808 lines
69 KiB
HTML
808 lines
69 KiB
HTML
<!DOCTYPE html>
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<title>fix electrode/conp command — LAMMPS documentation</title>
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<link rel="next" title="fix electron/stopping command" href="fix_electron_stopping.html" />
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="fixes.html">Fix Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="fix_accelerate_cos.html">fix accelerate/cos command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_acks2_reaxff.html">fix acks2/reaxff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt.html">fix adapt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt_fep.html">fix adapt/fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_add_heat.html">fix add/heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addforce.html">fix addforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addtorque.html">fix addtorque command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_alchemy.html">fix alchemy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_bitorsion.html">fix amoeba/bitorsion command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_pitorsion.html">fix amoeba/pitorsion command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_append_atoms.html">fix append/atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atc.html">fix atc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atom_swap.html">fix atom/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_atom.html">fix ave/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_chunk.html">fix ave/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate.html">fix ave/correlate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate_long.html">fix ave/correlate/long command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_grid.html">fix ave/grid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html">fix ave/histo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html#fix-ave-histo-weight-command">fix ave/histo/weight command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial.html">fix ave/spatial command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial_sphere.html">fix ave/spatial/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_time.html">fix ave/time command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_aveforce.html">fix aveforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_balance.html">fix balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bocs.html">fix bocs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_break.html">fix bond/break command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html">fix bond/create command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html#fix-bond-create-angle-command">fix bond/create/angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_react.html">fix bond/react command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_swap.html">fix bond/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_box_relax.html">fix box/relax command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html">fix brownian command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-sphere-command">fix brownian/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-asphere-command">fix brownian/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_charge_regulation.html">fix charge/regulation command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_cmap.html">fix cmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_colvars.html">fix colvars command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_controller.html">fix controller command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_damping_cundall.html">fix damping/cundall command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html">fix deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform_pressure.html">fix deform/pressure command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deposit.html">fix deposit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_energy.html">fix dpd/energy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html">fix edpd/source command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html#fix-tdpd-source-command">fix tdpd/source command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drag.html">fix drag command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude.html">fix drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html">fix drude/transform/direct command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html#fix-drude-transform-inverse-command">fix drude/transform/inverse command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dt_reset.html">fix dt/reset command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html">fix efield command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html#fix-efield-tip4p-command">fix efield/tip4p command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ehex.html">fix ehex command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">fix electrode/conp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#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-thermo-command">fix electrode/thermo 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="#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_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>
