663 lines
57 KiB
HTML
663 lines
57 KiB
HTML
<!DOCTYPE html>
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<title>fix hyper/global command — LAMMPS documentation</title>
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<link rel="next" title="fix hyper/local command" href="fix_hyper_local.html" />
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<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="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 current"><a class="current reference internal" href="#">fix hyper/global 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_hyper_local.html">fix hyper/local command</a></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>
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<li class="toctree-l2"><a class="reference internal" href="fix_numdiff_virial.html">fix numdiff/virial command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
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<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>
|
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<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>
|
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<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>
|
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<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>
|
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
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|
<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>
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|
<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>
|
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<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>
|
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<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>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-grid-command">fix ttm/grid command</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_viscous_sphere.html">fix viscous/sphere command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lepton-command">fix wall/lepton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-morse-command">fix wall/morse command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-table-command">fix wall/table command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polygon.html">fix wall/body/polygon command</a></li>
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<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>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_flow.html">fix wall/flow command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran_region.html">fix wall/gran/region command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_piston.html">fix wall/piston command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect_stochastic.html">fix wall/reflect/stochastic command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_widom.html">fix widom 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="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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<li class="breadcrumb-item active">fix hyper/global command</li>
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<a href="fix_hyper_local.html" class="btn btn-neutral float-right" title="fix hyper/local command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
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</div>
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<hr/>
|
|
</div>
|
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
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<div itemprop="articleBody">
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|
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
|
<section id="fix-hyper-global-command">
|
|
<span id="index-0"></span><h1>fix hyper/global command<a class="headerlink" href="#fix-hyper-global-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">global</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>
|
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</pre></div>
|
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</div>
|
|
<ul class="simple">
|
|
<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/global = 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 = height of bias potential (energy units)</p></li>
|
|
<li><p>Tequil = equilibration temperature (temperature units)</p></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">global</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>
|
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</pre></div>
|
|
</div>
|
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</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 global hyperdynamics (GHD) simulation. The role
|
|
of this fix is to a select a single pair of atoms in the system at
|
|
each timestep to add a global 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_local.html"><span class="doc">fix hyper/local</span></a>
|
|
command, which can be user to perform a local hyperdynamics (LHD)
|
|
simulation, by adding a local bias potential to multiple pairs 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
|
|
GHD follow the description given in <a class="reference internal" href="#voter2013ghd"><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="#mironghd"><span class="std std-ref">(Miron)</span></a>. In LAMMPS we use a
|
|
simplified version of bond-boost GHD where a single bond in the system
|
|
is biased at any one timestep.</p>
|
|
<p>Bonds are defined between each pair of atoms <em>ij</em>, whose <span class="math notranslate nohighlight">\(R^0_{ij}\)</span>
|
|
distance is less than <em>cutbond</em>, when the system is in a quenched state
|
|
(minimum) energy. Note that these are not “bonds” in a covalent
|
|
sense. A bond is simply any pair of atoms that meet the distance
|
|
criterion. <em>Cutbond</em> is an argument to this fix; it is discussed
|
|
below. A bond is only formed if one or both of the <em>ij</em> atoms are in
|
|
the specified group.</p>
|
|
<p>The current strain of bond <em>ij</em> (when running dynamics) is defined as</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[E_{ij} = \frac{R_{ij} - R^0_{ij}}{R^0_{ij}}\]</div>
|
|
<p>where <span class="math notranslate nohighlight">\(R_{ij}\)</span> is the current distance between atoms <em>i</em> and <em>j</em>,
|
|
and <span class="math notranslate nohighlight">\(R^0_{ij}\)</span> is the equilibrium distance in the quenched state.</p>
|
|
<p>The bias energy <span class="math notranslate nohighlight">\(V_{ij}\)</span> of any bond between atoms <em>i</em> and <em>j</em>
|
|
is defined as</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[V_{ij} = V^{max} \cdot \left( 1 - \left(\frac{E_{ij}}{q}\right)^2 \right) \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise}\]</div>
|
|
