980 lines
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HTML
980 lines
82 KiB
HTML
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<title>fix deform command — LAMMPS documentation</title>
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<link rel="next" title="fix deform/pressure command" href="fix_deform_pressure.html" />
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1"><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 current"><a class="current reference internal" href="#">fix deform 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_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>
|
||
<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>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
|
||
<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>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_numdiff.html">fix numdiff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_numdiff_virial.html">fix numdiff/virial command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_awpmd.html">fix nve/awpmd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_body.html">fix nve/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_bpm_sphere.html">fix nve/bpm/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_dot.html">fix nve/dot command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_dotc_langevin.html">fix nve/dotc/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_eff.html">fix nve/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_limit.html">fix nve/limit command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_line.html">fix nve/line command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_manifold_rattle.html">fix nve/manifold/rattle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_noforce.html">fix nve/noforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html">fix nve/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_spin.html">fix nve/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_tri.html">fix nve/tri command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvk.html">fix nvk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html">fix nvt/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_body.html">fix nvt/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html">fix nvt/sllod command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod_eff.html">fix nvt/sllod/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html">fix nvt/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_oneway.html">fix oneway command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_orient.html">fix orient/fcc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_orient_eco.html">fix orient/eco command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pafi.html">fix pafi command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pair.html">fix pair command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_phonon.html">fix phonon command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html">fix pimd/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html#fix-pimd-nvt-command">fix pimd/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimdb.html">fix pimdb/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimdb.html#fix-pimdb-nvt-command">fix pimdb/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_planeforce.html">fix planeforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_plumed.html">fix plumed command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html">fix polarize/bem/gmres command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html#fix-polarize-bem-icc-command">fix polarize/bem/icc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html#fix-polarize-functional-command">fix polarize/functional command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pour.html">fix pour command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_precession_spin.html">fix precession/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_press_berendsen.html">fix press/berendsen command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_press_langevin.html">fix press/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_print.html">fix print command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_propel_self.html">fix propel/self command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_property_atom.html">fix property/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_python_invoke.html">fix python/invoke command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_python_move.html">fix python/move command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qbmsst.html">fix qbmsst command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html">fix qeq/point command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-shielded-command">fix qeq/shielded command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-slater-command">fix qeq/slater command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-ctip-command">fix qeq/ctip command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-dynamic-command">fix qeq/dynamic command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-fire-command">fix qeq/fire command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html">fix qeq/comb command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reaxff.html">fix qeq/reaxff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qmmm.html">fix qmmm command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qtb.html">fix qtb command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_qtpie_reaxff.html">fix qtpie/reaxff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_reaxff_bonds.html">fix reaxff/bonds command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_reaxff_species.html">fix reaxff/species command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_recenter.html">fix recenter command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_restrain.html">fix restrain command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo.html">fix rheo command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_oxidation.html">fix rheo/oxidation command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_pressure.html">fix rheo/pressure command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_thermal.html">fix rheo/thermal command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_viscosity.html">fix rheo/viscosity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rhok.html">fix rhok command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html">fix rigid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-command">fix rigid/nve command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-command">fix rigid/npt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-command">fix rigid/nph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-small-command">fix rigid/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-small-command">fix rigid/nph/small command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rigid_meso.html">fix rigid/meso command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rx.html">fix rx command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_saed_vtk.html">fix saed/vtk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html">fix setforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html#fix-setforce-spin-command">fix