostostat update equation for each bond’s <span class="math notranslate nohighlight">\(C_{ij}\)</span> prefactor.
|
||
<em>Alpha</em> is specified in time units, similar to other thermostat or barostat
|
||
damping parameters. It is roughly the physical time it will take the
|
||
boostostat to adjust a <span class="math notranslate nohighlight">\(C_{ij}\)</span> value from a too high (or too low)
|
||
value to a correct one. An <em>alpha</em> setting of a few ps is typically good for
|
||
solid-state systems. Note that the <em>alpha</em> argument here is the
|
||
inverse of the alpha parameter discussed in
|
||
<a class="reference internal" href="#voter2013lhd"><span class="std std-ref">(Voter2013)</span></a>.</p>
|
||
<p>The <em>Btarget</em> argument is the desired time boost factor (a value > 1)
|
||
that all the atoms in the system will experience. The elapsed time
|
||
t_hyper for an LHD simulation running for <em>N</em> timesteps is simply</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[t_{hyper} = B_{target} \cdot N \cdot dt\]</div>
|
||
<p>where <em>dt</em> is the timestep size defined by the <a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a>
|
||
command. The effective time acceleration due to LHD is thus
|
||
<span class="math notranslate nohighlight">\(\frac{t_{hyper}}{N\cdot dt} = B_{target}\)</span>, where <span class="math notranslate nohighlight">\(N\cdot dt\)</span>
|
||
is the elapsed time for a normal MD run of N timesteps.</p>
|
||
<p>You cannot choose an arbitrarily large setting for <em>Btarget</em>. The
|
||
maximum value you should choose is</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[B_{target} = e^{\beta V_{small}}\]</div>
|
||
<p>where <span class="math notranslate nohighlight">\(V_{small}\)</span> is the smallest event barrier height in your
|
||
system, <span class="math notranslate nohighlight">\(\beta = \frac{1}{kT_{equil}}\)</span>, and <span class="math notranslate nohighlight">\(T_{equil}\)</span>
|
||
is the specified temperature of the system
|
||
(both by this fix and the Langevin thermostat).</p>
|
||
<p>Note that if <em>Btarget</em> is set smaller than this, the LHD simulation
|
||
will run correctly. There will just be fewer events because the hyper
|
||
time (t_hyper equation above) will be shorter.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you have no physical intuition as to the smallest barrier
|
||
height in your system, a reasonable strategy to determine the largest
|
||
<em>Btarget</em> you can use for an LHD model, is to run a sequence of
|
||
simulations with smaller and smaller <em>Btarget</em> values, until the event
|
||
rate does not change (as a function of hyper time).</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>Here is additional information on the optional keywords for this fix.</p>
|
||
<p>The <em>bound</em> keyword turns on min/max bounds for bias coefficients
|
||
<span class="math notranslate nohighlight">\(C_{ij}\)</span> for all bonds. <span class="math notranslate nohighlight">\(C_{ij}\)</span> is a prefactor for each bond on
|
||
the bias potential of maximum strength <span class="math notranslate nohighlight">\(V^{max}\)</span>. Depending on the
|
||
choice of <em>alpha</em> and <em>Btarget</em> and <em>Vmax</em>, the boostostatting can cause
|
||
individual <span class="math notranslate nohighlight">\(C_{ij}\)</span> values to fluctuate. If the fluctuations are too
|
||
large <span class="math notranslate nohighlight">\(C_{ij} \cdot V^{max}\)</span> can exceed low barrier heights and induce
|
||
bad event dynamics. Bounding the <span class="math notranslate nohighlight">\(C_{ij}\)</span> values is a way to prevent
|
||
this. If <em>Bfrac</em> is set to -1 or any negative value (the default) then no
|
||
bounds are enforced on <span class="math notranslate nohighlight">\(C_{ij}\)</span> values (except they must always
|
||
be >= 0.0). A <em>Bfrac</em> setting >= 0.0
|
||
sets a lower bound of 1.0 - Bfrac and upper bound of 1.0 + Bfrac on each
|
||
<span class="math notranslate nohighlight">\(C_{ij}\)</span> value. Note that all <span class="math notranslate nohighlight">\(C_{ij}\)</span> values are initialized
|
||
to 1.0 when a bond is created for the first time. Thus <em>Bfrac</em> limits the
|
||
bias potential height to <em>Vmax</em> +/- <em>Bfrac</em>*<em>Vmax</em>.</p>
|
||
<p>The <em>reset</em> keyword allow <em>Vmax</em> to be adjusted dynamically depending on the
|
||
average value of all <span class="math notranslate nohighlight">\(C_{ij}\)</span> prefactors. This can be useful if you
|
||
are unsure what value of <em>Vmax</em> will match the <em>Btarget</em> boost for the
|
||
system. The <span class="math notranslate nohighlight">\(C_{ij}\)</span> values will then adjust in aggregate (up or down)
|
||
so that <span class="math notranslate nohighlight">\(C_{ij} \cdot V^{max}\)</span> produces a boost of <em>Btarget</em>, but this
|
||
may conflict with the <em>bound</em> keyword settings. By using <em>bound</em> and <em>reset</em>
|
||
together, <span class="math notranslate nohighlight">\(V^{max}\)</span> itself can be reset, and desired bounds still applied
|
||
to the <span class="math notranslate nohighlight">\(C_{ij}\)</span> values.</p>
|
||
<p>A setting for <em>Rfreq</em> of -1 (the default) means <em>Vmax</em> never changes.
