forked from lijiext/lammps
681 lines
48 KiB
HTML
681 lines
48 KiB
HTML
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<!DOCTYPE html>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>fix bond/create command — LAMMPS documentation</title>
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<link rel="up" title="Fixes" href="fixes.html"/>
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<link rel="next" title="fix bond/swap command" href="fix_bond_swap.html"/>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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<p class="caption"><span class="caption-text">Index</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
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<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="fixes.html">Fixes</a><ul class="current">
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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_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_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_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_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_bond_break.html">fix bond/break command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">fix bond/create command</a><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="#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_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_deform.html">fix deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html#fix-deform-kk-command">fix deform/kk 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_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_ehex.html">fix ehex 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_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_gravity.html#fix-gravity-omp-command">fix gravity/omp 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_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.html#fix-langevin-kk-command">fix langevin/kk 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_lb_fluid.html">fix lb/fluid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_momentum.html">fix lb/momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_pc.html">fix lb/pc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_rigid_pc_sphere.html">fix lb/rigid/pc/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso.html">fix meso command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso_stationary.html">fix meso/stationary 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_move.html">fix move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-intel-command">fix nvt/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-kk-command">fix nvt/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-omp-command">fix nvt/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-intel-command">fix npt/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-kk-command">fix npt/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-omp-command">fix npt/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-kk-command">fix nph/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-omp-command">fix nph/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html#fix-nph-asphere-omp-command">fix nph/asphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html#fix-nph-sphere-omp-command">fix nph/sphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html#fix-nphug-omp-command">fix nphug/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html#fix-npt-asphere-omp-command">fix npt/asphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html">fix npt/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html#fix-npt-sphere-omp-command">fix npt/sphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-intel-command">fix nve/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-kk-command">fix nve/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-omp-command">fix nve/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html#fix-nve-asphere-intel-command">fix nve/asphere/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_body.html">fix nve/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_eff.html">fix nve/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_limit.html">fix nve/limit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_line.html">fix nve/line command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_manifold_rattle.html">fix nve/manifold/rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_noforce.html">fix nve/noforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html">fix nve/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html#fix-nve-sphere-omp-command">fix nve/sphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_tri.html">fix nve/tri command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html">fix nvt/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html#fix-nvt-asphere-omp-command">fix nvt/asphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_body.html">fix nvt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html">fix nvt/sllod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html#fix-nvt-sllod-intel-command">fix nvt/sllod/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html#fix-nvt-sllod-omp-command">fix nvt/sllod/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod_eff.html">fix nvt/sllod/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html">fix nvt/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html#fix-nvt-sphere-omp-command">fix nvt/sphere/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_oneway.html">fix oneway command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html">fix orient/fcc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_phonon.html">fix phonon command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html">fix pimd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_planeforce.html">fix planeforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_pour.html">fix pour command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_press_berendsen.html">fix press/berendsen command</a></li>
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<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_property_atom.html">fix property/atom command</a></li>
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|
<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-slater-command">fix qeq/slater command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-dynamic-command">fix qeq/dynamic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-fire-command">fix qeq/fire command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html">fix qeq/comb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html#fix-qeq-comb-omp-command">fix qeq/comb/omp command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reax.html">fix qeq/reax command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reax.html#fix-qeq-reax-kk-command">fix qeq/reax/kk command</a></li>
|
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_reax_bonds.html">fix reax/bonds command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_reax_bonds.html#fix-reax-c-bonds-command">fix reax/c/bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_reaxc_species.html">fix reax/c/species command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_recenter.html">fix recenter command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_restrain.html">fix restrain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html">fix rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-command">fix rigid/nve command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-command">fix rigid/npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-command">fix rigid/nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-small-command">fix rigid/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-small-command">fix rigid/nph/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rx.html">fix rx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_saed_vtk.html">fix saed/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html">fix setforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html#fix-setforce-kk-command">fix setforce/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shake.html">fix shake command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shake.html#fix-rattle-command">fix rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shardlow.html">fix shardlow