setforce/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sgcmc.html">fix sgcmc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_shake.html">fix shake command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_shake.html#fix-rattle-command">fix rattle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_shardlow.html">fix shardlow command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd.html">fix smd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_adjust_dt.html">fix smd/adjust_dt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_tlsph.html">fix smd/integrate_tlsph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_ulsph.html">fix smd/integrate_ulsph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_move_triangulated_surface.html">fix smd/move_tri_surf command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_setvel.html">fix smd/setvel command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_smd_wall_surface.html">fix smd/wall_surface command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sph.html">fix sph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sph_stationary.html">fix sph/stationary command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring.html">fix spring command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring_chunk.html">fix spring/chunk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring_rg.html">fix spring/rg command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_spring_self.html">fix spring/self command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_srd.html">fix srd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_store_force.html">fix store/force command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_store_state.html">fix store/state command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_berendsen.html">fix temp/berendsen command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html">fix temp/csvr command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html#fix-temp-csld-command">fix temp/csld command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale.html">fix temp/rescale command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tgnh_drude.html">fix tgnvt/drude command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tgnh_drude.html#fix-tgnpt-drude-command">fix tgnpt/drude command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-grid-command">fix ttm/grid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_viscosity.html">fix viscosity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_viscous.html">fix viscous command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_viscous_sphere.html">fix viscous/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lepton-command">fix wall/lepton command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-morse-command">fix wall/morse command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-table-command">fix wall/table command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polygon.html">fix wall/body/polygon command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polyhedron.html">fix wall/body/polyhedron command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_ees.html">fix wall/ees command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_ees.html#fix-wall-region-ees-command">fix wall/region/ees command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_flow.html">fix wall/flow command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran_region.html">fix wall/gran/region command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_piston.html">fix wall/piston command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect_stochastic.html">fix wall/reflect/stochastic command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_widom.html">fix widom command</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
||
</ul>
|
||
|
||
</div>
|
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</div>
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<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
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<li class="breadcrumb-item"><a href="fixes.html">Fix Styles</a></li>
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<li class="breadcrumb-item active">fix deform command</li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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|
||
<a href="fix_deform_pressure.html" class="btn btn-neutral float-right" title="fix deform/pressure command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
<hr/>
|
||
</div>
|
||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||
<div itemprop="articleBody">
|
||
|
||
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="fix-deform-command">
|
||
<span id="index-1"></span><span id="index-0"></span><h1>fix deform command<a class="headerlink" href="#fix-deform-command" title="Link to this heading"></a></h1>
|
||
<p>Accelerator Variants: <em>deform/kk</em></p>
|
||
<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">deform</span><span class="w"> </span><span class="n">N</span><span class="w"> </span><span class="n">parameter</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">args</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>N = perform box deformation every this many timesteps</p></li>
|
||
<li><p>one or more parameter/args sequences may be appended</p>
|
||
<pre class="literal-block">parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em> or <em>yz</em>
|
||
<em>x</em>, <em>y</em>, <em>z</em> args = style value(s)
|
||
style = <em>final</em> or <em>delta</em> or <em>scale</em> or <em>vel</em> or <em>erate</em> or <em>trate</em> or <em>volume</em> or <em>wiggle</em> or <em>variable</em> or <em>pressure</em> or <em>pressure/mean</em>
|
||
<em>final</em> values = lo hi
|
||
lo hi = box boundaries at end of run (distance units)
|
||
<em>delta</em> values = dlo dhi
|
||
dlo dhi = change in box boundaries at end of run (distance units)
|
||
<em>scale</em> values = factor
|
||
factor = multiplicative factor for change in box length at end of run
|
||
<em>vel</em> value = V
|
||
V = change box length at this velocity (distance/time units),
|
||
effectively an engineering strain rate
|
||
<em>erate</em> value = R
|
||
R = engineering strain rate (1/time units)
|
||
<em>trate</em> value = R
|
||
R = true strain rate (1/time units)
|
||
<em>volume</em> value = none = adjust this dim to preserve volume of system
|
||
<em>wiggle</em> values = A Tp
|
||
A = amplitude of oscillation (distance units)
|
||
Tp = period of oscillation (time units)
|
||
<em>variable</em> values = v_name1 v_name2
|
||
v_name1 = variable with name1 for box length change as function of time
|
||
v_name2 = variable with name2 for change rate as function of time
|
||
|
||
<em>xy</em>, <em>xz</em>, <em>yz</em> args = style value
|
||
style = <em>final</em> or <em>delta</em> or <em>vel</em> or <em>erate</em> or <em>trate</em> or <em>wiggle</em> or <em>variable</em>
|
||
<em>final</em> value = tilt
|
||
tilt = tilt factor at end of run (distance units)
|
||
<em>delta</em> value = dtilt
|
||
dtilt = change in tilt factor at end of run (distance units)
|
||
<em>vel</em> value = V
|
||
V = change tilt factor at this velocity (distance/time units),
|
||
effectively an engineering shear strain rate
|
||
<em>erate</em> value = R
|
||
R = engineering shear strain rate (1/time units)
|
||
<em>trate</em> value = R
|
||
