694 lines
61 KiB
HTML
694 lines
61 KiB
HTML
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<title>fix shake command — LAMMPS documentation</title>
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<link rel="next" title="fix shardlow command" href="fix_shardlow.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="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"><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>
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<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>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
|
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<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>
|
|
<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>
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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>
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|
<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>
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|
<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 current"><a class="current reference internal" href="#">fix shake command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="#fix-rattle-command">fix rattle command</a><ul>
|
|
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
|
|
<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>
|
|
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
|
|
</ul>
|
|
</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>
|
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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>
|
|
<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>
|
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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>
|
|
<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>
|
|
<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>
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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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</div>
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<li class="breadcrumb-item active">fix shake command</li>
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<a href="fix_shardlow.html" class="btn btn-neutral float-right" title="fix shardlow 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">
|
|
<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-shake-command">
|
|
<span id="index-2"></span><span id="index-1"></span><span id="index-0"></span><h1>fix shake command<a class="headerlink" href="#fix-shake-command" title="Link to this heading"></a></h1>
|
|
<p>Accelerator Variants: <em>shake/kk</em></p>
|
|
</section>
|
|
<section id="fix-rattle-command">
|
|
<h1>fix rattle command<a class="headerlink" href="#fix-rattle-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">style</span><span class="w"> </span><span class="n">tol</span><span class="w"> </span><span class="n">iter</span><span class="w"> </span><span class="n">N</span><span class="w"> </span><span class="n">constraint</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul>
|
|
<li><p>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p></li>
|
|
<li><p>style = shake or rattle = style name of this fix command</p></li>
|
|
<li><p>tol = accuracy tolerance of SHAKE solution</p></li>
|
|
<li><p>iter = max # of iterations in each SHAKE solution</p></li>
|
|
<li><p>N = print SHAKE statistics every this many timesteps (0 = never)</p></li>
|
|
<li><p>one or more constraint/value pairs are appended</p></li>
|
|
<li><p>constraint = <em>b</em> or <em>a</em> or <em>t</em> or <em>m</em></p>
|
|
<pre class="literal-block"><em>b</em> values = one or more bond types (may use type labels)
|
|
<em>a</em> values = one or more angle types (may use type labels)
|
|
<em>t</em> values = one or more atom types (may use type labels)
|
|
<em>m</em> value = one or more mass values</pre>
|
|
</li>
|
|
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
|
<li><p>keyword = <em>mol</em> or <em>kbond</em></p>
|
|
<pre class="literal-block"><em>mol</em> value = template-ID
|
|
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
|
|
<em>kbond</em> value = force constant
|
|
force constant = force constant used to apply a restraint force when used during minimization</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">sub</span><span class="w"> </span><span class="n">shake</span><span class="w"> </span><span class="m">0.0001</span><span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">b</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="m">19</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">2</span>
|
|
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">sub</span><span class="w"> </span><span class="n">shake</span><span class="w"> </span><span class="m">0.0001</span><span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">t</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">6</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="m">31</span>
|
|
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">sub</span><span class="w"> </span><span class="n">shake</span><span class="w"> </span><span class="m">0.0001</span><span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">t</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">6</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="m">31</span><span class="w"> </span><span class="n">mol</span><span class="w"> </span><span class="n">myMol</span>
|
|
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">sub</span><span class="w"> </span><span class="n">rattle</span><span class="w"> </span><span class="m">0.0001</span><span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">t</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">6</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="m">31</span>
|
|