command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd.html">fix smd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_adjust_dt.html">fix smd/adjust_dt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_tlsph.html">fix smd/integrate_tlsph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_ulsph.html">fix smd/integrate_ulsph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_move_triangulated_surface.html">fix smd/move_tri_surf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_setvel.html">fix smd/setvel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_wall_surface.html">fix smd/wall_surface command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring.html">fix spring command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_chunk.html">fix spring/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_rg.html">fix spring/rg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_self.html">fix spring/self command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_srd.html">fix srd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_store_force.html">fix store/force command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_store_state.html">fix store/state command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_berendsen.html">fix temp/berendsen command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html">fix temp/csvr command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html#fix-temp-csld-command">fix temp/csld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale.html">fix temp/rescale command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_viscosity.html">fix viscosity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_viscous.html">fix viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_piston.html">fix wall/piston command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html#fix-wall-reflect-kk-command">fix wall/reflect/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li>fix bond/create command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<div class="section" id="fix-bond-create-command">
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<span id="index-0"></span><h1>fix bond/create command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">bond</span><span class="o">/</span><span class="n">create</span> <span class="n">Nevery</span> <span class="n">itype</span> <span class="n">jtype</span> <span class="n">Rmin</span> <span class="n">bondtype</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
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</li>
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<li><p class="first">bond/create = style name of this fix command</p>
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</li>
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<li><p class="first">Nevery = attempt bond creation every this many steps</p>
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</li>
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<li><p class="first">itype,jtype = atoms of itype can bond to atoms of jtype</p>
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</li>
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<li><p class="first">Rmin = 2 atoms separated by less than Rmin can bond (distance units)</p>
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</li>
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<li><p class="first">bondtype = type of created bonds</p>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended to args</p>
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</li>
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<li><p class="first">keyword = <em>iparam</em> or <em>jparam</em> or <em>prob</em> or <em>atype</em> or <em>dtype</em> or <em>itype</em></p>
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<pre class="literal-block">
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<em>iparam</em> values = maxbond, newtype
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maxbond = max # of bonds of bondtype the itype atom can have
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newtype = change the itype atom to this type when maxbonds exist
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<em>jparam</em> values = maxbond, newtype
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maxbond = max # of bonds of bondtype the jtype atom can have
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newtype = change the jtype atom to this type when maxbonds exist
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<em>prob</em> values = fraction seed
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fraction = create a bond with this probability if otherwise eligible
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seed = random number seed (positive integer)
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<em>atype</em> value = angletype
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angletype = type of created angles
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<em>dtype</em> value = dihedraltype
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dihedraltype = type of created dihedrals
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<em>itype</em> value = impropertype
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impropertype = type of created impropers
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</pre>
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</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">5</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">create</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">0.8</span> <span class="mi">1</span>
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<span class="n">fix</span> <span class="mi">5</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">create</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mf">0.8</span> <span class="mi">1</span> <span class="n">prob</span> <span class="mf">0.5</span> <span class="mi">85784</span> <span class="n">iparam</span> <span class="mi">2</span> <span class="mi">3</span>
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|
<span class="n">fix</span> <span class="mi">5</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">create</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mf">0.8</span> <span class="mi">1</span> <span class="n">prob</span> <span class="mf">0.5</span> <span class="mi">85784</span> <span class="n">iparam</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">atype</span> <span class="mi">1</span> <span class="n">dtype</span> <span class="mi">2</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Create bonds between pairs of atoms as a simulation runs according to
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specified criteria. This can be used to model cross-linking of
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polymers, the formation of a percolation network, etc. In this
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context, a bond means an interaction between a pair of atoms computed
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by the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> command. Once the bond is created
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it will be permanently in place. Optionally, the creation of a bond
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can also create angle, dihedral, and improper interactions that bond
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is part of. See the discussion of the <em>atype</em>, <em>dtype</em>, and <em>itype</em>
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keywords below.</p>
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<p>This is different than a <a class="reference internal" href="pair_style.html"><span class="doc">pairwise</span></a> bond-order
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potential such as Tersoff or AIREBO which infers bonds and many-body
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interactions based on the current geometry of a small cluster of atoms
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and effectively creates and destroys bonds and higher-order many-body
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interactions from timestep to timestep as atoms move.</p>
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<p>A check for possible new bonds is performed every <em>Nevery</em> timesteps.