R = true shear strain rate (1/time units)
|
||
<em>wiggle</em> values = A Tp
|
||
A = amplitude of oscillation (distance units)
|
||
Tp = period of oscillation (time units)
|
||
<em>variable</em> values = v_name1 v_name2
|
||
v_name1 = variable with name1 for tilt change as function of time
|
||
v_name2 = variable with name2 for change rate as function of time</pre>
|
||
</li>
|
||
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>remap</em> or <em>flip</em> or <em>units</em> or <em>couple</em> or <em>vol/balance/p</em> or <em>max/rate</em> or <em>normalize/pressure</em></p>
|
||
<pre class="literal-block"><em>remap</em> value = <em>x</em> or <em>v</em> or <em>none</em>
|
||
x = remap coords of atoms in group into deforming box
|
||
v = remap velocities of atoms in group when they cross periodic boundaries
|
||
none = no remapping of x or v
|
||
<em>flip</em> value = <em>yes</em> or <em>no</em>
|
||
allow or disallow box flips when it becomes highly skewed
|
||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||
lattice = distances are defined in lattice units
|
||
box = distances are defined in simulation box units</pre>
|
||
</li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">deform</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="n">final</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">9.0</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">final</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">5.0</span><span class="w"> </span><span class="n">units</span><span class="w"> </span><span class="n">box</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">deform</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="n">trate</span><span class="w"> </span><span class="m">0.1</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="n">volume</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">volume</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">deform</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">xy</span><span class="w"> </span><span class="n">erate</span><span class="w"> </span><span class="m">0.001</span><span class="w"> </span><span class="n">remap</span><span class="w"> </span><span class="n">v</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">deform</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="n">delta</span><span class="w"> </span><span class="o">-</span><span class="m">0.5</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="n">xz</span><span class="w"> </span><span class="n">vel</span><span class="w"> </span><span class="m">1.0</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Change the volume and/or shape of the simulation box during a dynamics
|
||
run. Orthogonal simulation boxes have 3 adjustable parameters
|
||
(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
|
||
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
|
||
adjusted independently and simultaneously.</p>
|
||
<p>The <a class="reference internal" href="fix_deform_pressure.html"><span class="doc">fix deform/pressure</span></a> command extends
|
||
this command with additional keywords and arguments. The rest of this
|
||
page explains the options common to both commands. The <a class="reference internal" href="fix_deform_pressure.html"><span class="doc">fix
|
||
deform/pressure</span></a> page explains the options
|
||
available ONLY with the fix deform/pressure command. Note that a
|
||
simulation can define only a single deformation command: fix deform or
|
||
fix deform/pressure.</p>
|
||
<p>Both these fixes can be used to perform non-equilibrium MD (NEMD)
|
||
simulations of a continuously strained system. See the <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix
|
||
nvt/sllod</span></a> and <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> commands for more details. Note that
|
||
simulation of a continuously extended system (extensional flow) can be
|
||
modeled using the <a class="reference internal" href="Packages_details.html#pkg-uef"><span class="std std-ref">UEF package</span></a> and its <a class="reference internal" href="fix_nh_uef.html"><span class="doc">fix
|
||
commands</span></a>.</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Inconsistent trajectories due to image flags</p>
|
||
<p>When running long simulations while shearing the box or using a high
|
||
shearing rate, it is possible that the image flags used for storing
|
||
unwrapped atom positions will “wrap around”. When LAMMPS is compiled
|
||
with the default settings, case image flags are limited to a range of
|
||
<span class="math notranslate nohighlight">\(-512 \le i \le 511\)</span>, which will overflow when atoms starting
|
||
at zero image flag value have passed through a periodic box dimension
|
||
more than 512 times.</p>
|
||
<p>Changing the <a class="reference internal" href="Build_settings.html#size"><span class="std std-ref">size of LAMMPS integer types</span></a> to the
|
||
“bigbig” setting can make this overflow much less likely, since it
|
||
increases the image flag value range to <span class="math notranslate nohighlight">\(- 1,048,576 \le i \le
|
||
1\,048\,575\)</span></p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>For the <em>x</em>, <em>y</em>, <em>z</em> parameters, the associated dimension cannot be
|
||
shrink-wrapped. For the <em>xy</em>, <em>yz</em>, <em>xz</em> parameters, the associated
|
||
second dimension cannot be shrink-wrapped. Dimensions not varied by
|
||
this command can be periodic or non-periodic. Dimensions
|
||
corresponding to unspecified parameters can also be controlled by a
|
||
<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> command.</p>
|
||
<p>The size and shape of the simulation box at the beginning of the
|
||
simulation run were either specified by the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command used to setup the simulation initially if it
|
||
is the first run, or they are the values from the end of the previous
|
||
run. The <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>, <a class="reference internal" href="read_data.html"><span class="doc">read data</span></a>, and <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands specify
|
||
whether the simulation box is orthogonal or non-orthogonal (triclinic)
|
||
and explain the meaning of the xy,xz,yz tilt factors. If fix deform
|
||
changes the xy,xz,yz tilt factors, then the simulation box must be
|
||
triclinic, even if its initial tilt factors are 0.0.</p>
|
||
<p>As described below, the desired simulation box size and shape at the
|
||
end of the run are determined by the parameters of the fix deform
|
||
command. Every Nth timestep during the run, the simulation box is
|
||
expanded, contracted, or tilted to ramped values between the initial
|
||
and final values.</p>
|
||
<hr class="docutils" />
|
||
<p>For the <em>x</em>, <em>y</em>, and <em>z</em> parameters, this is the meaning of their
|
||
styles and values.</p>
|
||
<p>The <em>final</em>, <em>delta</em>, <em>scale</em>, <em>vel</em>, and <em>erate</em> styles all change
|
||
the specified dimension of the box via “constant displacement” which
|
||
is effectively a “constant engineering strain rate”. This means the
|
||
box dimension changes linearly with time from its initial to final
|
||
value.</p>
|
||
<p>For style <em>final</em>, the final lo and hi box boundaries of a dimension
|
||
are specified. The values can be in lattice or box distance units.
