1117 lines
92 KiB
HTML
1117 lines
92 KiB
HTML
<!DOCTYPE html>
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<title>fix bond/react command — LAMMPS documentation</title>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="next" title="fix bond/swap command" href="fix_bond_swap.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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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="fixes.html">Fix Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="fix_accelerate_cos.html">fix accelerate/cos command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_acks2_reaxff.html">fix acks2/reaxff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt.html">fix adapt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt_fep.html">fix adapt/fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_add_heat.html">fix add/heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addforce.html">fix addforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addtorque.html">fix addtorque command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_alchemy.html">fix alchemy command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_bitorsion.html">fix amoeba/bitorsion command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_pitorsion.html">fix amoeba/pitorsion command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_append_atoms.html">fix append/atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atc.html">fix atc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atom_swap.html">fix atom/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_atom.html">fix ave/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_chunk.html">fix ave/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate.html">fix ave/correlate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate_long.html">fix ave/correlate/long command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_grid.html">fix ave/grid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html">fix ave/histo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html#fix-ave-histo-weight-command">fix ave/histo/weight command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial.html">fix ave/spatial command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial_sphere.html">fix ave/spatial/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_time.html">fix ave/time command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_aveforce.html">fix aveforce command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="fix_balance.html">fix balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bocs.html">fix bocs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_break.html">fix bond/break command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html">fix bond/create command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html#fix-bond-create-angle-command">fix bond/create/angle command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">fix bond/react 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_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>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mdi_qm.html">fix mdi/qm command</a></li>
|
||
<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>
|
||
<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>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_move.html">fix move command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html">fix mvv/dpd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-edpd-command">fix mvv/edpd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-tdpd-command">fix mvv/tdpd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_neb_spin.html">fix neb/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html">fix nvt/uef command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html#fix-npt-uef-command">fix npt/uef command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nonaffine_displacement.html">fix nonaffine/displacement command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_cauchy.html">fix npt/cauchy command</a></li>
|
||
<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/react command</li>
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||
<a href="fix_bond_swap.html" class="btn btn-neutral float-right" title="fix bond/swap 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-react-command">
|
||
<span id="index-0"></span><h1>fix bond/react command<a class="headerlink" href="#fix-bond-react-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">bond</span><span class="o">/</span><span class="n">react</span><span class="w"> </span><span class="n">common_keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">react</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">react</span><span class="o">-</span><span class="n">group</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">Nevery</span><span class="w"> </span><span class="n">Rmin</span><span class="w"> </span><span class="n">Rmax</span><span class="w"> </span><span class="n">template</span><span class="o">-</span><span class="n">ID</span><span class="nv">(pre-reacted)</span><span class="w"> </span><span class="n">template</span><span class="o">-</span><span class="n">ID</span><span class="nv">(post-reacted)</span><span class="w"> </span><span class="n">map_file</span><span class="w"> </span><span class="n">individual_keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">react</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">react</span><span class="o">-</span><span class="n">group</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">Nevery</span><span class="w"> </span><span class="n">Rmin</span><span class="w"> </span><span class="n">Rmax</span><span class="w"> </span><span class="n">template</span><span class="o">-</span><span class="n">ID</span><span class="nv">(pre-reacted)</span><span class="w"> </span><span class="n">template</span><span class="o">-</span><span class="n">ID</span><span class="nv">(post-reacted)</span><span class="w"> </span><span class="n">map_file</span><span class="w"> </span><span class="n">individual_keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">react</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">react</span><span class="o">-</span><span class="n">group</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">Nevery</span><span class="w"> </span><span class="n">Rmin</span><span class="w"> </span><span class="n">Rmax</span><span class="w"> </span><span class="n">template</span><span class="o">-</span><span class="n">ID</span><span class="nv">(pre-reacted)</span><span class="w"> </span><span class="n">template</span><span class="o">-</span><span class="n">ID</span><span class="nv">(post-reacted)</span><span class="w"> </span><span class="n">map_file</span><span class="w"> </span><span class="n">individual_keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="o">&</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>bond/react = style name of this fix command</p></li>
|
||
<li><p>the common keyword/values may be appended directly after ‘bond/react’</p></li>
|
||
<li><p>common keywords apply to all reaction specifications</p></li>
|
||
<li><p>common_keyword = <em>stabilization</em> or <em>reset_mol_ids</em></p>
|
||
<pre class="literal-block"><em>stabilization</em> values = stabilize group_prefix xmax
|
||
stabilize = <em>yes</em> or <em>no</em>
|
||
<em>yes</em> = perform reaction site stabilization
|
||
<em>no</em> = no reaction site stabilization (default)
|
||
group_prefix = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
|
||
xmax = value that is used by an internally-created <a class="reference internal" href="fix_nve_limit.html"><span class="doc">nve/limit</span></a> integrator
|
||
<em>reset_mol_ids</em> values = <em>yes</em> or <em>no</em>
|
||
<em>yes</em> = update molecule IDs based on new global topology (default)
|
||
<em>no</em> = do not update molecule IDs</pre>
|
||
</li>
|
||
<li><p>react = mandatory argument indicating new reaction specification</p></li>
|
||
<li><p>react-ID = user-assigned name for the reaction</p></li>
|
||
<li><p>react-group-ID = only atoms in this group are considered for the reaction</p></li>
|
||
<li><p>Nevery = attempt reaction every this many steps</p></li>
|
||
<li><p>Rmin = initiator atoms must be separated by more than Rmin to initiate reaction (distance units)</p></li>