|
||
A setting of 0 means <span class="math notranslate nohighlight">\(V^{max}\)</span> is adjusted every time an event occurs and
|
||
bond pairs are recalculated. A setting of N > 0 timesteps means
|
||
<span class="math notranslate nohighlight">\(V^{max}\)</span> is adjusted on the first time an event occurs on a timestep >=
|
||
N steps after the previous adjustment. The adjustment to <span class="math notranslate nohighlight">\(V^{max}\)</span> is
|
||
computed as follows. The current average of all <span class="math notranslate nohighlight">\(C_{ij} \cdot V^{max}\)</span>
|
||
values is computed and the <span class="math notranslate nohighlight">\(V^{max}\)</span> is reset to that value. All
|
||
<span class="math notranslate nohighlight">\(C_{ij}\)</span> values are changed to new prefactors such the new
|
||
<span class="math notranslate nohighlight">\(C_{ij} \cdot V^{max}\)</span> is the same as it was previously. If the
|
||
<em>bound</em> keyword was used, those bounds are enforced on the new <span class="math notranslate nohighlight">\(C_{ij}\)</span>
|
||
values. Henceforth, new bonds are assigned a <span class="math notranslate nohighlight">\(C_{ij} = 1.0\)</span>, which
|
||
means their bias potential magnitude is the new <span class="math notranslate nohighlight">\(V^{max}\)</span>.</p>
|
||
<p>The <em>check/ghost</em> keyword turns on extra computation each timestep to
|
||
compute statistics about ghost atoms used to determine which bonds to
|
||
bias. The output of these stats are the vector values 14 and 15,
|
||
described below. If this keyword is not enabled, the output
|
||
of the stats will be zero.</p>
|
||
<p>The <em>check/bias</em> keyword turns on extra computation and communication
|
||
to check if any biased bonds are closer than <em>Dcut</em> to each other,
|
||
which should not be the case if LHD is operating correctly. Thus it
|
||
is a debugging check. The <em>Nevery</em> setting determines how often the
|
||
check is made. The <em>error</em>, <em>warn</em>, or <em>ignore</em> setting determines
|
||
what is done if the count of too-close bonds is not zero. Either the
|
||
code will exit, or issue a warning, or silently tally the count. The
|
||
count can be output as vector value 17, as described below. If this
|
||
keyword is not enabled, the output of that statistic will be 0.</p>
|
||
<p>Note that both of these computations are costly, hence they are only
|
||
enabled by these keywords.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Link to this heading"></a></h2>
|
||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
|
||
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by
|
||
this fix to add the energy of the bias potential to the global
|
||
potential energy of the system as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>. The default setting for this fix is <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify
|
||
energy no</span></a>.</p>
|
||
<p>This fix computes a global scalar and global vector of length 28,
|
||
which can be accessed by various <a class="reference internal" href="Howto_output.html"><span class="doc">output commands</span></a>. The scalar is the magnitude of the bias potential
|
||
(energy units) applied on the current timestep, summed over all biased
|
||
bonds. The vector stores the following quantities:</p>
|
||
<blockquote>
|
||
<div><ol class="arabic simple">
|
||
<li><p>average boost for all bonds on this step (unitless)</p></li>
|
||
<li><p># of biased bonds on this step</p></li>
|
||
<li><p>max strain <span class="math notranslate nohighlight">\(E_{ij}\)</span> of any bond on this step (absolute value, unitless)</p></li>
|
||
<li><p>value of <span class="math notranslate nohighlight">\(V^{max}\)</span> on this step (energy units)</p></li>
|
||
<li><p>average bias coeff for all bonds on this step (unitless)</p></li>
|
||
<li><p>min bias coeff for all bonds on this step (unitless)</p></li>
|
||
<li><p>max bias coeff for all bonds on this step (unitless)</p></li>
|
||
<li><p>average # of bonds/atom on this step</p></li>
|
||
<li><p>average neighbor bonds/bond on this step within <em>Dcut</em></p></li>
|
||
