682 lines
62 KiB
HTML
682 lines
62 KiB
HTML
<!DOCTYPE html>
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<title>fix bond/create command — LAMMPS documentation</title>
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<link rel="next" title="fix bond/react command" href="fix_bond_react.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="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 current"><a class="current reference internal" href="#">fix bond/create command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#fix-bond-create-angle-command">fix bond/create/angle 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_bond_react.html">fix bond/react command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_swap.html">fix bond/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_box_relax.html">fix box/relax command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html">fix brownian command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-sphere-command">fix brownian/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-asphere-command">fix brownian/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_charge_regulation.html">fix charge/regulation command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_cmap.html">fix cmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_colvars.html">fix colvars command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_controller.html">fix controller command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_damping_cundall.html">fix damping/cundall command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html">fix deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform_pressure.html">fix deform/pressure command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deposit.html">fix deposit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_energy.html">fix dpd/energy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html">fix edpd/source command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html#fix-tdpd-source-command">fix tdpd/source command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drag.html">fix drag command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude.html">fix drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html">fix drude/transform/direct command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html#fix-drude-transform-inverse-command">fix drude/transform/inverse command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_dt_reset.html">fix dt/reset command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html">fix efield command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html#fix-efield-tip4p-command">fix efield/tip4p command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ehex.html">fix ehex command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html">fix electrode/conp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html#fix-electrode-conq-command">fix electrode/conq command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html#fix-electrode-thermo-command">fix electrode/thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electron_stopping.html">fix electron/stopping command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_electron_stopping.html#fix-electron-stopping-fit-command">fix electron/stopping/fit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_enforce2d.html">fix enforce2d command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_cv.html">fix eos/cv command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table.html">fix eos/table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table_rx.html">fix eos/table/rx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_evaporate.html">fix evaporate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_external.html">fix external command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ffl.html">fix ffl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_filter_corotate.html">fix filter/corotate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_flow_gauss.html">fix flow/gauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_freeze.html">fix freeze command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gcmc.html">fix gcmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gld.html">fix gld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gle.html">fix gle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html">fix gravity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_grem.html">fix grem command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_halt.html">fix halt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_heat.html">fix heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_heat_flow.html">fix heat/flow command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_hyper_global.html">fix hyper/global command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_hyper_local.html">fix hyper/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_imd.html">fix imd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_indent.html">fix indent command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ipi.html">fix ipi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html">fix langevin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_drude.html">fix langevin/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_eff.html">fix langevin/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_spin.html">fix langevin/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_fluid.html">fix lb/fluid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_momentum.html">fix lb/momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mdi_qm.html">fix mdi/qm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mdi_qmmm.html">fix mdi/qmmm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso_move.html">fix meso/move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mol_swap.html">fix mol/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html">fix momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html#fix-momentum-chunk-command">fix momentum/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_move.html">fix move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html">fix mvv/dpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-edpd-command">fix mvv/edpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-tdpd-command">fix mvv/tdpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb_spin.html">fix neb/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html">fix nvt/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html#fix-npt-uef-command">fix npt/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nonaffine_displacement.html">fix nonaffine/displacement command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_cauchy.html">fix npt/cauchy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html">fix npt/sphere command</a></li>
|
||
<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>
|
||
|
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</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 bond/create command</li>
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||
<a href="fix_bond_react.html" class="btn btn-neutral float-right" title="fix bond/react 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-bond-create-command">
|
||
<span id="index-1"></span><span id="index-0"></span><h1>fix bond/create command<a class="headerlink" href="#fix-bond-create-command" title="Link to this heading"></a></h1>
|
||
</section>
|
||
<section id="fix-bond-create-angle-command">
|
||
<h1>fix bond/create/angle command<a class="headerlink" href="#fix-bond-create-angle-command" title="Link to this heading"></a></h1>
|
||
<section id="syntax">
|
||
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">Nevery</span><span class="w"> </span><span class="n">itype</span><span class="w"> </span><span class="n">jtype</span><span class="w"> </span><span class="n">Rmin</span><span class="w"> </span><span class="n">bondtype</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</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>bond/create</em> or <em>bond/create/angle</em></p></li>
|
||
<li><p>Nevery = attempt bond creation every this many steps</p></li>
|
||
<li><p>itype,jtype = atoms of itype can bond to atoms of jtype (1-Ntypes or type label)</p></li>