|
||
<li><p>Rmax = initiator atoms must be separated by less than Rmax to initiate reaction (distance units)</p></li>
|
||
<li><p>template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology</p></li>
|
||
<li><p>template-ID(post-reacted) = ID of a molecule template containing post-reaction topology</p></li>
|
||
<li><p>map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates</p></li>
|
||
<li><p>zero or more individual keyword/value pairs may be appended to each react argument</p></li>
|
||
<li><p>individual_keyword = <em>prob</em> or <em>rate_limit</em> or <em>max_rxn</em> or <em>stabilize_steps</em> or <em>custom_charges</em> or <em>rescale_charges</em> or <em>molecule</em> or <em>modify_create</em></p>
|
||
<pre class="literal-block"><em>prob</em> values = fraction seed
|
||
fraction = initiate reaction with this probability if otherwise eligible
|
||
seed = random number seed (positive integer)
|
||
<em>rate_limit</em> = Nlimit Nsteps
|
||
Nlimit = maximum number of reactions allowed to occur within interval
|
||
Nsteps = the interval (number of timesteps) over which to count reactions
|
||
<em>max_rxn</em> value = N
|
||
N = maximum number of reactions allowed to occur
|
||
<em>stabilize_steps</em> value = timesteps
|
||
timesteps = number of time steps to apply the internally-created <a class="reference internal" href="fix_nve_limit.html"><span class="doc">nve/limit</span></a> fix to reacting atoms
|
||
<em>custom_charges</em> value = <em>no</em> or fragment-ID
|
||
<em>no</em> = update all atomic charges (default)
|
||
fragment-ID = ID of molecule fragment whose charges are updated
|
||
<em>rescale_charges</em> value = <em>no</em> or <em>yes</em>
|
||
<em>no</em> = do not rescale atomic charges (default)
|
||
<em>yes</em> = rescale charges such that total charge does not change during reaction
|
||
<em>molecule</em> value = <em>off</em> or <em>inter</em> or <em>intra</em>
|
||
<em>off</em> = allow both inter- and intramolecular reactions (default)
|
||
<em>inter</em> = search for reactions between molecules with different IDs
|
||
<em>intra</em> = search for reactions within the same molecule
|
||
<em>modify_create</em> values = keyword arg
|
||
<em>fit</em> arg = <em>all</em> or fragment-ID
|
||
<em>all</em> = use all eligible atoms for create-atoms fit (default)
|
||
fragment-ID = ID of molecule fragment used for create-atoms fit
|
||
<em>overlap</em> value = R
|
||
R = only insert atom/molecule if further than R from existing particles (distance units)</pre>
|
||
</li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<p>For unabridged example scripts and files, see examples/PACKAGES/reaction.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">molecule</span><span class="w"> </span><span class="n">mol1</span><span class="w"> </span><span class="n">pre_reacted_topology.txt</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">mol2</span><span class="w"> </span><span class="n">post_reacted_topology.txt</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">react</span><span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">myrxn1</span><span class="w"> </span><span class="n">all</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">3.25</span><span class="w"> </span><span class="n">mol1</span><span class="w"> </span><span class="n">mol2</span><span class="w"> </span><span class="n">map_file.txt</span>
|
||
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">mol1</span><span class="w"> </span><span class="n">pre_reacted_rxn1.txt</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">mol2</span><span class="w"> </span><span class="n">post_reacted_rxn1.txt</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">mol3</span><span class="w"> </span><span class="n">pre_reacted_rxn2.txt</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">mol4</span><span class="w"> </span><span class="n">post_reacted_rxn2.txt</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">react</span><span class="w"> </span><span class="n">stabilization</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">nvt_grp</span><span class="w"> </span><span class="n">.03</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">myrxn1</span><span class="w"> </span><span class="n">all</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">3.25</span><span class="w"> </span><span class="n">mol1</span><span class="w"> </span><span class="n">mol2</span><span class="w"> </span><span class="n">map_file_rxn1.txt</span><span class="w"> </span><span class="n">prob</span><span class="w"> </span><span class="m">0.50</span><span class="w"> </span><span class="m">12345</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">myrxn2</span><span class="w"> </span><span class="n">all</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">2.75</span><span class="w"> </span><span class="n">mol3</span><span class="w"> </span><span class="n">mol4</span><span class="w"> </span><span class="n">map_file_rxn2.txt</span><span class="w"> </span><span class="n">prob</span><span class="w"> </span><span class="m">0.25</span><span class="w"> </span><span class="m">12345</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">6</span><span class="w"> </span><span class="nv nv-Identifier">nvt_grp_REACT</span><span class="w"> </span><span class="n">nvt</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="c"># set thermostat after bond/react</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Initiate complex covalent bonding (topology) changes. These topology
|
||
changes will be referred to as ‘reactions’ throughout this
|
||
documentation. Topology changes are defined in pre- and post-reaction
|
||
molecule templates and can include creation and deletion of bonds,
|
||
angles, dihedrals, impropers, bond types, angle types, dihedral types,
|
||
atom types, or atomic charges. In addition, reaction by-products or
|
||
other molecules can be identified and deleted. Finally, atoms can be
|
||
created and inserted at specific positions relative to the reaction
|
||
site.</p>
|
||
<p>Fix bond/react does not use quantum mechanical (e.g., <a class="reference internal" href="fix_qmmm.html"><span class="doc">fix qmmm</span></a>) or
|
||
pairwise bond-order potential (e.g., <a class="reference internal" href="pair_tersoff.html"><span class="doc">Tersoff</span></a> or
|
||
<a class="reference internal" href="pair_airebo.html"><span class="doc">AIREBO</span></a>) methods to
|
||
determine bonding changes a priori. Rather, it uses a distance-based
|
||
probabilistic criteria to effect predetermined topology changes in
|
||
simulations using standard force fields.</p>
|
||
<p>This fix was created to facilitate the dynamic creation of polymeric,
|
||
amorphous or highly cross-linked systems. A suggested workflow for
|
||
using this fix is</p>
|
||
<blockquote>
|
||
<div><ol class="arabic simple">
|
||
<li><p>identify a reaction to be simulated</p></li>
|
||
<li><p>build a molecule template of the reaction site before the reaction has occurred</p></li>
|
||
<li><p>build a molecule template of the reaction site after the reaction has occurred</p></li>
|
||
<li><p>create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates</p></li>
|
||
<li><p>fill a simulation box with molecules and run a simulation with fix bond/react.</p></li>
|
||
</ol>
|
||
</div></blockquote>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 15Sep2022.</span></p>
|
||
</div>
|
||
<p><a class="reference internal" href="Howto_type_labels.html"><span class="doc">Type labels</span></a> allow for molecule templates
|
||
and data files to use alphanumeric atom types that match those of
|
||
a force field. Input files that use type labels are inherently
|
||
compatible with each other and portable between different
|
||
simulations. Therefore, it is highly recommended to use type labels
|
||
to specify atom, bond, etc. types when using fix bond/react.</p>
|
||
</div>
|
||
<p>Only one ‘fix bond/react’ command can be used at a time. Multiple
|
||
reactions can be simultaneously applied by specifying multiple <em>react</em>
|
||
arguments to a single ‘fix bond/react’ command. This syntax is
|
||
necessary because the “common” keywords are applied to all reactions.</p>
|
||
<p>The <em>stabilization</em> keyword enables reaction site stabilization.