|
||
See the discussion of the units keyword below.</p>
|
||
<p>For style <em>delta</em>, plus or minus changes in the lo/hi box boundaries
|
||
of a dimension are specified. The values can be in lattice or box
|
||
distance units. See the discussion of the units keyword below.</p>
|
||
<p>For style <em>scale</em>, a multiplicative factor to apply to the box length
|
||
of a dimension is specified. For example, if the initial box length
|
||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||
factor less than 1.0 means compression.</p>
|
||
<p>For style <em>vel</em>, a velocity at which the box length changes is
|
||
specified in units of distance/time. This is effectively a “constant
|
||
engineering strain rate”, where rate = V/L0 and L0 is the initial box
|
||
length. The distance can be in lattice or box distance units. See
|
||
the discussion of the units keyword below. For example, if the
|
||
initial box length is 100 Angstroms, and V is 10 Angstroms/ps, then
|
||
after 10 ps, the box length will have doubled. After 20 ps, it
|
||
will have tripled.</p>
|
||
<p>The <em>erate</em> style changes a dimension of the box at a “constant
|
||
engineering strain rate”. The units of the specified strain rate are
|
||
1/time. See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units
|
||
associated with different choices of simulation units,
|
||
e.g. picoseconds for “metal” units). Tensile strain is unitless and
|
||
is defined as delta/L0, where L0 is the original box length and delta
|
||
is the change relative to the original length. The box length L as a
|
||
function of time will change as</p>
|
||
<pre class="literal-block">L(t) = L0 (1 + erate*dt)</pre>
|
||
<p>where dt is the elapsed time (in time units). Thus if <em>erate</em> R is
|
||
specified as 0.1 and time units are picoseconds, this means the box
|
||
length will increase by 10% of its original length every picosecond.
|
||
I.e. strain after 1 ps = 0.1, strain after 2 ps = 0.2, etc. R =
|
||
-0.01 means the box length will shrink by 1% of its original length
|
||
every picosecond. Note that for an “engineering” rate the change is
|
||
based on the original box length, so running with R = 1 for 10
|
||
picoseconds expands the box length by a factor of 11 (strain of 10),
|
||
which is different that what the <em>trate</em> style would induce.</p>
|
||
<p>The <em>trate</em> style changes a dimension of the box at a “constant true
|
||
strain rate”. Note that this is not an “engineering strain rate”, as
|
||
the other styles are. Rather, for a “true” rate, the rate of change
|
||
is constant, which means the box dimension changes non-linearly with
|
||
time from its initial to final value. The units of the specified
|
||
strain rate are 1/time. See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the
|
||
time units associated with different choices of simulation units,
|
||
e.g. picoseconds for “metal” units). Tensile strain is unitless and
|
||
is defined as delta/L0, where L0 is the original box length and delta
|
||
is the change relative to the original length.</p>
|
||
<p>The box length L as a function of time will change as</p>
|
||
<pre class="literal-block">L(t) = L0 exp(trate*dt)</pre>
|
||
<p>where dt is the elapsed time (in time units). Thus if <em>trate</em> R is
|
||
specified as ln(1.1) and time units are picoseconds, this means the
|
||
box length will increase by 10% of its current (not original) length
|
||
every picosecond. I.e. strain after 1 ps = 0.1, strain after 2 ps
|
||
= 0.21, etc. R = ln(2) or ln(3) means the box length will double or
|
||
triple every picosecond. R = ln(0.99) means the box length will
|
||
shrink by 1% of its current length every picosecond. Note that for a
|
||
“true” rate the change is continuous and based on the current length,
|
||
so running with R = ln(2) for 10 picoseconds does not expand the box
|
||
length by a factor of 11 as it would with <em>erate</em>, but by a factor of
|
||
1024 since the box length will double every picosecond.</p>
|
||
<p>Note that to change the volume (or cross-sectional area) of the
|
||
simulation box at a constant rate, you can change multiple dimensions
|
||
via <em>erate</em> or <em>trate</em>. E.g. to double the box volume in a picosecond
|
||
picosecond, you could set “x erate M”, “y erate M”, “z erate M”, with
|
||
M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%,
|
||
the box volume doubles. Or you could set “x trate M”, “y trate M”, “z
|
||
trate M”, with M = ln(1.26) = 0.231, and the box volume would double
|
||
every picosecond.</p>
|
||
<p>The <em>volume</em> style changes the specified dimension in such a way that
|
||
the box volume remains constant while other box dimensions are changed
|
||
explicitly via the styles discussed above. For example, “x scale 1.1
|
||
y scale 1.1 z volume” will shrink the z box length as the x,y box