|
||
<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>
|
||
<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>
|
||
</div>
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</nav>
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
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<li class="breadcrumb-item"><a href="fixes.html">Fix Styles</a></li>
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<li class="breadcrumb-item active">fix electrode/conp command</li>
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<li class="wy-breadcrumbs-aside">
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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</li>
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</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
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<a href="fix_ehex.html" class="btn btn-neutral float-left" title="fix ehex command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="fix_electron_stopping.html" class="btn btn-neutral float-right" title="fix electron/stopping 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/>
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</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-electrode-conp-command">
|
||
<span id="index-5"></span><span id="index-4"></span><span id="index-3"></span><span id="index-2"></span><span id="index-1"></span><span id="index-0"></span><h1>fix electrode/conp command<a class="headerlink" href="#fix-electrode-conp-command" title="Link to this heading"></a></h1>
|
||
<p>Accelerator Variant: <em>electrode/conp/intel</em></p>
|
||
</section>
|
||
<section id="fix-electrode-conq-command">
|
||
<h1>fix electrode/conq command<a class="headerlink" href="#fix-electrode-conq-command" title="Link to this heading"></a></h1>
|
||
<p>Accelerator Variant: <em>electrode/conq/intel</em></p>
|
||
</section>
|
||
<section id="fix-electrode-thermo-command">
|
||
<h1>fix electrode/thermo command<a class="headerlink" href="#fix-electrode-thermo-command" title="Link to this heading"></a></h1>
|
||
<p>Accelerator Variant: <em>electrode/thermo/intel</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">style</span><span class="w"> </span><span class="n">args</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 = <em>electrode/conp</em> or <em>electrode/conq</em> or <em>electrode/thermo</em></p></li>
|
||
<li><p>args = arguments used by a particular style</p>
|
||
<pre class="literal-block"><em>electrode/conp</em> args = potential eta
|
||
<em>electrode/conq</em> args = charge eta
|
||
<em>electrode/thermo</em> args = potential eta <em>temp</em> values
|
||
potential = electrode potential
|
||
charge = electrode charge
|
||
eta = reciprocal width of electrode charge smearing (can be NULL if eta keyword is used)
|
||
<em>temp</em> values = T_v tau_v rng_v
|
||
T_v = temperature of thermo-potentiostat
|
||
tau_v = time constant of thermo-potentiostat
|
||
rng_v = integer used to initialize random number generator</pre>
|
||
</li>
|
||
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>algo</em> or <em>symm</em> or <em>couple</em> or <em>etypes</em> or <em>ffield</em> or <em>write_mat</em> or <em>write_inv</em> or <em>read_mat</em> or <em>read_inv</em> or <em>qtotal</em> or <em>eta</em></p></li>
|
||
</ul>
|
||
<pre class="literal-block"><em>algo</em> values = <em>mat_inv</em> or <em>mat_cg</em> tol or <em>cg</em> tol
|
||
specify the algorithm used to compute the electrode charges
|
||
<em>symm</em> value = <em>on</em> or <em>off</em>
|
||
turn on/off charge neutrality constraint for the electrodes
|
||
<em>couple</em> values = group-ID val
|
||
group-ID = group of atoms treated as additional electrode
|
||
val = electric potential or charge on this electrode
|
||
<em>etypes</em> value = <em>on</em> or <em>off</em>
|
||
turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap)
|
||
<em>ffield</em> value = <em>on</em> or <em>off</em>
|
||
turn on/off finite-field implementation
|
||
<em>write_mat</em> value = filename
|
||
filename = file to which to write elastance matrix
|
||
<em>write_inv</em> value = filename
|
||
filename = file to which to write inverted matrix
|
||
<em>read_mat</em> value = filename
|
||
filename = file from which to read elastance matrix
|
||
<em>read_inv</em> value = filename
|
||
filename = file from which to read inverted matrix
|
||
<em>qtotal</em> value = number or <em>v_</em> equal-style variable
|
||
add overall potential so that all electrode charges add up to <em>qtotal</em>
|
||
<em>eta</em> value = d_propname
|
||
d_propname = a custom double vector defined via fix property/atom</pre>
|
||