|
||
Reaction site stabilization is performed by including reacting atoms
|
||
in an internally-created fix <a class="reference internal" href="fix_nve_limit.html"><span class="doc">nve/limit</span></a> time
|
||
integrator for a set number of time steps given by the
|
||
<em>stabilize_steps</em> keyword. While reacting atoms are being time
|
||
integrated by the internal nve/limit, they are prevented from being
|
||
involved in any new reactions. The <em>xmax</em> value keyword should
|
||
typically be set to the maximum distance that non-reacting atoms move
|
||
during the simulation.</p>
|
||
<p>Fix bond/react creates and maintains two important dynamic groups of
|
||
atoms when using the <em>stabilization</em> keyword. The first group contains
|
||
all atoms currently involved in a reaction; this group is
|
||
automatically time-integrated by an internally-created
|
||
<a class="reference internal" href="fix_nve_limit.html"><span class="doc">nve/limit</span></a> integrator. The second group contains
|
||
all atoms currently not involved in a reaction. This group should be
|
||
controlled by a thermostat in order to time integrate the system. The name
|
||
of this group of non-reacting atoms is created by appending ‘_REACT’
|
||
to the group-ID argument of the <em>stabilization</em> keyword, as shown in
|
||
the second example above.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When using reaction stabilization, you should generally <strong>not</strong> have
|
||
a separate thermostat that acts on the “all” group.</p>
|
||
</div>
|
||
<p>The group-ID set using the <em>stabilization</em> keyword can be an existing
|
||
static group or a previously-unused group-ID. It cannot be specified
|
||
as “all”. If the group-ID is previously unused, the fix bond/react
|
||
command creates a <a class="reference internal" href="group.html"><span class="doc">dynamic group</span></a> that is initialized to
|
||
include all atoms. If the group-ID is that of an existing static
|
||
group, the group is used as the parent group of new,
|
||
internally-created dynamic group. In both cases, this new dynamic
|
||
group is named by appending ‘_REACT’ to the group-ID (e.g.,
|
||
nvt_grp_REACT). By specifying an existing group, you may thermostat
|
||
constant-topology parts of your system separately. The dynamic group
|
||
contains only atoms not involved in a reaction at a given time step,
|
||
and therefore should be used by a subsequent system-wide time
|
||
integrator such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, or
|
||
<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, as shown in the second example
|
||
above (full examples can be found in examples/PACKAGES/reaction). The time
|
||
integration command should be placed after the fix bond/react command
|
||
due to the internal dynamic grouping performed by fix bond/react.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If the group-ID is an existing static group, react-group-IDs
|
||
should also be specified as this static group or a subset.</p>
|
||
</div>
|
||
<p>The <em>reset_mol_ids</em> keyword invokes the <a class="reference internal" href="reset_atoms.html"><span class="doc">reset_atoms mol</span></a> command after a reaction occurs, to ensure that
|
||
molecule IDs are consistent with the new bond topology. The group-ID
|
||
used for <a class="reference internal" href="reset_atoms.html"><span class="doc">reset_atoms mol</span></a> is the group-ID for this
|
||
fix. Resetting molecule IDs is necessarily a global operation, so it
|
||
can be slow for very large systems.</p>
|
||
<p>The following comments pertain to each <em>react</em> argument (in other
|
||
words, they can be customized for each reaction, or reaction step):</p>
|
||
<p>A check for possible new reaction sites is performed every <em>Nevery</em>
|
||
time steps. <em>Nevery</em> can be specified with an equal-style
|
||
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, whose value is rounded up to the nearest
|
||
integer.</p>
|
||
<p>Three physical conditions must be met for a reaction to occur. First,
|
||
an initiator atom pair must be identified within the reaction distance
|
||
cutoffs. Second, the topology surrounding the initiator atom pair must
|
||
match the topology of the pre-reaction template. Only atom types and
|
||
bond connectivity are used to identify a valid reaction site (not bond
|
||
types, etc.). Finally, any reaction constraints listed in the map file
|
||
(see below) must be satisfied. If all of these conditions are met, the
|
||
reaction site is eligible to be modified to match the post-reaction
|
||
template.</p>
|
||
<p>An initiator atom pair will be identified if several conditions are
|
||
met. First, a pair of atoms <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(j\)</span> within the specified
|
||
react-group-ID of type <em>itype</em> and <em>jtype</em> must be separated by a distance
|
||
between <em>Rmin</em> and <em>Rmax</em>. <em>Rmin</em> and <em>Rmax</em> can be specified with
|
||
equal-style <a class="reference internal" href="variable.html"><span class="doc">variables</span></a>. For example, these reaction cutoffs
|
||
can be functions of the reaction conversion using the following commands:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">rmax</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="c"># initialize variable before bond/react</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">myrxn</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">react</span><span class="w"> </span><span class="n">react</span><span class="w"> </span><span class="n">myrxn1</span><span class="w"> </span><span class="n">all</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="n">v_rmax</span><span class="w"> </span><span class="n">mol1</span><span class="w"> </span><span class="n">mol2</span><span class="w"> </span><span class="n">map_file.txt</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">rmax</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">3</span><span class="o">+</span><span class="n">f_myrxn[1]</span><span class="o">/</span><span class="m">100</span><span class="w"> </span><span class="c"># arbitrary function of reaction count</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The following criteria are used if multiple candidate initiator atom