|
||
lengths increase, to keep the volume constant (product of x,y,z
|
||
lengths). If “x scale 1.1 z volume” is specified and parameter <em>y</em> is
|
||
unspecified, then the z box length will shrink as x increases to keep
|
||
the product of x,z lengths constant. If “x scale 1.1 y volume z
|
||
volume” is specified, then both the y,z box lengths will shrink as x
|
||
increases to keep the volume constant (product of x,y,z lengths). In
|
||
this case, the y,z box lengths shrink so as to keep their relative
|
||
aspect ratio constant.</p>
|
||
<p>For solids or liquids, note that when one dimension of the box is
|
||
expanded via fix deform (i.e. tensile strain), it may be physically
|
||
undesirable to hold the other 2 box lengths constant (unspecified by
|
||
fix deform) since that implies a density change. Using the <em>volume</em>
|
||
style for those 2 dimensions to keep the box volume constant may make
|
||
more physical sense, but may also not be correct for materials and
|
||
potentials whose Poisson ratio is not 0.5. An alternative is to use
|
||
<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt aniso</span></a> with zero applied pressure on those 2
|
||
dimensions, so that they respond to the tensile strain dynamically.</p>
|
||
<p>The <em>wiggle</em> style oscillates the specified box length dimension
|
||
sinusoidally with the specified amplitude and period. I.e. the box
|
||
length L as a function of time is given by</p>
|
||
<pre class="literal-block">L(t) = L0 + A sin(2*pi t/Tp)</pre>
|
||
<p>where L0 is its initial length. If the amplitude A is a positive
|
||
number the box initially expands, then contracts, etc. If A is
|
||
negative then the box initially contracts, then expands, etc. The
|
||
amplitude can be in lattice or box distance units. See the discussion
|
||
of the units keyword below.</p>
|
||
<p>The <em>variable</em> style changes the specified box length dimension by
|
||
evaluating a variable, which presumably is a function of time. The
|
||
variable with <em>name1</em> must be an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> and should calculate a change in box length in units of
|
||
distance. Note that this distance is in box units, not lattice units;
|
||
see the discussion of the <em>units</em> keyword below. The formula
|
||
associated with variable <em>name1</em> can reference the current timestep.
|
||
Note that it should return the “change” in box length, not the
|
||
absolute box length. This means it should evaluate to 0.0 when
|
||
invoked on the initial timestep of the run following the definition of
|
||
fix deform. It should evaluate to a value > 0.0 to dilate the box at
|
||
future times, or a value < 0.0 to compress the box.</p>
|
||
<p>The variable <em>name2</em> must also be an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> and should calculate the rate of box length change, in
|
||
units of distance/time, i.e. the time-derivative of the <em>name1</em>
|
||
variable. This quantity is used internally by LAMMPS to reset atom
|
||
velocities when they cross periodic boundaries. It is computed
|
||
internally for the other styles, but you must provide it when using an
|
||
arbitrary variable.</p>
|
||
<p>Here is an example of using the <em>variable</em> style to perform the same
|
||
box deformation as the <em>wiggle</em> style formula listed above, where we
|
||
assume that the current timestep = 0.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">A</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">5.0</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">Tp</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">10.0</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">displace</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="s">"v_A * sin(2*PI * step*dt/v_Tp)"</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">rate</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="s">"2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">deform</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="k">variable </span><span class="nv nv-Identifier">v_displace</span><span class="w"> </span><span class="n">v_rate</span><span class="w"> </span><span class="n">remap</span><span class="w"> </span><span class="n">v</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>For the <em>scale</em>, <em>vel</em>, <em>erate</em>, <em>trate</em>, <em>volume</em>, <em>wiggle</em>, and
|
||
<em>variable</em> styles, the box length is expanded or compressed around its
|
||
mid point.</p>
|
||
<hr class="docutils" />
|
||
<p>For the <em>xy</em>, <em>xz</em>, and <em>yz</em> parameters, this is the meaning of their
|
||
styles and values. Note that changing the tilt factors of a triclinic
|
||
box does not change its volume.</p>
|
||
<p>The <em>final</em>, <em>delta</em>, <em>vel</em>, and <em>erate</em> styles all change the shear