|
||
<li><p>Rmin = two atoms separated by less than Rmin can bond (distance units)</p></li>
|
||
<li><p>bondtype = type of created bonds (integer or type label)</p></li>
|
||
<li><p>zero or more keyword/value pairs may be appended to args</p></li>
|
||
<li><p>keyword = <em>iparam</em> or <em>jparam</em> or <em>prob</em> or <em>atype</em> or <em>dtype</em> or <em>itype</em> or <em>aconstrain</em></p>
|
||
<pre class="literal-block"><em>iparam</em> values = maxbond, newtype
|
||
maxbond = max # of bonds of bondtype the itype atom can have
|
||
newtype = change the itype atom to this type when maxbonds exist (1-Ntypes or type label)
|
||
<em>jparam</em> values = maxbond, newtype
|
||
maxbond = max # of bonds of bondtype the jtype atom can have
|
||
newtype = change the jtype atom to this type when maxbonds exist (1-Ntypes or type label)
|
||
<em>prob</em> values = fraction seed
|
||
fraction = create a bond with this probability if otherwise eligible
|
||
seed = random number seed (positive integer)
|
||
<em>atype</em> value = angletype
|
||
angletype = type of created angles (integer or type label)
|
||
<em>dtype</em> value = dihedraltype
|
||
dihedraltype = type of created dihedrals (integer or type label)
|
||
<em>itype</em> value = impropertype
|
||
impropertype = type of created impropers (integer or type label)
|
||
<em>aconstrain</em> value = amin amax
|
||
amin = minimal angle at which new bonds can be created
|
||
amax = maximal angle at which new bonds can be created</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">5</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">create</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.8</span><span class="w"> </span><span class="m">1</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">5</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">create</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">0.8</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">prob</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">85784</span><span class="w"> </span><span class="n">iparam</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">3</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">5</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">create</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">0.8</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">prob</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">85784</span><span class="w"> </span><span class="n">iparam</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="n">atype</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">dtype</span><span class="w"> </span><span class="m">2</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">5</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">create</span><span class="o">/</span><span class="n">angle</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">1.122</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">aconstrain</span><span class="w"> </span><span class="m">120</span><span class="w"> </span><span class="m">180</span><span class="w"> </span><span class="n">prob</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">4928459</span><span class="w"> </span><span class="n">iparam</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">jparam</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span>
|
||
|
||
<span class="k">labelmap</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">c1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="n">n2</span>
|
||
<span class="k">labelmap</span><span class="w"> </span><span class="n">bond</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">c1</span><span class="o">-</span><span class="n">n2</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">5</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">create</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">c1</span><span class="w"> </span><span class="n">n2</span><span class="w"> </span><span class="m">0.8</span><span class="w"> </span><span class="n">c1</span><span class="o">-</span><span class="n">n2</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Create bonds between pairs of atoms as a simulation runs according to
|
||
specified criteria. This can be used to model the cross-linking of
|
||
polymers, the formation of a percolation network, etc. In this
|
||
context, a bond means an interaction between a pair of atoms computed
|
||
by the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> command. Once the bond is created
|
||
it will be permanently in place. Optionally, the creation of a bond
|
||
can also create angle, dihedral, and improper interactions that the bond
|
||
is part of. See the discussion of the <em>atype</em>, <em>dtype</em>, and <em>itype</em>
|
||
keywords below.</p>
|
||
<p>This process is different than a <a class="reference internal" href="pair_style.html"><span class="doc">pair-wise</span></a> bond-order
|
||
potential such as Tersoff or AIREBO, which infer bonds and many-body
|
||
interactions based on the current geometry of a small cluster of atoms
|
||
and effectively create and destroy bonds and higher-order many-body
|
||
interactions from time step to time step as the atoms move.</p>
|
||
<p>A check for possible new bonds is performed every <em>Nevery</em> time steps.
|
||
If two atoms <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span> are within a distance <em>Rmin</em> of each
|
||
other, atom <span class="math notranslate nohighlight">\(i\)</span> is of type <em>itype</em>, atom <span class="math notranslate nohighlight">\(j\)</span> is of type <em>jtype</em>,
|
||
and both <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span> are in the specified fix group, then if a bond
|
||
does not already exist between atoms <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span>, and if both
|
||
<span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span> meet their respective <em>maxbond</em> requirements (explained
|
||
below), then <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span> are labeled as a “possible” bond pair.</p>
|
||
<p>If several atoms are close to an atom, it may have multiple possible
|
||
bond partners. Every atom checks its list of possible bond partners
|
||
and labels the closest such partner as its “sole” bond partner. After
|
||
this is done, if atom <span class="math notranslate nohighlight">\(i\)</span> has atom <span class="math notranslate nohighlight">\(j\)</span> as its sole partner and
|
||
atom <span class="math notranslate nohighlight">\(j\)</span> has atom <span class="math notranslate nohighlight">\(i\)</span> as its sole partner, then the
|
||
<span class="math notranslate nohighlight">\(i,j\)</span> bond is “eligible” to be formed.</p>
|
||
<p>Note that these rules mean that an atom will only be part of at most one
|
||
created bond on a given time step. It also means that if atom <span class="math notranslate nohighlight">\(i\)</span>
|
||
chooses atom <span class="math notranslate nohighlight">\(j\)</span> as its sole partner, but atom <span class="math notranslate nohighlight">\(j\)</span> chooses atom
|
||
<span class="math notranslate nohighlight">\(k\)</span> as its sole partner (because <span class="math notranslate nohighlight">\(R_{jk} < R_{ij}\)</span>), then atom
|
||
<span class="math notranslate nohighlight">\(i\)</span> will not form a bond on this time step, even if it has other possible
|
||
bond partners.</p>
|
||
<p>It is permissible to have <em>itype</em> = <em>jtype</em>. <em>Rmin</em> must be <span class="math notranslate nohighlight">\(\leq\)</span> the
|
||
pair-wise cutoff distance between <em>itype</em> and <em>jtype</em> atoms, as defined
|
||
by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> command.</p>
|
||
<p>The <em>iparam</em> and <em>jparam</em> keywords can be used to limit the bonding
|
||
functionality of the participating atoms. Each atom keeps track of
|
||
how many bonds of <em>bondtype</em> it already has. If atom <span class="math notranslate nohighlight">\(i\)</span> of type
|
||
<em>itype</em> already has <em>maxbond</em> bonds (as set by the <em>iparam</em>
|
||
keyword), then it will not form any more, and likewise for atom <span class="math notranslate nohighlight">\(j\)</span>.