<p>where the prefactor <span class="math notranslate nohighlight">\(V^{max}\)</span> and the cutoff <em>qfactor</em> are arguments to
|
|
this fix; they are discussed below. This functional form is an
|
|
inverse parabola centered at 0.0 with height <span class="math notranslate nohighlight">\(V^{max}\)</span> and
|
|
which goes to 0.0 at +/- qfactor.</p>
|
|
<p>Let <span class="math notranslate nohighlight">\(E^{max}\)</span> be the maximum of <span class="math notranslate nohighlight">\(\left| E_{ij} \right|\)</span>
|
|
for all <em>ij</em> bonds in the system on a
|
|
given timestep. On that step, <span class="math notranslate nohighlight">\(V_{ij}\)</span> is added as a bias potential
|
|
to only the single bond with strain <span class="math notranslate nohighlight">\(E^{max}\)</span>, call it
|
|
<span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span>. Note that <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> will be 0.0
|
|
if <span class="math notranslate nohighlight">\(E^{max} >= \textrm{qfactor}\)</span> on that timestep. Also note
|
|
that <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> is added to the normal interatomic potential
|
|
that is computed between all atoms in the system at every step.</p>
|
|
<p>The derivative of <span class="math notranslate nohighlight">\(V^{max}_{ij}\)</span> with respect to the position of
|
|
each atom in the <span class="math notranslate nohighlight">\(E^{max}\)</span> 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">
|
|
\[F^{max}_{ij} = - \frac{dV^{max}_{ij}}{dE_{ij}} = \frac{2 V^{max} E-{ij}}{\textrm{qfactor}^2} \textrm{ for } \left|E_{ij}\right| < \textrm{qfactor} \textrm{ or } 0 \textrm{ otherwise}\]</div>
|
|
<p>which can be decomposed into an equal and opposite force acting on
|
|
only the two <em>ij</em> atoms in the <span class="math notranslate nohighlight">\(E^{max}\)</span> bond.</p>
|
|
<p>The time boost factor for the system is given each timestep I by</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[B_i = e^{\beta V^{max}_{ij}}\]</div>
|
|
<p>where <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. Note that
|
|
<span class="math notranslate nohighlight">\(B_i >= 1\)</span> at every step.</p>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note</p>
|
|
<p>To run a GHD 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>The elapsed time <span class="math notranslate nohighlight">\(t_{hyper}\)</span> for a GHD simulation running for <em>N</em>
|
|
timesteps is simply</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[t_{hyper} = \sum_{i=1,N} B-i \cdot dt\]</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 GHD is thus t_hyper /
|
|
N*dt, where N*dt is elapsed time for a normal MD run of N timesteps.</p>
|
|
<p>Note that in GHD, the boost factor varies from timestep to timestep.
|
|
Likewise, which bond has <span class="math notranslate nohighlight">\(E^{max}\)</span> strain and thus which pair of
|
|
atoms the bias potential is added to, will also vary from timestep to timestep.
|
|
This is in contrast to local hyperdynamics (LHD) where the boost
|
|
factor is an input parameter; see the <a class="reference internal" href="fix_hyper_local.html"><span class="doc">fix hyper/local</span></a> page for details.</p>
|
|
<hr class="docutils" />
|
|
<p>Here is additional information on the input parameters for GHD.</p>
|
|
<p>The <em>cutbond</em> argument is the cutoff distance for defining bonds between
|
|
pairs of nearby atoms. A pair of <em>ij</em> 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 is 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 reasonable.</p>
|
|
<p>The <em>Vmax</em> argument is the prefactor on the bias potential. Ideally,
|
|
tt should be set to a value slightly 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 <em>Vmax</em> 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 GHD that guarantee an accelerated
|
|
time-accurate trajectory of the system.</p>
|
|
<p>Note that if <em>Vmax</em> is set too small, the GHD 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>Vmax</em> you can use for a GHD model, is to run a sequence of
|
|
simulations with smaller and smaller <em>Vmax</em> values, until the event
|
|
rate does not change (as a function of hyper time).</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.</p>
|
|
<p>In general, the lower the value of <em>Tequil</em> and the higher the value
|
|
of <em>Vmax</em>, the more time boost will be achievable by the GHD
|
|
algorithm.</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 12,
|
|
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. The vector stores the
|
|
following quantities:</p>
|
|
<blockquote>
|
|
<div><ol class="arabic simple">
|
|
<li><p>boost factor on this step (unitless)</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>ID of first atom in the max-strain bond</p></li>
|
|
<li><p>ID of second atom in the max-strain bond</p></li>
|
|
<li><p>average # of bonds/atom on this step</p></li>
|
|
<li><p>fraction of timesteps where the biased bond has bias = 0.0 during this run</p></li>
|
|
<li><p>fraction of timesteps where the biased bond has negative strain during this run</p></li>
|
|
<li><p>max drift distance of any atom during this run (distance units)</p></li>
|
|
<li><p>max bond length during this run (distance units)</p></li>
|
|
<li><p>cumulative hyper time since fix was defined (time units)</p></li>
|
|
<li><p>cumulative count of event timesteps since fix was defined</p></li>
|
|
<li><p>cumulative count of atoms in events since fix was defined</p></li>
|
|
</ol>
|
|
</div></blockquote>
|
|
<p>The first 5 quantities are for the current timestep. Quantities 6-9
|
|
are for the current hyper run. They are reset each time a new hyper
|
|
run is performed. Quantities 19-12 are cumulative across multiple
|
|
runs (since the point in the input script the fix was defined).</p>
|
|
<p>For value 8, 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 value 11, 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 12, 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 11 is
|
|
the cumulative count of the number of atoms participating in any of
|
|
the events that were found.</p>
|
|
<p>The scalar and vector values calculated by this fix are all
|
|
“intensive”.</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 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> 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_local.html"><span class="doc">fix hyper/local</span></a></p>
|
|
</section>
|
|
<section id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
|
<p>none</p>
|
|
<hr class="docutils" />
|
|
<p id="voter2013ghd"><strong>(Voter2013)</strong> S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
|
|
144110 (2013).</p>
|
|
<p id="mironghd"><strong>(Miron)</strong> R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).</p>
|
|
</section>
|
|
</section>
|
|
|
|
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