|
||
strain at a “constant engineering shear strain rate”. This means the
|
||
tilt factor changes linearly with time from its initial to final
|
||
value.</p>
|
||
<p>For style <em>final</em>, the final tilt factor is specified. The value
|
||
can be in lattice or box distance units. See the discussion of the
|
||
units keyword below.</p>
|
||
<p>For style <em>delta</em>, a plus or minus change in the tilt factor is
|
||
specified. The value can be in lattice or box distance units. See
|
||
the discussion of the units keyword below.</p>
|
||
<p>For style <em>vel</em>, a velocity at which the tilt factor changes is
|
||
specified in units of distance/time. This is effectively an
|
||
“engineering shear strain rate”, where rate = V/L0 and L0 is the
|
||
initial box length perpendicular to the direction of shear. The
|
||
distance can be in lattice or box distance units. See the discussion
|
||
of the units keyword below. For example, if the initial tilt factor
|
||
is 5 Angstroms, and the V is 10 Angstroms/ps, then after 1 ps, the
|
||
tilt factor will be 15 Angstroms. After 2 ps, it will be 25
|
||
Angstroms.</p>
|
||
<p>The <em>erate</em> style changes a tilt factor at a “constant engineering
|
||
shear strain rate”. The units of the specified shear strain rate are
|
||
1/time. See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units
|
||
associated with different choices of simulation units,
|
||
e.g. picoseconds for “metal” units). Shear strain is unitless and is
|
||
defined as offset/length, where length is the box length perpendicular
|
||
to the shear direction (e.g. y box length for xy deformation) and
|
||
offset is the displacement distance in the shear direction (e.g. x
|
||
direction for xy deformation) from the unstrained orientation.</p>
|
||
<p>The tilt factor T as a function of time will change as</p>
|
||
<pre class="literal-block">T(t) = T0 + L0*erate*dt</pre>
|
||
<p>where T0 is the initial tilt factor, L0 is the original length of the
|
||
box perpendicular to the shear direction (e.g. y box length for xy
|
||
deformation), and dt is the elapsed time (in time units). Thus if
|
||
<em>erate</em> R is specified as 0.1 and time units are picoseconds, this
|
||
means the shear strain will increase by 0.1 every picosecond. I.e. if
|
||
the xy shear strain was initially 0.0, then strain after 1 ps = 0.1,
|
||
strain after 2 ps = 0.2, etc. Thus the tilt factor would be 0.0 at
|
||
time 0, 0.1*ybox at 1 ps, 0.2*ybox at 2 ps, etc, where ybox is the
|
||
original y box length. R = 1 or 2 means the tilt factor will increase
|
||
by 1 or 2 every picosecond. R = -0.01 means a decrease in shear
|
||
strain by 0.01 every picosecond.</p>
|
||
<p>The <em>trate</em> style changes a tilt factor at a “constant true shear
|
||
strain rate”. Note that this is not an “engineering shear strain
|
||
rate”, as the other styles are. Rather, for a “true” rate, the rate
|
||
of change is constant, which means the tilt factor changes
|
||
non-linearly with time from its initial to final value. The units of
|
||
the specified shear strain rate are 1/time. See the
|
||
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units associated with
|
||
different choices of simulation units, e.g. picoseconds for “metal”
|
||
units). Shear strain is unitless and is defined as offset/length,
|
||
where length is the box length perpendicular to the shear direction
|
||
(e.g. y box length for xy deformation) and offset is the displacement
|
||
distance in the shear direction (e.g. x direction for xy deformation)
|
||
from the unstrained orientation.</p>
|
||
<p>The tilt factor T as a function of time will change as</p>
|
||
<pre class="literal-block">T(t) = T0 exp(trate*dt)</pre>
|
||
<p>where T0 is the initial tilt factor and dt is the elapsed time (in
|
||
time units). Thus if <em>trate</em> R is specified as ln(1.1) and time units
|
||
are picoseconds, this means the shear strain or tilt factor will
|
||
increase by 10% every picosecond. I.e. if the xy shear strain was
|
||
initially 0.1, then strain after 1 ps = 0.11, strain after 2 ps =
|
||
0.121, etc. R = ln(2) or ln(3) means the tilt factor will double or
|
||
triple every picosecond. R = ln(0.99) means the tilt factor will
|
||
shrink by 1% every picosecond. Note that the change is continuous, so
|
||
running with R = ln(2) for 10 picoseconds does not change the tilt
|
||
factor by a factor of 10, but by a factor of 1024 since it doubles
|
||
every picosecond. Note that the initial tilt factor must be non-zero
|
||
to use the <em>trate</em> option.</p>
|
||
<p>Note that shear strain is defined as the tilt factor divided by the
|
||
perpendicular box length. The <em>erate</em> and <em>trate</em> styles control the
|
||
tilt factor, but assume the perpendicular box length remains constant.