|
||
If <em>maxbond</em> is set to 0, then there is no limit on the number of bonds
|
||
that can be formed with that atom.</p>
|
||
<p>The <em>newtype</em> value for <em>iparam</em> and <em>jparam</em> can be used to change
|
||
the atom type of atom <span class="math notranslate nohighlight">\(i\)</span> or <span class="math notranslate nohighlight">\(j\)</span> when it reaches <em>maxbond</em> number
|
||
of bonds of type <em>bondtype</em>. This means it can now interact in a pair-wise
|
||
fashion with other atoms in a different way by specifying different
|
||
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> coefficients. If you do not wish the
|
||
atom type to change, simply specify <em>newtype</em> as <em>itype</em> or <em>jtype</em>.</p>
|
||
<p>The <em>prob</em> keyword can also affect whether an eligible bond is
|
||
actually created. The <em>fraction</em> setting must be a value between 0.0
|
||
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
|
||
the eligible bond is only created if the random number is less than <em>fraction</em>.</p>
|
||
<p>The <em>aconstrain</em> keyword is only available with the fix
|
||
bond/create/angle command. It allows one to specify minimum and maximum
|
||
angles <em>amin</em> and <em>amax</em>, respectively, between the two prospective bonding
|
||
partners and a third particle that is already bonded to one of the two
|
||
partners. Such a criterion can be important when new angles are defined
|
||
together with the formation of a new bond. Without a restriction on the
|
||
permissible angle, and for stiffer angle potentials, very large energies
|
||
can arise and lead to unphysical behavior.</p>
|
||
<p>Any bond that is created is assigned a bond type of <em>bondtype</em>.</p>
|
||
<p>When a bond is created, data structures within LAMMPS that store bond
|
||
topologies are updated to reflect the creation. If the bond is part of
|
||
new 3-body (angle) or 4-body (dihedral, improper) interactions, you
|
||
can choose to create new angles, dihedrals, and impropers as well using
|
||
the <em>atype</em>, <em>dtype</em>, and <em>itype</em> keywords. All of these changes
|
||
typically affect pair-wise interactions between atoms that are now part
|
||
of new bonds, angles, etc.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>One data structure that is not updated when a bond breaks are
|
||
the molecule IDs stored by each atom. Even though two molecules
|
||
become one molecule due to the created bond, all atoms in the new
|
||
molecule retain their original molecule IDs.</p>
|
||
</div>
|
||
<p>If the <em>atype</em> keyword is used and if an angle potential is defined
|
||
via the <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a> command, then any new 3-body
|
||
interactions inferred by the creation of a bond will create new angles
|
||
of type <em>angletype</em>, with parameters assigned by the corresponding
|
||
<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command. Likewise, the <em>dtype</em> and
|
||
<em>itype</em> keywords will create new dihedrals and impropers of type
|
||
<em>dihedraltype</em> and <em>impropertype</em>.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>To create a new bond, the internal LAMMPS data structures that
|
||
store this information must have space for it. When LAMMPS is
|
||
initialized from a data file, the list of bonds is scanned and the
|
||
maximum number of bonds per atom is tallied. If some atom will
|
||
acquire more bonds than this limit as this fix operates, then the
|
||
“extra bond per atom” parameter must be set to allow for it. Ditto
|
||
for “extra angle per atom”, “extra dihedral per atom”, and “extra
|
||
improper per atom” if angles, dihedrals, or impropers are being added
|
||
when bonds are created. See the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
|
||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command for more details. Note that a
|
||
data file with no atoms can be used if you wish to add non-bonded
|
||
atoms via the <a class="reference internal" href="create_atoms.html"><span class="doc">create atoms</span></a> command (e.g., for a
|
||
percolation simulation).</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>LAMMPS stores and maintains a data structure with a list of the
|
||
first, second, and third neighbors of each atom (within the bond topology of
|
||
the system) for use in weighting pair-wise interactions for bonded
|
||
atoms. Note that adding a single bond always adds a new first neighbor
|
||
but may also induce <strong>many</strong> new second and third neighbors, depending on the
|
||
molecular topology of your system. The “extra special per atom”
|
||
parameter must typically be set to allow for the new maximum total
|
||
size (first + second + third neighbors) of this per-atom list. There are two
|
||
ways to do this. See the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
|
||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> commands for details.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Even if you do not use the <em>atype</em>, <em>dtype</em>, or <em>itype</em>