|
||
pairs are identified within the cutoff distance:</p>
|
||
<blockquote>
|
||
<div><ol class="arabic simple">
|
||
<li><p>If the initiator atoms in the pre-reaction template are not 1–2
|
||
neighbors (i.e., not directly bonded) the closest potential partner is
|
||
chosen.</p></li>
|
||
<li><p>Otherwise, if the initiator atoms in the pre-reaction template are 1–2
|
||
neighbors (i.e. directly bonded) the farthest potential partner is
|
||
chosen.</p></li>
|
||
<li><p>Then, if both an atom <span class="math notranslate nohighlight">\(i\)</span> and atom <span class="math notranslate nohighlight">\(j\)</span> have each other as
|
||
initiator partners, these two atoms are identified as the initiator atom
|
||
pair of the reaction site.</p></li>
|
||
</ol>
|
||
</div></blockquote>
|
||
<p>Note that it can be helpful to select unique atom types for the
|
||
initiator atoms: if an initiator atom pair is identified, as described
|
||
in the previous steps, but it does not correspond to the same pair
|
||
specified in the pre-reaction template, an otherwise eligible reaction
|
||
could be prevented from occurring. Once this unique initiator atom
|
||
pair is identified for each reaction, there could be two or more
|
||
reactions that involve the same atom on the same time step. If this is
|
||
the case, only one such reaction is permitted to occur. This reaction
|
||
is chosen randomly from all potential reactions involving the
|
||
overlapping atom. This capability allows, for example, different
|
||
reaction pathways to proceed from identical reaction sites with
|
||
user-specified probabilities.</p>
|
||
<p>The pre-reacted molecule template is specified by a molecule command.
|
||
This molecule template file contains a sample reaction site and its
|
||
surrounding topology. As described below, the initiator atom pairs of
|
||
the pre-reacted template are specified by atom ID in the map file. The
|
||
pre-reacted molecule template should contain as few atoms as possible
|
||
while still completely describing the topology of all atoms affected
|
||
by the reaction (which includes all atoms that change atom type or
|
||
connectivity, and all bonds that change bond type). For example, if
|
||
the force field contains dihedrals, the pre-reacted template should
|
||
contain any atom within three bonds of reacting atoms.</p>
|
||
<p>Some atoms in the pre-reacted template that are not reacting may have
|
||
missing topology with respect to the simulation. For example, the
|
||
pre-reacted template may contain an atom that, in the simulation, is
|
||
currently connected to the rest of a long polymer chain. These are
|
||
referred to as edge atoms, and are also specified in the map file. All
|
||
pre-reaction template atoms should be linked to an initiator atom, via
|
||
at least one path that does not involve edge atoms. When the
|
||
pre-reaction template contains edge atoms, not all atoms, bonds,
|
||
charges, etc. specified in the reaction templates will be updated.
|
||
Specifically, topology that involves only atoms that are “too near” to
|
||
template edges will not be updated. The definition of “too near the
|
||
edge” depends on which interactions are defined in the simulation. If
|
||
the simulation has defined dihedrals, atoms within two bonds of edge
|
||
atoms are considered “too near the edge.” If the simulation defines
|
||
angles, but not dihedrals, atoms within one bond of edge atoms are
|
||
considered “too near the edge.” If just bonds are defined, only edge
|
||
atoms are considered “too near the edge.”</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Small molecules (i.e., ones that have all their atoms contained
|
||
within the reaction templates) never have edge atoms.</p>
|
||
</div>
|
||
<p>Note that some care must be taken when a building a molecule template
|
||
for a given simulation. All atom types in the pre-reacted template
|
||
must be the same as those of a potential reaction site in the
|
||
simulation. A detailed discussion of matching molecule template atom
|
||
types with the simulation is provided on the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a>
|
||
command page. It is highly recommended to use <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Type labels</span></a>
|
||
(added in version 15Sep2022) in both molecule templates and data
|
||
files, which automates the process of syncing atom types between
|
||
different input files.</p>
|
||
<p>The post-reacted molecule template contains a sample of the reaction
|
||
site and its surrounding topology after the reaction has occurred. It
|
||
must contain the same number of atoms as the pre-reacted template
|
||
(unless there are created atoms). A one-to-one correspondence between
|
||
the atom IDs in the pre- and post-reacted templates is specified in
|
||
the map file as described below. Note that during a reaction, an atom,
|
||
bond, etc. type may change to one that was previously not present in
|
||
the simulation. These new types must also be defined during the setup
|
||
of a given simulation. A discussion of correctly handling this is also
|
||
provided on the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command page.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When a reaction occurs, it is possible that the resulting
|
||
topology/atom (e.g., special bonds, dihedrals) exceeds that of
|
||
the existing system and reaction templates. As when inserting
|
||
molecules, enough space for this increased topology/atom must be
|
||
reserved by using the relevant “extra” keywords to 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.</p>
|
||
</div>
|
||
<p>The map file is a text document with the following format:</p>
|
||
<p>A map file has a header and a body. The header of map file the