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">sub</span><span class="w"> </span><span class="n">rattle</span><span class="w"> </span><span class="m">0.0001</span><span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">t</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">6</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="m">31</span><span class="w"> </span><span class="n">mol</span><span class="w"> </span><span class="n">myMol</span>
|
|
</pre></div>
|
|
</div>
|
|
</section>
|
|
<section id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
|
<p>Apply bond and angle constraints to specified bonds and angles in the
|
|
simulation by either the SHAKE or RATTLE algorithms. This typically
|
|
enables a longer timestep. The SHAKE or RATTLE constraint algorithms,
|
|
however, can <em>only</em> be applied during molecular dynamics runs.</p>
|
|
<div class="versionchanged">
|
|
<p><span class="versionmodified changed">Changed in version 15Sep2022.</span></p>
|
|
</div>
|
|
<p>These fixes may now also be used during minimization. In that case the
|
|
constraints are <em>approximated</em> by strong harmonic restraints.</p>
|
|
<p><strong>SHAKE vs RATTLE:</strong></p>
|
|
<p>The SHAKE algorithm was invented for schemes such as standard Verlet
|
|
timestepping, where only the coordinates are integrated and the
|
|
velocities are approximated as finite differences to the trajectories
|
|
(<a class="reference internal" href="#ryckaert"><span class="std std-ref">Ryckaert et al. (1977)</span></a>). If the velocities are
|
|
integrated explicitly, as with velocity Verlet which is what LAMMPS
|
|
uses as an integration method, a second set of constraining forces is
|
|
required in order to eliminate velocity components along the bonds
|
|
(<a class="reference internal" href="#andersen3"><span class="std std-ref">Andersen (1983)</span></a>).</p>
|
|
<p>In order to formulate individual constraints for SHAKE and RATTLE,
|
|
focus on a single molecule whose bonds are constrained. Let Ri and Vi
|
|
be the position and velocity of atom <em>i</em> at time <em>n</em>, for
|
|
<em>i</em> =1,…,<em>N</em>, where <em>N</em> is the number of sites of our reference
|
|
molecule. The distance vector between sites <em>i</em> and <em>j</em> is given by</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[\mathbf r^{n+1}_{ij} = \mathbf r^n_j - \mathbf r^n_i\]</div>
|
|
<p>The constraints can then be formulated as</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[\begin{split}\mathbf r^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= d^2_{ij} \quad \text{and} \\
|
|
\mathbf v^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= 0\end{split}\]</div>
|
|
<p>The SHAKE algorithm satisfies the first condition, i.e. the sites at
|
|
time <em>n+1</em> will have the desired separations Dij immediately after the
|
|
coordinates are integrated. If we also enforce the second condition,
|
|
the velocity components along the bonds will vanish. RATTLE satisfies
|
|
both conditions. As implemented in LAMMPS, <em>fix rattle</em> uses fix shake
|
|
for satisfying the coordinate constraints. Therefore the settings and
|
|
optional keywords are the same for both fixes, and all the information
|
|
below about SHAKE is also relevant for RATTLE.</p>
|
|
<p><strong>SHAKE:</strong></p>
|
|
<p>Each timestep the specified bonds and angles are reset to their
|
|
equilibrium lengths and angular values via the SHAKE algorithm
|
|
(<a class="reference internal" href="#ryckaert"><span class="std std-ref">Ryckaert et al. (1977)</span></a>). This is done by applying an
|
|
additional constraint force so that the new positions preserve the
|
|
desired atom separations. The equations for the additional force are
|
|
solved via an iterative method that typically converges to an accurate
|
|
solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1
|
|
part in 10000) and maximum # of iterations are specified as arguments.
|
|
Setting the N argument will print statistics to the screen and log
|
|
file about regarding the lengths of bonds and angles that are being
|
|
constrained. Small delta values mean SHAKE is doing a good job.</p>
|
|
<p>In LAMMPS, only small clusters of atoms can be constrained. This is
|
|
so the constraint calculation for a cluster can be performed by a
|
|
single processor, to enable good parallel performance. A cluster is
|
|
defined as a central atom connected to others in the cluster by
|
|
constrained bonds. LAMMPS allows for the following kinds of clusters
|
|
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
|
|
one central atom bonded to 2 others and the angle between the three atoms
|
|
also constrained. This means water molecules or CH2 or CH3 groups may
|
|
be constrained, but not all the C-C backbone bonds of a long polymer
|
|
chain.</p>
|
|
<p>The <em>b</em> constraint lists bond types that will be constrained. The <em>t</em>
|
|
constraint lists atom types. All bonds connected to an atom of the
|
|
specified type will be constrained. The <em>m</em> constraint lists atom
|
|
masses. All bonds connected to atoms of the specified masses will be
|
|
constrained (within a fudge factor of MASSDELTA specified in
|
|
<code class="docutils literal notranslate"><span class="pre">src/RIGID/fix_shake.cpp</span></code>). The <em>a</em> constraint lists angle types. If
|
|
both bonds in the angle are constrained then the angle will also be
|
|
constrained if its type is in the list.</p>
|
|
<div class="versionchanged">
|
|
<p><span class="versionmodified changed">Changed in version 29Aug2024.</span></p>
|
|
</div>
|
|
<p>The types may be given as type labels <em>only</em> if there is no atom, bond,
|
|
or angle type label named <em>b</em>, <em>a</em>, <em>t</em>, or <em>m</em> defined in the
|
|
simulation. If that is the case, type labels cannot be used as
|
|
constraint type index with these two fixes, because the type labels
|
|
would be incorrectly treated as a new type of constraint instead.