|
||
If this is not the case (e.g. it changes due to another fix deform
|
||
parameter), then this effect on the shear strain is ignored.</p>
|
||
<p>The <em>wiggle</em> style oscillates the specified tilt factor sinusoidally
|
||
with the specified amplitude and period. I.e. the tilt factor T as a
|
||
function of time is given by</p>
|
||
<pre class="literal-block">T(t) = T0 + A sin(2*pi t/Tp)</pre>
|
||
<p>where T0 is its initial value. If the amplitude A is a positive
|
||
number the tilt factor initially becomes more positive, then more
|
||
negative, etc. If A is negative then the tilt factor initially
|
||
becomes more negative, then more positive, etc. The amplitude can be
|
||
in lattice or box distance units. See the discussion of the units
|
||
keyword below.</p>
|
||
<p>The <em>variable</em> style changes the specified tilt factor by evaluating a
|
||
variable, which presumably is a function of time. The variable with
|
||
<em>name1</em> must be an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> and should
|
||
calculate a change in tilt in units of distance. Note that this
|
||
distance is in box units, not lattice units; see the discussion of the
|
||
<em>units</em> keyword below. The formula associated with variable <em>name1</em>
|
||
can reference the current timestep. Note that it should return the
|
||
“change” in tilt factor, not the absolute tilt factor. This means it
|
||
should evaluate to 0.0 when invoked on the initial timestep of the run
|
||
following the definition of fix deform.</p>
|
||
<p>The variable <em>name2</em> must also be an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> and should calculate the rate of tilt change, in units of
|
||
distance/time, i.e. the time-derivative of the <em>name1</em> variable. This
|
||
quantity is used internally by LAMMPS to reset atom velocities when
|
||
they cross periodic boundaries. It is computed internally for the
|
||
other styles, but you must provide it when using an arbitrary
|
||
variable.</p>
|
||
<p>Here is an example of using the <em>variable</em> style to perform the same
|
||
box deformation as the <em>wiggle</em> style formula listed above, where we
|
||
assume that the current timestep = 0.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">A</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">5.0</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">Tp</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">10.0</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">displace</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="s">"v_A * sin(2*PI * step*dt/v_Tp)"</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">rate</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="s">"2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">deform</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">xy</span><span class="w"> </span><span class="k">variable </span><span class="nv nv-Identifier">v_displace</span><span class="w"> </span><span class="n">v_rate</span><span class="w"> </span><span class="n">remap</span><span class="w"> </span><span class="n">v</span>
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>All of the tilt styles change the xy, xz, yz tilt factors during a
|
||
simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
|
||
are normally bounded by half the distance of the parallel box length.
|
||
See the discussion of the <em>flip</em> keyword below, to allow this bound to
|
||
be exceeded, if desired.</p>
|
||
<p>For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
|
||
the xy tilt factor must be between -5 and 5. Similarly, both xz and
|
||
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
|
||
not a limitation, since if the maximum tilt factor is 5 (as in this
|
||
example), then configurations with tilt = …, -15, -5, 5, 15, 25,
|
||
… are all equivalent.</p>
|
||
<p>To obey this constraint and allow for large shear deformations to be
|
||
applied via the <em>xy</em>, <em>xz</em>, or <em>yz</em> parameters, the following
|
||
algorithm is used. If <em>prd</em> is the associated parallel box length (10
|
||
in the example above), then if the tilt factor exceeds the accepted
|
||
range of -5 to 5 during the simulation, then the box is flipped to the
|
||
other limit (an equivalent box) and the simulation continues. Thus
|
||
for this example, if the initial xy tilt factor was 0.0 and “xy final
|
||
100.0” was specified, then during the simulation the xy tilt factor
|
||
would increase from 0.0 to 5.0, the box would be flipped so that the
|
||
tilt factor becomes -5.0, the tilt factor would increase from -5.0 to
|
||
5.0, the box would be flipped again, etc. The flip occurs 10 times
|
||
and the final tilt factor at the end of the simulation would be 0.0.
|
||
During each flip event, atoms are remapped into the new box in the
|
||
appropriate manner.</p>
|
||
<p>The one exception to this rule is if the first dimension in the tilt
|
||
factor (x for xy) is non-periodic. In that case, the limits on the
|
||
tilt factor are not enforced, since flipping the box in that dimension
|
||
does not change the atom positions due to non-periodicity. In this
|
||
mode, if you tilt the system to extreme angles, the simulation will
|
||
simply become inefficient due to the highly skewed simulation box.</p>
|
||
<hr class="docutils" />
|
||
<p>Each time the box size or shape is changed, the <em>remap</em> keyword
|
||
determines whether atom positions are remapped to the new box. If
|
||
<em>remap</em> is set to <em>x</em> (the default), atoms in the fix group are
|
||
remapped; otherwise they are not. Note that their velocities are not
|
||
changed, just their positions are altered. If <em>remap</em> is set to <em>v</em>,
|
||
then any atom in the fix group that crosses a periodic boundary will
|
||
have a delta added to its velocity equal to the difference in
|
||
velocities between the lo and hi boundaries. Note that this velocity
|
||
difference can include tilt components, e.g. a delta in the x velocity
|
||
when an atom crosses the y periodic boundary. If <em>remap</em> is set to
|
||
<em>none</em>, then neither of these remappings take place.</p>
|
||
<p>Conceptually, setting <em>remap</em> to <em>x</em> forces the atoms to deform via an
|
||
affine transformation that exactly matches the box deformation. This
|
||
setting is typically appropriate for solids. Note that though the
|
||
atoms are effectively “moving” with the box over time, it is not due
|
||
to their having a velocity that tracks the box change, but only due to
|
||
the remapping. By contrast, setting <em>remap</em> to <em>v</em> is typically
|
||
appropriate for fluids, where you want the atoms to respond to the
|
||
change in box size/shape on their own and acquire a velocity that
|
||
matches the box change, so that their motion will naturally track the
|
||
box without explicit remapping of their coordinates.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When non-equilibrium MD (NEMD) simulations are performed using
|
||
this fix, the option “remap v” should normally be used. This is
|
||
because <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a> adjusts the atom positions
|
||
and velocities to induce a velocity profile that matches the changing
|
||
box size/shape. Thus atom coordinates should NOT be remapped by fix
|
||
deform, but velocities SHOULD be when atoms cross periodic boundaries,
|
||
since that is consistent with maintaining the velocity profile already
|
||
created by fix nvt/sllod. LAMMPS will warn you if the <em>remap</em> setting
|
||
is not consistent with fix nvt/sllod.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>For non-equilibrium MD (NEMD) simulations using “remap v” it is
|
||
usually desirable that the fluid (or flowing material,
|
||
e.g. granular particles) stream with a velocity profile consistent
|
||
with the deforming box. As mentioned above, using a thermostat
|
||
such as <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix lavgevin</span></a> (with a bias provided by <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>), will typically accomplish that. If you do
|
||
not use a thermostat, then there is no driving force pushing the
|
||
atoms to flow in a manner consistent with the deforming box.