</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">fxconp</span><span class="w"> </span><span class="nv nv-Identifier">bot</span><span class="w"> </span><span class="n">electrode</span><span class="o">/</span><span class="n">conp</span><span class="w"> </span><span class="o">-</span><span class="m">1.0</span><span class="w"> </span><span class="m">1.805</span><span class="w"> </span><span class="n">couple</span><span class="w"> </span><span class="n">top</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">couple</span><span class="w"> </span><span class="n">ref</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="n">write_inv</span><span class="w"> </span><span class="n">inv.csv</span><span class="w"> </span><span class="n">symm</span><span class="w"> </span><span class="n">on</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">fxconp</span><span class="w"> </span><span class="nv nv-Identifier">electrodes</span><span class="w"> </span><span class="n">electrode</span><span class="o">/</span><span class="n">conq</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.805</span><span class="w"> </span><span class="n">algo</span><span class="w"> </span><span class="n">cg</span><span class="w"> </span><span class="m">1e-5</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">fxconp</span><span class="w"> </span><span class="nv nv-Identifier">bot</span><span class="w"> </span><span class="n">electrode</span><span class="o">/</span><span class="n">thermo</span><span class="w"> </span><span class="o">-</span><span class="m">1.0</span><span class="w"> </span><span class="m">1.805</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="m">298</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">couple</span><span class="w"> </span><span class="n">top</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>The <em>electrode</em> fixes implement the constant potential method (CPM)
|
||
(<a class="reference internal" href="#siepmann"><span class="std std-ref">Siepmann</span></a>, <a class="reference internal" href="#reed3"><span class="std std-ref">Reed</span></a>), and modern variants,
|
||
to accurately model electrified, conductive electrodes. This is
|
||
primarily useful for studying electrode-electrolyte interfaces,
|
||
especially at high potential differences or ionicities, with non-planar
|
||
electrodes such as nanostructures or nanopores, and to study dynamic
|
||
phenomena such as charging or discharging time scales or conductivity or
|
||
ionic diffusivities.</p>
|
||
<p>Each <em>electrode</em> fix allows users to set additional electrostatic
|
||
relationships between the specified groups which model useful
|
||
electrostatic configurations:</p>
|
||
<ul class="simple">
|
||
<li><p><em>electrode/conp</em> sets potentials or potential differences between electrodes</p>
|
||
<ul>
|
||
<li><p>(resulting in changing electrode total charges)</p></li>
|
||
</ul>
|
||
</li>
|
||
<li><p><em>electrode/conq</em> sets the total charge on each electrode</p>
|
||
<ul>
|
||
<li><p>(resulting in changing electrode potentials)</p></li>
|
||
</ul>
|
||
</li>
|
||
<li><p><em>electrode/thermo</em> sets a thermopotentiostat
|
||
<a class="reference internal" href="#deissenbeck"><span class="std std-ref">(Deissenbeck)</span></a> between two electrodes</p>
|
||
<ul>
|
||
<li><p>(resulting in changing charges and potentials with appropriate
|
||
average potential difference and thermal variance)</p></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<p>The first group-ID provided to each fix specifies the first electrode
|
||
group, and more group(s) are added using the <em>couple</em> keyword for each
|
||
additional group. While <em>electrode/thermo</em> only accepts two groups,
|
||
<em>electrode/conp</em> and <em>electrode/conq</em> accept any number of groups, up to
|
||
LAMMPS’s internal restrictions (see Restrictions below). Electrode
|
||
groups must not overlap, i.e. the fix will issue an error if any
|
||
particle is detected to belong to at least two electrode groups.</p>
|
||
<p>CPM involves updating charges on groups of electrode particles, per time
|
||
step, so that the system’s total energy is minimized with respect to
|
||
those charges. From basic electrostatics, this is equivalent to making
|
||
each group conductive, or imposing an equal electrostatic potential on
|
||
every particle in the same group (hence the name CPM). The charges are
|
||
usually modelled as a Gaussian distribution to make the charge-charge
|
||
interaction matrix invertible (<a class="reference internal" href="#gingrich"><span class="std std-ref">Gingrich</span></a>). The keyword
|
||
<em>eta</em> specifies the distribution’s width in units of inverse length.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>Three algorithms are available to minimize the energy, varying in how
|
||
matrices are pre-calculated before a run to provide computational
|
||
speedup. These algorithms can be selected using the keyword <em>algo</em>:</p>
|
||
<ul class="simple">
|
||
<li><p><em>algo mat_inv</em> pre-calculates the capacitance matrix and obtains the
|
||
charge configuration in one matrix-vector calculation per time step</p></li>
|
||
<li><p><em>algo mat_cg</em> pre-calculates the elastance matrix (inverse of
|
||
capacitance matrix) and obtains the charge configuration using a
|
||
conjugate gradient solver in multiple matrix-vector calculations per
|
||
time step</p></li>
|
||
<li><p><em>algo cg</em> does not perform any pre-calculation and obtains the charge
|
||
configuration using a conjugate gradient solver and multiple
|
||
calculations of the electric potential per time step.</p></li>
|
||