<li><p>average boost for all bonds during this run (unitless)</p></li>
|
||
<li><p>average # of biased bonds/step during this run</p></li>
|
||
<li><p>fraction of biased bonds with no bias during this run</p></li>
|
||
<li><p>fraction of biased bonds with negative strain during this run</p></li>
|
||
<li><p>max bond length during this run (distance units)</p></li>
|
||
<li><p>average bias coeff for all bonds during this run (unitless)</p></li>
|
||
<li><p>min bias coeff for any bond during this run (unitless)</p></li>
|
||
<li><p>max bias coeff for any bond during this run (unitless)</p></li>
|
||
<li><p>max drift distance of any bond atom during this run (distance units)</p></li>
|
||
<li><p>max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)</p></li>
|
||
<li><p>max distance outside my box of any ghost atom with any maxstrain during this run (distance units)</p></li>
|
||
<li><p>count of ghost atoms that could not be found on reneighbor steps during this run</p></li>
|
||
<li><p>count of bias overlaps (< <em>Dcut</em>) found during this run</p></li>
|
||
<li><p>cumulative hyper time since fix created (time units)</p></li>
|
||
<li><p>cumulative count of event timesteps since fix created</p></li>
|
||
<li><p>cumulative count of atoms in events since fix created</p></li>
|
||
<li><p>cumulative # of new bonds formed since fix created</p></li>
|
||
<li><p>average boost for biased bonds on this step (unitless)</p></li>
|
||
<li><p># of bonds with absolute strain >= q on this step</p></li>
|
||
</ol>
|
||
</div></blockquote>
|
||
<p>Quantities 1-9 are for the current timestep. Quantities 10-22
|
||
are for the current hyper run. They are reset each time a new
|
||
hyper run is performed. Quantities 23-26 are cumulative across
|
||
multiple runs (since the point in the input script the fix was
|
||
defined).</p>
|
||
<p>For value 10, each bond instantaneous boost factor is given by the
|
||
equation for <span class="math notranslate nohighlight">\(B_{ij}\)</span> above. The total system boost (average across all
|
||
bonds) fluctuates, but should average to a value close to the
|
||
specified <span class="math notranslate nohighlight">\(B_{target}\)</span>.</p>
|
||
<p>For value 12, the numerator is a count of all biased bonds on each
|
||
timestep whose bias energy = 0.0 due to <span class="math notranslate nohighlight">\(E_{ij} >= qfactor\)</span>. The
|
||
denominator is the count of all biased bonds on all timesteps.</p>
|
||
<p>For value 13, the numerator is a count of all biased bonds on each
|
||
timestep with negative strain. The denominator is the count of all
|
||
biased bonds on all timesteps.</p>
|
||
<p>Values 18-22 are mostly useful for debugging and diagnostic purposes.</p>
|
||
<p>For value 18, drift is the distance an atom moves between two quenched
|
||
states when the second quench determines an event has occurred. Atoms
|
||
involved in an event will typically move the greatest distance since
|
||
others typically remain near their original quenched position.</p>
|
||
<p>For values 19-21, neighbor atoms in the full neighbor list with cutoff
|
||
<em>Dcut</em> may be ghost atoms outside a processor’s sub-box. Before the
|
||
next event occurs they may move further than <em>Dcut</em> away from the
|
||
sub-box boundary. Value 19 is the furthest (from the sub-box) any
|
||
ghost atom in the neighbor list with maxstrain < <em>qfactor</em> was
|
||
accessed during the run. Value 20 is the same except that the ghost
|
||
atom’s maxstrain may be >= <em>qfactor</em>, which may mean it is about to
|
||
participate in an event. Value 21 is a count of how many ghost atoms
|
||
could not be found on reneighbor steps, presumably because they moved
|
||
too far away due to their participation in an event (which will likely
|
||
be detected at the next quench).</p>
|
||
<p>Typical values for 19 and 20 should be slightly larger than <em>Dcut</em>,
|
||
which accounts for ghost atoms initially at a <em>Dcut</em> distance moving
|
||
thermally before the next event takes place.</p>
|
||
<p>Note that for values 19 and 20 to be computed, the optional keyword
|
||
<em>check/ghost</em> must be specified. Otherwise these values will be zero.