|
||
contains one mandatory keyword and five optional keywords. The
|
||
mandatory keyword is <em>equivalences</em>:</p>
|
||
<pre class="literal-block">N <em>equivalences</em> = # of atoms N in the reaction molecule templates</pre>
|
||
<p>The optional keywords are <em>edgeIDs</em>, <em>deleteIDs</em>, <em>chiralIDs</em>, and
|
||
<em>constraints</em>:</p>
|
||
<pre class="literal-block">N <em>edgeIDs</em> = # of edge atoms N in the pre-reacted molecule template
|
||
N <em>deleteIDs</em> = # of atoms N that are deleted
|
||
N <em>createIDs</em> = # of atoms N that are created
|
||
N <em>chiralIDs</em> = # of chiral centers N
|
||
N <em>constraints</em> = # of reaction constraints N</pre>
|
||
<p>The body of the map file contains two mandatory sections and five
|
||
optional sections. The first mandatory section begins with the keyword
|
||
“InitiatorIDs” and lists the two atom IDs of the initiator atom pair
|
||
in the pre-reacted molecule template. The second mandatory section
|
||
begins with the keyword “Equivalences” and lists a one-to-one
|
||
correspondence between atom IDs of the pre- and post-reacted
|
||
templates. The first column is an atom ID of the pre-reacted molecule
|
||
template, and the second column is the corresponding atom ID of the
|
||
post-reacted molecule template. The first optional section begins with
|
||
the keyword “EdgeIDs” and lists the atom IDs of edge atoms in the
|
||
pre-reacted molecule template. The second optional section begins with
|
||
the keyword “DeleteIDs” and lists the atom IDs of pre-reaction
|
||
template atoms to delete. The third optional section begins with the
|
||
keyword “CreateIDs” and lists the atom IDs of the post-reaction
|
||
template atoms to create. The fourth optional section begins with the
|
||
keyword “ChiralIDs” lists the atom IDs of chiral atoms whose
|
||
handedness should be enforced. The fifth optional section begins with
|
||
the keyword “Constraints” and lists additional criteria that must be
|
||
satisfied in order for the reaction to occur. Currently, there are
|
||
six types of constraints available, as discussed below: “distance”,
|
||
“angle”, “dihedral”, “arrhenius”, “rmsd”, and “custom”.</p>
|
||
<p>A sample map file is given below:</p>
|
||
<hr class="docutils" />
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span># this is a map file
|
||
|
||
7 equivalences
|
||
2 edgeIDs
|
||
|
||
InitiatorIDs
|
||
|
||
3
|
||
5
|
||
|
||
EdgeIDs
|
||
|
||
1
|
||
7
|
||
|
||
Equivalences
|
||
|
||
1 1
|
||
2 2
|
||
3 3
|
||
4 4
|
||
5 5
|
||
6 6
|
||
7 7
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>A user-specified set of atoms can be deleted by listing their
|
||
pre-reaction template IDs in the DeleteIDs section. A deleted atom
|
||
must still be included in the post-reaction molecule template, in
|
||
which it cannot be bonded to an atom that is not deleted. In addition
|
||
to deleting unwanted reaction by-products, this feature can be used to
|
||
remove specific topologies, such as small rings, that may be otherwise
|
||
indistinguishable.</p>
|
||
<p>Atoms can be created by listing their post-reaction template IDs in
|
||
the CreateIDs section. A created atom should not be included in the
|
||
pre-reaction template. The inserted positions of created atoms are
|
||
determined by the coordinates of the post-reaction template, after
|
||
optimal translation and rotation of the post-reaction template to the
|
||
reaction site (using a fit with atoms that are neither created nor
|
||
deleted). The <em>modify_create</em> keyword can be used to modify the
|
||
default behavior when creating atoms. The <em>modify_create</em> keyword has
|
||
two sub-keywords, <em>fit</em> and <em>overlap</em>. One or more of the sub-keywords
|
||
may be used after the <em>modify_create</em> keyword. The <em>fit</em> sub-keyword
|
||
can be used to specify which post-reaction atoms are used for the
|
||
optimal translation and rotation of the post-reaction template. The
|
||
fragment-ID value of the <em>fit</em> sub-keyword must be the name of a
|
||
molecule fragment defined in the post-reaction <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> template, and only atoms in this fragment are used for the
|
||
fit. Atoms are created only if no current atom in the simulation is
|
||
within a distance <span class="math notranslate nohighlight">\(R\)</span> of any created atom, including the effect of
|
||
periodic boundary conditions if applicable. <span class="math notranslate nohighlight">\(R\)</span> is defined by the
|
||
<em>overlap</em> sub-keyword. Note that the default value for <span class="math notranslate nohighlight">\(R\)</span> is 0.0, which
|
||
will allow atoms to strongly overlap if you are inserting where other
|
||
atoms are present. The velocity of each created atom is initialized in
|
||
a random direction with a magnitude calculated from the instantaneous
|
||
temperature of the reaction site.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>The ‘Coords’ section must be included in the post-reaction template
|
||
when creating atoms because these coordinates are used to determine
|
||
where new atoms are inserted.</p>
|
||
</div>
|
||
<p>The handedness of atoms that are chiral centers can be enforced by
|
||
listing their IDs in the ChiralIDs section. A chiral atom must be
|
||
bonded to four atoms with mutually different atom types. This feature
|
||
uses the coordinates and types of the involved atoms in the
|
||
pre-reaction template to determine handedness. Three atoms bonded to
|
||
the chiral center are arbitrarily chosen, to define an oriented plane,
|
||
and the relative position of the fourth bonded atom determines the
|
||
chiral center’s handedness.</p>
|
||
<p>Any number of additional constraints may be specified in the
|
||
Constraints section of the map file. The constraint of type “distance”
|
||
has syntax as follows:</p>
|
||
<pre class="literal-block">distance <em>ID1</em> <em>ID2</em> <em>rmin</em> <em>rmax</em></pre>
|
||