|
|
Thus, LAMMPS will print a warning and type label handling is disabled
|
|
and numeric types must be used.</p>
|
|
<p>For all constraints, a particular bond is only constrained if <em>both</em>
|
|
atoms in the bond are in the group specified with the SHAKE fix.</p>
|
|
<p>The degrees-of-freedom removed by SHAKE bonds and angles are accounted
|
|
for in temperature and pressure computations. Similarly, the SHAKE
|
|
contribution to the pressure of the system (virial) is also accounted
|
|
for.</p>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note</p>
|
|
<p>This command works by using the current forces on atoms to calculate
|
|
an additional constraint force which when added will leave the atoms
|
|
in positions that satisfy the SHAKE constraints (e.g. bond length)
|
|
after the next time integration step. If you define fixes
|
|
(e.g. <a class="reference internal" href="fix_efield.html"><span class="doc">fix efield</span></a>) that add additional force to
|
|
the atoms after <em>fix shake</em> operates, then this fix will not take them
|
|
into account and the time integration will typically not satisfy the
|
|
SHAKE constraints. The solution for this is to make sure that fix
|
|
shake is defined in your input script after any other fixes which add
|
|
or change forces (to atoms that <em>fix shake</em> operates on).</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The <em>mol</em> keyword should be used when other commands, such as <a class="reference internal" href="fix_deposit.html"><span class="doc">fix
|
|
deposit</span></a> or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, add molecules
|
|
on-the-fly during a simulation, and you wish to constrain the new
|
|
molecules via SHAKE. You specify a <em>template-ID</em> previously defined
|
|
using the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads a file that
|
|
defines the molecule. You must use the same <em>template-ID</em> that the
|
|
command adding molecules uses. The coordinates, atom types, special
|
|
bond restrictions, and SHAKE info can be specified in the molecule file.
|
|
See the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for details. The only
|
|
settings required to be in this file (by this command) are the SHAKE
|
|
info of atoms in the molecule.</p>
|
|
<p>The <em>kbond</em> keyword sets the restraint force constant when <em>fix shake</em>
|
|
or fix rattle are used during minimization. In that case the constraint
|
|
algorithms are <em>not</em> applied and restraint forces are used instead to
|
|
maintain the geometries similar to the constraints. How well the
|
|
geometries are maintained and how quickly a minimization converges,
|
|
depends largely on the force constant <em>kbond</em>: larger values will reduce
|
|
the deviation from the desired geometry, but can also lead to slower
|
|
convergence of the minimization or lead to instabilities depending on
|
|
the minimization algorithm requiring to reduce the value of
|
|
<a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a>. Even though the restraints will not
|
|
preserve the bond lengths and angles as closely as the constraints
|
|
during the MD, they are generally close enough so that the constraints
|
|
will be fulfilled to the desired accuracy within a few MD steps
|
|
following the minimization. The default value for <em>kbond</em> depends on the
|
|
<a class="reference internal" href="units.html"><span class="doc">units</span></a> setting and is 1.0e6*k_B.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed on the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a>
|
|
page. The accelerated styles take the same arguments and should
|
|
produce the same results, except for round-off and precision issues.</p>
|
|
<p>These accelerated styles are part of the GPU, INTEL, KOKKOS,
|
|
OPENMP, and OPT packages, respectively. They are only enabled if
|
|
LAMMPS was built with those packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
|
<p>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <a class="reference internal" href="Run_options.html"><span class="doc">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can use the
|
|
<a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
|
<p>See the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a> page for more
|
|
instructions on how to use the accelerated styles effectively.</p>
|
|
<hr class="docutils" />
|
|
<p><strong>RATTLE:</strong></p>
|
|
<p>The velocity constraints lead to a linear system of equations which
|
|
can be solved analytically. The implementation of the algorithm in
|
|
LAMMPS closely follows (<a class="reference internal" href="#andersen3"><span class="std std-ref">Andersen (1983)</span></a>).</p>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note</p>
|
|
<p>The <em>fix rattle</em> command modifies forces and velocities and thus
|
|
should be defined after all other integration fixes in your input