|
||
This is because computing them incurs overhead, so the values are only
|
||
computed if requested.</p>
|
||
<p>Value 21 should be zero or small. As explained above a small count
|
||
likely means some ghost atoms were participating in their own events
|
||
and moved a longer distance. If the value is large, it likely means
|
||
the communication cutoff for ghosts is too close to <em>Dcut</em> leading to
|
||
many not-found ghost atoms before the next event. This may lead to a
|
||
reduced number of bonds being selected for biasing, since the code
|
||
assumes those atoms are part of highly strained bonds. As explained
|
||
above, the <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify cutoff</span></a> command can be used
|
||
to set a longer cutoff.</p>
|
||
<p>For value 22, no two bonds should be biased if they are within a
|
||
<em>Dcut</em> distance of each other. This value should be zero, indicating
|
||
that no pair of biased bonds are closer than <em>Dcut</em> from each other.</p>
|
||
<p>Note that for value 22 to be computed, the optional keyword
|
||
<em>check/bias</em> must be specified and it determines how often this check
|
||
is performed. This is because performing the check incurs overhead,
|
||
so if only computed as often as requested.</p>
|
||
<p>The result at the end of the run is the cumulative total from every
|
||
timestep the check was made. Note that the value is a count of atoms
|
||
in bonds which found other atoms in bonds too close, so it is almost
|
||
always an over-count of the number of too-close bonds.</p>
|
||
<p>Value 23 is simply the specified <em>boost</em> factor times the number of
|
||
timesteps times the timestep size.</p>
|
||
<p>For value 24, events are checked for by the <a class="reference internal" href="hyper.html"><span class="doc">hyper</span></a> command
|
||
once every <em>Nevent</em> timesteps. This value is the count of those
|
||
timesteps on which one (or more) events was detected. It is NOT the
|
||
number of distinct events, since more than one event may occur in the
|
||
same <em>Nevent</em> time window.</p>
|
||
<p>For value 25, each time the <a class="reference internal" href="hyper.html"><span class="doc">hyper</span></a> command checks for an
|
||
event, it invokes a compute to flag zero or more atoms as
|
||
participating in one or more events. E.g. atoms that have displaced
|
||
more than some distance from the previous quench state. Value 25 is
|
||
the cumulative count of the number of atoms participating in any of
|
||
the events that were found.</p>
|
||
<p>Value 26 tallies the number of new bonds created by the bond reset
|
||
operation. Bonds between a specific I,J pair of atoms may persist for
|
||
the entire hyperdynamics simulation if neither I or J are involved in
|
||
an event.</p>
|
||
<p>Value 27 computes the average boost for biased bonds only on this step.</p>
|
||
<p>Value 28 is the count of bonds with an absolute value of strain >= q
|
||
on this step.</p>
|
||
<p>The scalar value and vector values are all “intensive”.</p>
|
||
<p>This fix also computes a local vector of length the number of bonds
|
||
currently in the system. The value for each bond is its <span class="math notranslate nohighlight">\(C_{ij}\)</span>
|
||
prefactor (bias coefficient). These values can be can be accessed by various
|
||
<a class="reference internal" href="Howto_output.html"><span class="doc">output commands</span></a>. A particularly useful one is the
|
||
<a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> command which can be used to
|
||
histogram the Cij values to see if they are distributed reasonably
|
||
close to 1.0, which indicates a good choice of <span class="math notranslate nohighlight">\(V^{max}\)</span>.</p>
|
||
<p>The local values calculated by this fix are unitless.</p>
|
||
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
||
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during
|
||
<a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This fix is part of the REPLICA package. It is only enabled if LAMMPS
|
||
was built with that 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="hyper.html"><span class="doc">hyper</span></a>, <a class="reference internal" href="fix_hyper_global.html"><span class="doc">fix hyper/global</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The default settings for optimal keywords are bounds = -1 and reset =
|
||
-1. The check/ghost and check/bias keywords are not enabled by
|
||
default.</p>
|
||
<hr class="docutils" />
|
||
<p id="voter2013lhd"><strong>(Voter2013)</strong> S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
|
||
144110 (2013).</p>
|
||
<p id="mironlhd"><strong>(Miron)</strong> R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
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<a href="fix_hyper_global.html" class="btn btn-neutral float-left" title="fix hyper/global command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="fix_imd.html" class="btn btn-neutral float-right" title="fix imd command" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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