<p>where “distance” is the required keyword, <em>ID1</em> and <em>ID2</em> are
|
||
pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
|
||
two atoms must be separated by a distance between <em>rmin</em> and <em>rmax</em>
|
||
for the reaction to occur.</p>
|
||
<p>The constraint of type “angle” has the following syntax:</p>
|
||
<pre class="literal-block">angle <em>ID1</em> <em>ID2</em> <em>ID3</em> <em>amin</em> <em>amax</em></pre>
|
||
<p>where “angle” is the required keyword, <em>ID1</em>, <em>ID2</em> and <em>ID3</em> are
|
||
pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
|
||
three atoms must form an angle between <em>amin</em> and <em>amax</em> for the
|
||
reaction to occur (where <em>ID2</em> is the central atom). Angles must be
|
||
specified in degrees. This constraint can be used to enforce a certain
|
||
orientation between reacting molecules.</p>
|
||
<p>The constraint of type “dihedral” has the following syntax:</p>
|
||
<pre class="literal-block">dihedral <em>ID1</em> <em>ID2</em> <em>ID3</em> <em>ID4</em> <em>amin</em> <em>amax</em> <em>amin2</em> <em>amax2</em></pre>
|
||
<p>where “dihedral” is the required keyword, and <em>ID1</em>, <em>ID2</em>, <em>ID3</em>
|
||
and <em>ID4</em> are pre-reaction atom IDs (or molecule-fragment IDs, see
|
||
below). Dihedral angles are calculated in the interval <span class="math notranslate nohighlight">\((-180^\circ,180^\circ]\)</span>.
|
||
Refer to the <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral style</span></a> documentation for
|
||
further details on convention. If <em>amin</em> is less than <em>amax</em>, these
|
||
four atoms must form a dihedral angle greater than <em>amin</em> <strong>and</strong> less
|
||
than <em>amax</em> for the reaction to occur. If <em>amin</em> is greater than
|
||
<em>amax</em>, these four atoms must form a dihedral angle greater than
|
||
<em>amin</em> <strong>or</strong> less than <em>amax</em> for the reaction to occur. Angles must
|
||
be specified in degrees. Optionally, a second range of permissible
|
||
angles <em>amin2</em> to <em>amax2</em> can be specified.</p>
|
||
<p>For the ‘distance’, ‘angle’, and ‘dihedral’ constraints (explained
|
||
above), atom IDs can be replaced by pre-reaction molecule-fragment
|
||
IDs. The molecule-fragment ID must begin with a letter. The location
|
||
of the ID is the geometric center of all atom positions in the
|
||
fragment. The molecule fragment must have been defined in the
|
||
<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for the pre-reaction template.</p>
|
||
<p>The constraint of type ‘arrhenius’ imposes an additional reaction
|
||
probability according to the modified Arrhenius equation,</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[k = AT^{n}e^{-E_{a}/k_{B}T}.\]</div>
|
||
<p>The Arrhenius constraint has the following syntax:</p>
|
||
<pre class="literal-block">arrhenius <em>A</em> <em>n</em> <em>E_a</em> <em>seed</em></pre>
|
||
<p>where “arrhenius” is the required keyword, <em>A</em> is the pre-exponential
|
||
factor, <em>n</em> is the exponent of the temperature dependence, <span class="math notranslate nohighlight">\(E_a\)</span>
|
||
is the activation energy (<a class="reference internal" href="units.html"><span class="doc">units</span></a> of energy), and <em>seed</em> is a
|
||
random number seed. The temperature is defined as the instantaneous
|
||
temperature averaged over all atoms in the reaction site and is
|
||
calculated in the same manner as for example
|
||
<a class="reference internal" href="compute_temp_chunk.html"><span class="doc">compute temp/chunk</span></a>. Currently, there are no
|
||
options for additional temperature averaging or velocity-biased
|
||
temperature calculations. A uniform random number between 0 and 1 is
|
||
generated using <em>seed</em>; if this number is less than the result of the
|
||
Arrhenius equation above, the reaction is permitted to occur.</p>
|
||
<p>The constraint of type ‘rmsd’ has the following syntax:</p>
|
||
<pre class="literal-block">rmsd <em>RMSDmax</em> <em>molfragment</em></pre>
|
||
<p>where “rmsd” is the required keyword, and <em>RMSDmax</em> is the maximum
|
||
root-mean-square deviation between atom positions of the pre-reaction
|
||
template and the local reaction site (distance units), after optimal
|
||
translation and rotation of the pre-reaction template. Optionally, the
|
||
name of a molecule fragment (of the pre-reaction template) can be
|
||
specified by <em>molfragment</em>. If a molecule fragment is specified,
|
||
only atoms that are part of this molecule fragment are used to
|
||
determine the RMSD. A molecule fragment must have been defined in the
|
||
<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for the pre-reaction template. For
|
||
example, the molecule fragment could consist of only the backbone
|
||
atoms of a polymer chain. This constraint can be used to enforce a
|
||
specific relative position and orientation between reacting molecules.</p>
|
||
<div class="versionchanged">
|
||
<p><span class="versionmodified changed">Changed in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>The constraint of type “custom” has the following syntax:</p>
|
||
<pre class="literal-block">custom <em>varstring</em></pre>
|
||
<p>where ‘custom’ is the required keyword, and <em>varstring</em> is a variable
|
||
expression. The expression must be a valid equal-style variable
|
||
formula that can be read by the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command,
|
||
after any special reaction functions are evaluated. If the resulting
|
||
expression is zero, the reaction is prevented from occurring;
|
||
otherwise, it is permitted to occur. There are three special reaction
|
||
functions available, ‘rxnbond’, ‘rxnsum’, and ‘rxnave’. The ‘rxnbond’
|
||
function allows per-bond values to be included in the variable strings
|
||
of the custom constraint. The ‘rxnbond’ function has two mandatory
|
||
arguments. The first argument is the ID of a previously defined
|
||
‘compute bond/local’ command. This ‘compute bond/local’ must compute