|
|
script. If you define other fixes that modify velocities or forces
|
|
after <em>fix rattle</em> operates, then <em>fix rattle</em> will not take them
|
|
into account and the overall time integration will typically not
|
|
satisfy the RATTLE constraints. You can check whether the
|
|
constraints work correctly by setting the value of RATTLE_DEBUG in
|
|
<code class="docutils literal notranslate"><span class="pre">src/RIGID/fix_rattle.cpp</span></code> to 1 and recompiling LAMMPS.</p>
|
|
</div>
|
|
</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 these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart
|
|
files</span></a>.</p>
|
|
<p>Both fix <em>shake</em> and fix <em>rattle</em> behave differently during a minimization
|
|
in comparison to a molecular dynamics run:</p>
|
|
<ul>
|
|
<li><p>When used during a minimization, the SHAKE or RATTLE constraint
|
|
algorithms themselves are <strong>not</strong> applied. Instead the constraints
|
|
are replaced by harmonic restraint forces. The energy and virial
|
|
contributions due to the restraint forces are tallied into global and
|
|
per-atom accumulators. The total restraint energy is also accessible
|
|
as a global scalar property of the fix.</p></li>
|
|
<li><p>During molecular dynamics runs, however, the fixes do apply the
|
|
requested SHAKE or RATTLE constraint algorithms.</p>
|
|
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>virial</em> option is supported by
|
|
these fixes to add the contribution due to the added constraint forces
|
|
on atoms to both the global pressure and per-atom stress of the system
|
|
via the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> and <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute
|
|
stress/atom</span></a> commands. The former can be
|
|
accessed by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
|
|
<p>The default setting for this fix is <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify virial yes</span></a>. No global or per-atom quantities are stored by these
|
|
fixes for access by various <a class="reference internal" href="Howto_output.html"><span class="doc">output commands</span></a> during
|
|
an MD run. No parameter of these fixes 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.</p>
|
|
</li>
|
|
</ul>
|
|
</section>
|
|
<section id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
|
<p>These fixes are part of the RIGID package. They are 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> page for more info.</p>
|
|
<p>For computational efficiency, there can only be one shake or rattle
|
|
fix defined in a simulation.</p>
|
|
<p>If you use a tolerance that is too large or a max-iteration count that
|
|
is too small, the constraints will not be enforced very strongly,
|
|
which can lead to poor energy conservation. You can test for this in
|
|
your system by running a constant NVE simulation with a particular set
|
|
of SHAKE parameters and monitoring the energy versus time.</p>
|
|
<p>SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
|
|
(e.g. a linear CO2 molecule). This causes a divergence when solving the
|
|
constraint equations numerically. You can use <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid or fix
|
|
rigid/small</span></a> instead to make a linear molecule rigid.</p>
|
|
<p>When used during minimization choosing a too large value of the <em>kbond</em>
|
|
can make minimization very inefficient and also cause stability problems
|
|
with some minimization algorithms. Sometimes those can be avoided by
|
|
reducing the <a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a>.</p>
|
|
</section>
|
|
<section id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
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<p><a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>, <a class="reference internal" href="fix_ehex.html"><span class="doc">fix ehex</span></a>,
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<a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a></p>
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</section>
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<section id="default">
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<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
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<p>kbond = 1.0e9*k_B</p>
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<hr class="docutils" />
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<p id="ryckaert"><strong>(Ryckaert)</strong> J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
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J of Comp Phys, 23, 327-341 (1977).</p>
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<p id="andersen3"><strong>(Andersen)</strong> H. Andersen, J of Comp Phys, 52, 24-34 (1983).</p>
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