|
||
keywords, the list of topological neighbors is updated for atoms
|
||
affected by the new bond. This in turn affects which neighbors are
|
||
considered for pair-wise interactions, using the weighting rules set by
|
||
the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command. Consider a new bond
|
||
created between atoms <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span>. If <span class="math notranslate nohighlight">\(j\)</span> has a bonded
|
||
neighbor <span class="math notranslate nohighlight">\(k\)</span>, then <span class="math notranslate nohighlight">\(k\)</span> becomes a second neighbor of <span class="math notranslate nohighlight">\(i\)</span>.
|
||
Even if the <em>atype</em> keyword is not used to create angle <span class="math notranslate nohighlight">\(\angle ijk\)</span>,
|
||
the pair-wise interaction between <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(k\)</span> could potentially
|
||
be turned off or weighted by the 1–3 weighting specified
|
||
by the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command. This is the case
|
||
even if the “angle yes” option was used with that command. The same
|
||
is true for third neighbors (1–4 interactions), the <em>dtype</em> keyword, and
|
||
the “dihedral yes” option used with the
|
||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command.</p>
|
||
</div>
|
||
<p>Note that even if your simulation starts with no bonds, you must
|
||
define a <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> and use the
|
||
<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command to specify coefficients for the
|
||
<em>bondtype</em>. Similarly, if new atom types are specified by the
|
||
<em>iparam</em> or <em>jparam</em> keywords, they must be within the range of atom
|
||
types allowed by the simulation and pair-wise coefficients must be
|
||
specified for the new types.</p>
|
||
<p>Computationally, each time step this fix is invoked, it loops over
|
||
neighbor lists and computes distances between pairs of atoms in the
|
||
list. It also communicates between neighboring processors to
|
||
coordinate which bonds are created. Moreover, if any bonds are
|
||
created, neighbor lists must be immediately updated on the same
|
||
time step. This is to ensure that any pair-wise interactions that
|
||
should be turned “off” due to a bond creation, because they are now
|
||
excluded by the presence of the bond and the settings of the
|
||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command, will be immediately
|
||
recognized. All of these operations increase the cost of a time step.
|
||
Thus, you should be cautious about invoking this fix too frequently.</p>
|
||
<p>You can dump out snapshots of the current bond topology via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Creating a bond typically alters the energy of a system. You
|
||
should be careful not to choose bond creation criteria that induce a
|
||
dramatic change in energy. For example, if you define a very stiff
|
||
harmonic bond and create it when two atoms are separated by a distance
|
||
far from the equilibrium bond length, then the two atoms will oscillate
|
||
dramatically when the bond is formed. More generally, you may need to
|
||
thermostat your system to compensate for energy changes resulting from
|
||
created bonds (and angles, dihedrals, impropers).</p>
|
||
</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Link to this heading"></a></h2>
|
||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are
|
||
relevant to this fix.</p>
|
||
<p>This fix computes two statistics which it stores in a global vector of
|
||
length 2, which can be accessed by various <a class="reference internal" href="Howto_output.html"><span class="doc">output commands</span></a>. The vector values calculated by this fix are
|
||
“intensive”.</p>
|
||
<p>The two quantities in the global vector are</p>
|
||
<blockquote>
|
||
<div><ol class="arabic simple">
|
||
<li><p>number of bonds created on the most recent creation time step</p></li>
|
||
<li><p>cumulative number of bonds created</p></li>
|
||
</ol>
|
||
</div></blockquote>
|
||
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
||
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
|
||
built with that package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a>
|
||
doc page for more info.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>, <a class="reference internal" href="fix_bond_react.html"><span class="doc">fix bond/react</span></a>, <a class="reference internal" href="fix_bond_swap.html"><span class="doc">fix bond/swap</span></a>,
|
||
<a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>, <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</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 iparam = (0,itype), jparam = (0,jtype), and
|
||
prob = 1.0.</p>
|
||
</section>
|
||
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