|
||
only one value, e.g. bond force. This value is returned by the
|
||
‘rxnbond’ function. The second argument is the name of a molecule
|
||
fragment in the pre-reaction template. The fragment must contain
|
||
exactly two atoms, corresponding to the atoms involved in the bond
|
||
whose value should be calculated. An example of a constraint that uses
|
||
the force experienced by a bond is provided below. The ‘rxnsum’ and
|
||
‘rxnave’ functions operate over the atoms in a given reaction site,
|
||
and have one mandatory argument and one optional argument. The
|
||
mandatory argument is the identifier for an atom-style variable. The
|
||
second, optional argument is the name of a molecule fragment in the
|
||
pre-reaction template, and can be used to operate over a subset of
|
||
atoms in the reaction site. The ‘rxnsum’ function sums the atom-style
|
||
variable over the reaction site, while the ‘rxnave’ returns the
|
||
average value. For example, a constraint on the total potential energy
|
||
of atoms involved in the reaction can be imposed as follows:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">pe</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="c"># in LAMMPS input script</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">my_pe</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="n">c_1</span><span class="w"> </span><span class="c"># in LAMMPS input script</span>
|
||
</pre></div>
|
||
</div>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="n">custom</span><span class="w"> </span><span class="s">"rxnsum(v_my_pe) > 100"</span><span class="w"> </span><span class="c"># in Constraints section of map file</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The above example prevents the reaction from occurring unless the
|
||
total potential energy of the reaction site is above 100. As a second
|
||
example, this time using the ‘rxnbond’ function, consider a modified
|
||
Arrhenius constraint that depends on the bond force of a specific bond:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="c"># in LAMMPS input script</span>
|
||
|
||
<span class="k">compute </span><span class="nv nv-Identifier">bondforce</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">local</span><span class="w"> </span><span class="n">force</span>
|
||
|
||
<span class="k">compute </span><span class="nv nv-Identifier">ke_atom</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">ke</span><span class="o">/</span><span class="n">atom</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">ke</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="n">c_ke_atom</span>
|
||
|
||
<span class="k">variable </span><span class="nv nv-Identifier">E_a</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="c"># activation energy</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">l0</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="c"># characteristic length</span>
|
||
</pre></div>
|
||
</div>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="c"># in Constraints section of map file</span>
|
||
|
||
<span class="n">custom</span><span class="w"> </span><span class="s">"exp(-(v_E_a-rxnbond(c_bondforce,bond1frag)*v_l0)/(2/3*rxnave(v_ke))) < random(0,1,12345)"</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>By using an inequality and the ‘random(x,y,z)’ function, the left-hand
|
||
side can be interpreted as the probability of the reaction occurring,
|
||
similar to the ‘arrhenius’ constraint above.</p>
|
||
<p>By default, all constraints must be satisfied for the reaction to
|
||
occur. In other words, constraints are evaluated as a series of
|
||
logical values using the logical AND operator “&&”. More complex logic
|
||
can be achieved by explicitly adding the logical AND operator “&&” or
|
||
the logical OR operator “||” after a given constraint command. If a
|
||
logical operator is specified after a constraint, it must be placed
|
||
after all constraint parameters, on the same line as the constraint
|
||
(one per line). Similarly, parentheses can be used to group
|
||
constraints. The expression that results from concatenating all
|
||
constraints should be a valid logical expression that can be read by
|
||
the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command after converting each
|
||
constraint to a logical value. Because exactly one constraint is
|
||
allowed per line, having a valid logical expression implies that left
|
||
parentheses “(” should only appear before a constraint, and right
|
||
parentheses “)” should only appear after a constraint and before any
|
||
logical operator.</p>
|
||
<p>Once a reaction site has been successfully identified, data structures
|
||
within LAMMPS that store bond topology are updated to reflect the
|
||
post-reacted molecule template. All force fields with fixed bonds,
|
||
angles, dihedrals or impropers are supported.</p>
|
||
<p>A few capabilities to note:</p>
|
||
<blockquote>
|
||
<div><ol class="arabic simple">
|
||
<li><p>You may specify as many <em>react</em> arguments as desired. For example, you
|
||
could break down a complicated reaction mechanism into several reaction
|
||
steps, each defined by its own <em>react</em> argument.</p></li>
|
||
<li><p>While typically a bond is formed or removed between the initiator atoms
|
||
specified in the pre-reacted molecule template, this is not required.</p></li>
|
||
<li><p>By reversing the order of the pre- and post-reacted molecule templates in
|
||
another <em>react</em> argument, you can allow for the possibility of one or
|
||
more reverse reactions.</p></li>
|
||
</ol>
|
||
</div></blockquote>
|
||
<p>The optional keywords deal with the probability of a given reaction
|
||
occurring as well as the stable equilibration of each reaction site as
|
||
it occurs.</p>
|
||
<p>The <em>prob</em> keyword can affect whether or not an eligible reaction
|
||
actually occurs. The fraction setting must be a value between 0.0 and
|
||
1.0, and can be specified with an equal-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.