</ul>
|
||
<p>For both <em>cg</em> methods, the command must specify the conjugate gradient
|
||
tolerance. <em>fix electrode/thermo</em> currently only supports the <em>mat_inv</em>
|
||
algorithm.</p>
|
||
<p>The keyword <em>symm</em> can be set <em>on</em> (or <em>off</em>) to turn on (or turn off)
|
||
the capacitance matrix constraint that sets total electrode charge to be
|
||
zero. This has slightly different effects for each <em>fix electrode</em>
|
||
variant. For <em>fix electrode/conp</em>, with <em>symm off</em>, the potentials
|
||
specified are absolute potentials, but the charge configurations
|
||
satisfying them may add up to an overall non-zero, varying charge for
|
||
the electrodes (and thus the simulation box). With <em>symm on</em>, the total
|
||
charge over all electrode groups is constrained to zero, and potential
|
||
differences rather than absolute potentials are the physically relevant
|
||
quantities.</p>
|
||
<p>For <em>fix electrode/conq</em>, with <em>symm off</em>, overall neutrality is
|
||
explicitly obeyed or violated by the user input (which is not
|
||
checked!). With <em>symm on</em>, overall neutrality is ensured by ignoring the
|
||
user-input charge for the last listed electrode (instead, its charge
|
||
will always be minus the total sum of all other electrode charges). For
|
||
<em>fix electrode/thermo</em>, overall neutrality is always automatically
|
||
imposed for any setting of <em>symm</em>, but <em>symm on</em> allows finite-field
|
||
mode (<em>ffield on</em>, described below) for faster simulations.</p>
|
||
<p>For all three fixes, any potential (or charge for <em>conq</em>) can be
|
||
specified as an equal-style variable prefixed with “v_”. For example,
|
||
the following code will ramp the potential difference between electrodes
|
||
from 0.0V to 2.0V over the course of the simulation:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">fxconp</span><span class="w"> </span><span class="nv nv-Identifier">bot</span><span class="w"> </span><span class="n">electrode</span><span class="o">/</span><span class="n">conp</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.805</span><span class="w"> </span><span class="n">couple</span><span class="w"> </span><span class="n">top</span><span class="w"> </span><span class="n">v_v</span><span class="w"> </span><span class="n">symm</span><span class="w"> </span><span class="n">on</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">v</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="n">ramp</span><span class="nv">(0.0, 2.0)</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Note that these fixes only parse their supplied variable name when
|
||
starting a run, and so these fixes will accept equal-style variables
|
||
defined <em>after</em> the fix definition, including variables dependent on the
|
||
fix’s own output. This is useful, for example, in the fix’s internal
|
||
finite-field commands (see below). For an advanced example of this see
|
||
the in.conq2 input file in the directory
|
||
<code class="docutils literal notranslate"><span class="pre">examples/PACKAGES/electrode/graph-il</span></code>.</p>
|
||
<p>This fix necessitates the use of a long range solver that calculates and
|
||
provides the matrix of electrode-electrode interactions and a vector of
|
||
electrode-electrolyte interactions. The Kspace styles
|
||
<em>ewald/electrode</em>, <em>pppm/electrode</em> and <em>pppm/electrode/intel</em> are
|
||
created specifically for this task <a class="reference internal" href="#ahrens-iwers"><span class="std std-ref">(Ahrens-Iwers)</span></a>.</p>
|
||
<p>For systems with non-periodic boundaries in one or two directions dipole
|
||
corrections are available with the <a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a>.
|
||
For ewald/electrode a two-dimensional Ewald summation <a class="reference internal" href="#hu"><span class="std std-ref">(Hu)</span></a>
|
||
can be used by setting “slab ew2d”:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">kspace_modify</span><span class="w"> </span><span class="n">slab</span><span class="w"> </span><span class="o"><</span><span class="n">slab_factor</span><span class="o">></span>
|
||
<span class="k">kspace_modify</span><span class="w"> </span><span class="n">wire</span><span class="w"> </span><span class="o"><</span><span class="n">wire_factor</span><span class="o">></span>
|
||
<span class="k">kspace_modify</span><span class="w"> </span><span class="n">slab</span><span class="w"> </span><span class="n">ew2d</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Two implementations for the calculation of the elastance matrix are
|
||
available with pppm and can be selected using the <em>amat onestep/twostep</em>
|
||
keyword. <em>onestep</em> is the default; <em>twostep</em> can be faster for large
|
||
electrodes and a moderate mesh size but requires more memory.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">kspace_modify</span><span class="w"> </span><span class="n">amat</span><span class="w"> </span><span class="n">onestep</span><span class="o">/</span><span class="n">twostep</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>For all versions of the fix, the keyword-value <em>ffield on</em> enables the