|
||
E.g. for a shearing system the box deformation velocity may vary
|
||
from 0 at the bottom to 10 at the top of the box. But the stream
|
||
velocity profile of the atoms may vary from -5 at the bottom to +5
|
||
at the top. You can monitor these effects using the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix
|
||
ave/chunk</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>, and <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a> commands. One way to induce atoms to
|
||
stream consistent with the box deformation is to give them an
|
||
initial velocity profile, via the <a class="reference internal" href="velocity.html"><span class="doc">velocity ramp</span></a>
|
||
command, that matches the box deformation rate. This also
|
||
typically helps the system come to equilibrium more quickly, even
|
||
if a thermostat is used.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If a <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> is defined for rigid bodies, and
|
||
<em>remap</em> is set to <em>x</em>, then the center-of-mass coordinates of rigid
|
||
bodies will be remapped to the changing simulation box. This will
|
||
be done regardless of whether atoms in the rigid bodies are in the
|
||
fix deform group or not. The velocity of the centers of mass are
|
||
not remapped even if <em>remap</em> is set to <em>v</em>, since <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix
|
||
nvt/sllod</span></a> does not currently do anything special
|
||
for rigid particles. If you wish to perform a NEMD simulation of
|
||
rigid particles, you can either thermostat them independently or
|
||
include a background fluid and thermostat the fluid via <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix
|
||
nvt/sllod</span></a>.</p>
|
||
</div>
|
||
<p>The <em>flip</em> keyword allows the tilt factors for a triclinic box to
|
||
exceed half the distance of the parallel box length, as discussed
|
||
above. If the <em>flip</em> value is set to <em>yes</em>, the bound is enforced by
|
||
flipping the box when it is exceeded. If the <em>flip</em> value is set to
|
||
<em>no</em>, the tilt will continue to change without flipping. Note that if
|
||
you apply large deformations, this means the box shape can tilt
|
||
dramatically LAMMPS will run less efficiently, due to the large volume
|
||
of communication needed to acquire ghost atoms around a processor’s
|
||
irregular-shaped subdomain. For extreme values of tilt, LAMMPS may
|
||
also lose atoms and generate an error.</p>
|
||
<p>The <em>units</em> keyword determines the meaning of the distance units used
|
||
to define various arguments. A <em>box</em> value selects standard distance
|
||
units as defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for
|
||
units = real or metal. A <em>lattice</em> value means the distance units are
|
||
in lattice spacings. The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have
|
||
been previously used to define the lattice spacing. Note that the
|
||
units choice also affects the <em>vel</em> style parameters since it is
|
||
defined in terms of distance/time. Also note that the units keyword
|
||
does not affect the <em>variable</em> style. You should use the <em>xlat</em>,
|
||
<em>ylat</em>, <em>zlat</em> keywords of the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>
|
||
command if you want to include lattice spacings in a variable formula.</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>
|
||
</section>
|
||
<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>This fix will restore the initial box settings from <a class="reference internal" href="restart.html"><span class="doc">binary
|
||
restart files</span></a>, which allows the fix to be properly continue
|
||
deformation, when using the start/stop options of the <a class="reference internal" href="run.html"><span class="doc">run</span></a>
|
||
command. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are
|
||
relevant to this fix. No global or per-atom quantities are stored by
|
||
this fix for access by various <a class="reference internal" href="Howto_output.html"><span class="doc">output commands</span></a>.</p>
|
||
<p>This fix can perform deformation over multiple runs, using the <em>start</em>
|
||
and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
|
||
<a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of how to do this.</p>
|
||
<p>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>You cannot apply x, y, or z deformations to a dimension that is
|
||
shrink-wrapped via the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command.</p>
|
||
<p>You cannot apply xy, yz, or xz deformations to a second dimension (y
|
||
in xy) that is shrink-wrapped via the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>
|
||
command.</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="fix_deform_pressure.html"><span class="doc">fix deform/pressure</span></a>,
|
||
<a class="reference internal" href="change_box.html"><span class="doc">change_box</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The option defaults are remap = x, flip = yes, and units = lattice.</p>
|
||
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