|
||
A uniform random number between 0.0 and 1.0 is generated and the
|
||
eligible reaction only occurs if the random number is less than the
|
||
fraction. Up to <span class="math notranslate nohighlight">\(N\)</span> reactions are permitted to occur, as optionally
|
||
specified by the <em>max_rxn</em> keyword.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>The <em>rate_limit</em> keyword can enforce an upper limit on the overall
|
||
rate of the reaction. The number of reaction occurrences is limited to
|
||
Nlimit within an interval of Nsteps timesteps. No reactions are
|
||
permitted to occur within the first Nsteps timesteps of the first run
|
||
after reading a data file. Nlimit can be specified with an equal-style
|
||
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.</p>
|
||
<p>The <em>stabilize_steps</em> keyword allows for the specification of how many
|
||
time steps a reaction site is stabilized before being returned to the
|
||
overall system thermostat. In order to produce the most physical
|
||
behavior, this “reaction site equilibration time” should be tuned to
|
||
be as small as possible while retaining stability for a given system
|
||
or reaction step. After a limited number of case studies, this number
|
||
has been set to a default of 60 time steps. Ideally, it should be
|
||
individually tuned for each fix reaction step. Note that in some
|
||
situations, decreasing rather than increasing this parameter will
|
||
result in an increase in stability.</p>
|
||
<p>The <em>custom_charges</em> keyword can be used to specify which atoms’
|
||
atomic charges are updated. When the value is set to <em>no</em>, all atomic
|
||
charges are updated to those specified by the post-reaction template
|
||
(default). Otherwise, the value should be the name of a molecule
|
||
fragment defined in the pre-reaction molecule template. In this case,
|
||
only the atomic charges of atoms in the molecule fragment are updated.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>The <em>rescale_charges</em> keyword can be used to ensure the total charge
|
||
of the system does not change as reactions occur. When the argument is
|
||
set to <em>yes</em>, a fixed value is added to the charges of post-reaction
|
||
atoms such that their total charge equals that of the pre-reaction
|
||
site. If only a subset of atomic charges are updated via the
|
||
<em>custom_charges</em> keyword, this rescaling is applied to the subset.
|
||
This keyword could be useful for systems that contain different
|
||
molecules with the same reactive site, if the partial charges on the
|
||
reaction site vary from molecule to molecule, or when removing
|
||
reaction by-products.</p>
|
||
<p>The <em>molecule</em> keyword can be used to force the reaction to be
|
||
intermolecular, intramolecular or either. When the value is set to
|
||
<em>off</em>, molecule IDs are not considered when searching for reactions
|
||
(default). When the value is set to <em>inter</em>, the initiator atoms must
|
||
have different molecule IDs in order to be considered for the
|
||
reaction. When the value is set to <em>intra</em>, only initiator atoms with
|
||
the same molecule ID are considered for the reaction.</p>
|
||
<p>A few other considerations:</p>
|
||
<p>Optionally, you can enforce additional behaviors on reacting atoms.
|
||
For example, it may be beneficial to force reacting atoms to remain at
|
||
a certain temperature. For this, you can use the internally-created
|
||
dynamic group named “bond_react_MASTER_group”, which consists of all
|
||
atoms currently involved in a reaction. For example, adding the
|
||
following command would add an additional thermostat to the group of
|
||
all currently-reacting atoms:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">bond_react_MASTER_group</span><span class="w"> </span><span class="n">temp</span><span class="o">/</span><span class="n">rescale</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">1</span>
|
||
</pre></div>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>This command must be added after the fix bond/react command, and
|
||
will apply to all reactions.</p>
|
||
</div>
|
||
<p>Computationally, each time step this fix is invoked, it loops over
|
||
neighbor lists (for bond-forming reactions) and computes distances
|
||
between pairs of atoms in the list. It also communicates between
|
||
neighboring processors to coordinate which bonds are created and/or
|
||
removed. 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>
|
||
</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>Cumulative reaction counts for each reaction are written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.
|
||
These values are associated with the reaction name (react-ID).
|
||
Additionally, internally-created per-atom properties are stored to
|
||
allow for smooth restarts. 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 one statistic for each <em>react</em> argument that it
|
||
stores in a global vector, of length (number of react arguments), that
|
||
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>There is one quantity in the global vector for each <em>react</em> argument:</p>
|
||
<blockquote>
|
||
<div><ol class="arabic simple">
|
||
<li><p>cumulative number of reactions that occurred</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>
|
||
<p>When fix bond/react is “<a class="reference internal" href="unfix.html"><span class="doc">unfixed</span></a>”, all internally-created
|
||
groups are deleted. Therefore, fix bond/react can only be unfixed after
|
||
unfixing all other fixes that use any group created by fix bond/react.</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 REACTION 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> 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_create.html"><span class="doc">fix bond/create</span></a>,
|
||
<a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</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 stabilization = no, prob = 1.0, stabilize_steps = 60,
|
||
reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = <em>fit all</em></p>
|
||
<hr class="docutils" />
|
||
<p id="gissinger"><strong>(Gissinger2017)</strong> Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).</p>
|
||
<p id="gissinger2020"><strong>(Gissinger2020)</strong> Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).</p>
|
||
<p id="gissinger2024"><strong>(Gissinger2024)</strong> Gissinger, Jensen and Wise, Computer Physics Communications, 304, 109287 (2024).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
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|
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