|
||
finite-field mode (<a class="reference internal" href="#dufils"><span class="std std-ref">Dufils</span></a>, <a class="reference internal" href="#tee"><span class="std std-ref">Tee</span></a>), which uses
|
||
an electric field across a periodic cell instead of non-periodic
|
||
boundary conditions to impose a potential difference between the two
|
||
electrodes bounding the cell. The fix (with name <em>fix-ID</em>) detects which
|
||
of the two electrodes is “on top” (has the larger maximum <em>z</em>-coordinate
|
||
among all particles). Assuming the first electrode group is on top, it
|
||
then issues the following commands internally:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">fix-ID_ffield_zfield</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="nv">(f_fix-ID[2]-f_fix-ID[1])</span><span class="o">/</span><span class="n">lz</span>
|
||
<span class="n">efield</span><span class="w"> </span><span class="n">fix</span><span class="o">-</span><span class="n">ID_efield</span><span class="w"> </span><span class="n">all</span><span class="w"> </span><span class="n">efield</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="n">v_fix</span><span class="o">-</span><span class="n">ID_ffield_zfield</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>which implements the required electric field as the potential difference
|
||
divided by cell length. The internal commands use variable so that the
|
||
electric field will correctly vary with changing potentials in the
|
||
correct way (for example with equal-style potential difference or with
|
||
<em>fix electrode/conq</em>). This keyword requires two electrodes and will
|
||
issue an error with any other number of electrodes. This keyword
|
||
requires electroneutrality to be imposed (<em>symm on</em>) and will issue an
|
||
error otherwise.</p>
|
||
<div class="versionchanged">
|
||
<p><span class="versionmodified changed">Changed in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>For all versions of the fix, the keyword-value <em>etypes on</em> enables
|
||
type-based optimized neighbor lists. With this feature enabled, LAMMPS
|
||
provides the fix with an occasional neighbor list restricted to
|
||
electrode-electrode interactions for calculating the electrode matrix,
|
||
and a perpetual neighbor list restricted to electrode-electrolyte
|
||
interactions for calculating the electrode potentials, using particle
|
||
types to list only desired interactions, and typically resulting in
|
||
5–10% less computational time. Without this feature the fix will
|
||
simply use the active pair style’s neighbor list. This feature cannot
|
||
be enabled if any electrode particle has the same type as any
|
||
electrolyte particle (which would be unusual in a typical simulation)
|
||
and the fix will issue an error in that case.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 17Apr2024.</span></p>
|
||
</div>
|
||
<p>The keyword <em>qtotal</em> causes <em>fix electrode/conp</em> and <em>fix
|
||
electrode/thermo</em> to add an overall potential to all electrodes so that
|
||
the total charge on the electrodes is a specified amount (which may be
|
||
an equal-style variable). For example, if a user wanted to simulate a
|
||
solution of excess cations such that the total electrolyte charge is +2,
|
||
setting <em>qtotal -2</em> would cause the total electrode charge to be -2, so
|
||
that the simulation box remains overall electroneutral. Since <em>fix
|
||
electrode/conq</em> constrains the total charges of individual electrodes,
|
||
and since <em>symm on</em> constrains the total charge of all electrodes to be
|
||
zero, either option is incompatible with the <em>qtotal</em> keyword (even if
|
||
<em>qtotal</em> is set to zero).</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 17Apr2024.</span></p>
|
||
</div>
|
||
<p>The keyword <em>eta</em> takes the name of a custom double vector defined via
|
||
fix property/atom. The values will be used instead of the standard eta
|
||
value. The property/atom fix must be for vector of double values and
|
||
use the <em>ghost on</em> option.</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 currently does not write any information to restart files.</p>
|
||
<p>The <em>fix_modify tf</em> option enables the Thomas-Fermi metallicity model
|
||
(<a class="reference internal" href="#scalfi"><span class="std std-ref">Scalfi</span></a>) and allows parameters to be set for each atom type.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix_modify </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="n">tf</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">length</span><span class="w"> </span><span class="n">voronoi</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>If this option is used, these two parameters must be set for
|
||
all atom types of the electrode:</p>
|
||
<ul class="simple">
|
||
<li><p><cite>tf</cite> is the Thomas-Fermi length <span class="math notranslate nohighlight">\(l_{TF}\)</span></p></li>
|
||
<li><p><cite>voronoi</cite> is the Voronoi volume per atom in units of length cubed</p></li>
|
||
</ul>
|
||
<p>Different types may have different <cite>tf</cite> and <cite>voronoi</cite> values.
|
||
The following self-energy term is then added for all electrode atoms:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[A_{ii} += \frac{1}{4 \pi \epsilon_0} \times \frac{4 \pi l_{TF}^2}{\mathrm{Voronoi volume}}\]</div>
|
||
<p>The <em>fix_modify timer</em> option turns on (off) additional timer outputs in the log
|
||
file, for code developers to track optimization.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix_modify </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="n">timer</span><span class="w"> </span><span class="n">on</span><span class="o">/</span><span class="n">off</span>
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>These fixes compute a global (extensive) scalar, a global (intensive)
|
||
vector, and a global array, which can be accessed by various
|
||
<a class="reference internal" href="Howto_output.html"><span class="doc">output commands</span></a>.</p>
|
||
<p>The global scalar outputs the energy added to the system by this fix,
|
||
which is the negative of the total charge on each electrode multiplied
|
||
by that electrode’s potential.</p>
|
||
<p>The global vector outputs the potential on each electrode (and thus has
|
||
<em>N</em> entries if the fix manages <em>N</em> electrode groups), in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of electric field multiplied by distance (thus volts for <em>real</em>
|
||
and <em>metal</em> units). The electrode groups’ ordering follows the order in
|
||
which they were input in the fix command using <em>couple</em>. The global
|
||
vector output is useful for <em>fix electrode/conq</em> and <em>fix
|
||
electrode/thermo</em>, where potential is dynamically updated based on
|
||
electrolyte configuration instead of being directly set.</p>
|
||
<p>The global array has <em>N</em> rows and <em>2N+1</em> columns, where the fix manages
|
||
<em>N</em> electrode groups managed by the fix. For the <em>I</em>-th row of the
|
||
array, the elements are:</p>
|
||
<ul class="simple">
|
||
<li><p>array[I][1] = total charge that group <em>I</em> would have had <em>if it were
|
||
at 0 V applied potential</em></p></li>
|
||
<li><p>array[I][2 to <em>N</em> + 1] = the <em>N</em> entries
|
||
of the <em>I</em>-th row of the electrode capacitance matrix (definition
|
||
follows)</p></li>
|
||
<li><p>array[I][<em>N</em> + 2 to <em>2N</em> + 1] = the <em>N</em> entries of the
|
||
<em>I</em>-th row of the electrode elastance matrix (the inverse of the
|
||
electrode capacitance matrix)</p></li>
|
||
</ul>
|
||
<p>The <span class="math notranslate nohighlight">\(N \times N\)</span> electrode capacitance matrix, denoted <span class="math notranslate nohighlight">\(\mathbf{C}\)</span>
|
||
in the following equation, summarizes how the total charge induced on each
|
||
electrode (<span class="math notranslate nohighlight">\(\mathbf{Q}\)</span> as an <em>N</em>-vector) is related to the potential on
|
||
each electrode, <span class="math notranslate nohighlight">\(\mathbf{V}\)</span>, and the charge-at-0V <span class="math notranslate nohighlight">\(\mathbf{Q}_{0V}\)</span>
|
||
(which is influenced by the local electrolyte structure):</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V}\]</div>
|
||
<p>The charge-at-0V, electrode capacitance and elastance matrices are internally
|
||
used to calculate the potentials required to induce the specified total
|
||
electrode charges in <em>fix electrode/conq</em> and <em>fix electrode/thermo</em>. With the
|
||
<em>symm on</em> option, the electrode capacitance matrix would be singular, and thus
|
||
its last row is replaced with <em>N</em> copies of its top-left entry
|
||
(<span class="math notranslate nohighlight">\(\mathbf{C}_{11}\)</span>) for invertibility.</p>
|
||
<p>The global array output is mainly useful for quickly determining the ‘vacuum
|
||
capacitance’ of the system (capacitance with only electrodes, no electrolyte),
|
||
and can also be used for advanced simulations setting the potential as some
|
||
function of the charge-at-0V (such as the <code class="docutils literal notranslate"><span class="pre">in.conq2</span></code> example mentioned above).</p>
|
||
<p>Please cite <a class="reference internal" href="#ahrens-iwers2"><span class="std std-ref">(Ahrens-Iwers2022)</span></a> in any publication that
|
||
uses this implementation. Please cite also the publication on the combination
|
||
of the CPM with PPPM if you use <em>pppm/electrode</em> <a class="reference internal" href="#ahrens-iwers"><span class="std std-ref">(Ahrens-Iwers)</span></a>.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>For algorithms that use a matrix for the electrode-electrode
|
||
interactions, positions of electrode particles have to be immobilized at
|
||
all times.</p>
|
||
<p>With <em>ffield off</em> (i.e. the default), the box geometry is expected to be
|
||
<em>z</em>-non-periodic (i.e. <em>boundary p p f</em>), and this fix will issue an
|
||
error if the box is <em>z</em>-periodic. With <em>ffield on</em>, the box geometry is
|
||
expected to be <em>z</em>-periodic, and this fix will issue an error if the box
|
||
is <em>z</em>-non-periodic.</p>
|
||
<p>The parallelization for the fix works best if electrode atoms are evenly
|
||
distributed across processors. For a system with two electrodes at the bottom
|
||
and top of the cell this can be achieved with <em>processors * * 2</em>, or with the
|
||
line</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">if</span><span class="w"> </span><span class="s">"$(extract_setting(world_size) % 2) == 0"</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="s">"processors * * 2"</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>which avoids an error if the script is run on an odd number of
|
||
processors (such as on just one processor for testing).</p>
|
||
<p>The fix creates an additional group named <em>[fix-ID]_group</em> which is the
|
||
union of all electrode groups supplied to LAMMPS. This additional group
|
||
counts towards LAMMPS’s limitation on the total number of groups
|
||
(currently 32), which may not allow scripts that use that many groups to
|
||
run with this fix.</p>
|
||
<p>The matrix-based algorithms (<em>algo mat_inv</em> and <em>algo mat_cg</em>) currently
|
||
store an interaction matrix (either elastance or capacitance) of <em>N</em> by
|
||
<em>N</em> doubles for each MPI process. This memory requirement may be
|
||
prohibitive for large electrode groups. The fix will issue a warning if
|
||
it expects to use more than 0.5 GiB of memory.</p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The default keyword-option settings are <em>algo mat_inv</em>, <em>symm off</em>,
|
||
<em>etypes off</em> and <em>ffield off</em>.</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 id="siepmann"><strong>(Siepmann)</strong> Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).</p>
|
||
<p id="reed3"><strong>(Reed)</strong> Reed <em>et al.</em>, J. Chem. Phys. 126, 084704 (2007).</p>
|
||
<p id="deissenbeck"><strong>(Deissenbeck)</strong> Deissenbeck <em>et al.</em>, Phys. Rev. Letters 126, 136803 (2021).</p>
|
||
<p id="gingrich"><strong>(Gingrich)</strong> Gingrich, <cite>MSc thesis</cite> <<a class="reference external" href="https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf">https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf</a>>` (2010).</p>
|
||
<p id="ahrens-iwers"><strong>(Ahrens-Iwers)</strong> Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).</p>
|
||
<p id="hu"><strong>(Hu)</strong> Hu, J. Chem. Theory Comput. 10, 5254 (2014).</p>
|
||
<p id="dufils"><strong>(Dufils)</strong> Dufils <em>et al.</em>, Phys. Rev. Letters 123, 195501 (2019).</p>
|
||
<p id="tee"><strong>(Tee)</strong> Tee and Searles, J. Chem. Phys. 156, 184101 (2022).</p>
|
||
<p id="scalfi"><strong>(Scalfi)</strong> Scalfi <em>et al.</em>, J. Chem. Phys., 153, 174704 (2020).</p>
|
||
<p id="ahrens-iwers2"><strong>(Ahrens-Iwers2022)</strong> Ahrens-Iwers <em>et al.</em>, J. Chem. Phys. 157, 084801 (2022).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
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|
||
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|
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