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If two atoms I,J are within a distance <em>Rmin</em> of each other, if I is
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of atom type <em>itype</em>, if J is of atom type <em>jtype</em>, if both I and J
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are in the specified fix group, if a bond does not already exist
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between I and J, and if both I and J meet their respective <em>maxbond</em>
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requirement (explained below), then I,J is labeled as a “possible”
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bond pair.</p>
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<p>If several atoms are close to an atom, it may have multiple possible
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bond partners. Every atom checks its list of possible bond partners
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and labels the closest such partner as its “sole” bond partner. After
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this is done, if atom I has atom J as its sole partner, and atom J has
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atom I as its sole partner, then the I,J bond is “eligible” to be
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formed.</p>
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<p>Note that these rules mean an atom will only be part of at most one
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created bond on a given timestep. It also means that if atom I
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chooses atom J as its sole partner, but atom J chooses atom K is its
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|
sole partner (due to Rjk < Rij), then this means atom I will not form
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a bond on this timestep, even if it has other possible bond partners.</p>
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|
<p>It is permissible to have <em>itype</em> = <em>jtype</em>. <em>Rmin</em> must be <= the
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|
pairwise cutoff distance between <em>itype</em> and <em>jtype</em> atoms, as defined
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|
by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> command.</p>
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|
<p>The <em>iparam</em> and <em>jparam</em> keywords can be used to limit the bonding
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|
functionality of the participating atoms. Each atom keeps track of
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|
how many bonds of <em>bondtype</em> it already has. If atom I of
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|
itype already has <em>maxbond</em> bonds (as set by the <em>iparam</em>
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|
keyword), then it will not form any more. Likewise for atom J. If
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<em>maxbond</em> is set to 0, then there is no limit on the number of bonds
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that can be formed with that atom.</p>
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|
<p>The <em>newtype</em> value for <em>iparam</em> and <em>jparam</em> can be used to change
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|
the atom type of atom I or J when it reaches <em>maxbond</em> number of bonds
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|
of type <em>bondtype</em>. This means it can now interact in a pairwise
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|
fashion with other atoms in a different way by specifying different
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|
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> coefficients. If you do not wish the
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|
atom type to change, simply specify <em>newtype</em> as <em>itype</em> or <em>jtype</em>.</p>
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|
<p>The <em>prob</em> keyword can also effect whether an eligible bond is
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|
actually created. The <em>fraction</em> setting must be a value between 0.0
|
|
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
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|
the eligible bond is only created if the random number < fraction.</p>
|
|
<p>Any bond that is created is assigned a bond type of <em>bondtype</em></p>
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|
<p>When a bond is created, data structures within LAMMPS that store bond
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|
topology are updated to reflect the creation. If the bond is part of
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|
new 3-body (angle) or 4-body (dihedral, improper) interactions, you
|
|
can choose to create new angles, dihedrals, impropers as well, using
|
|
the <em>atype</em>, <em>dtype</em>, and <em>itype</em> keywords. All of these changes
|
|
typically affect pairwise interactions between atoms that are now part
|
|
of new bonds, angles, etc.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">One data structure that is not updated when a bond breaks are
|
|
the molecule IDs stored by each atom. Even though two molecules
|
|
become one moleclue due to the created bond, all atoms in the new
|
|
moleclue retain their original molecule IDs.</p>
|
|
</div>
|
|
<p>If the <em>atype</em> keyword is used and if an angle potential is defined
|
|
via the <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a> command, then any new 3-body
|
|
interactions inferred by the creation of a bond will create new angles
|
|
of type <em>angletype</em>, with parameters assigned by the corresponding
|
|
<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command. Likewise, the <em>dtype</em> and
|
|
<em>itype</em> keywords will create new dihedrals and impropers of type
|
|
<em>dihedraltype</em> and <em>impropertype</em>.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">To create a new bond, the internal LAMMPS data structures that
|
|
store this information must have space for it. When LAMMPS is
|
|
initialized from a data file, the list of bonds is scanned and the
|
|
maximum number of bonds per atom is tallied. If some atom will
|
|
acquire more bonds than this limit as this fix operates, then the
|
|
“extra bond per atom” parameter must be set to allow for it. Ditto
|
|
for “extra angle per atom”, “extra dihedral per atom”, and “extra
|
|
improper per atom” if angles, dihedrals, or impropers are being added
|
|
when bonds are created. See the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
|
|
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command for more details. Note that a
|
|
data file with no atoms can be used if you wish to add unbonded atoms
|
|
via the <a class="reference internal" href="create_atoms.html"><span class="doc">create atoms</span></a> command, e.g. for a
|
|
percolation simulation.</p>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">LAMMPS stores and maintains a data structure with a list of the
|
|
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
|
|
the system) for use in weighting pairwise interactions for bonded
|
|
atoms. Note that adding a single bond always adds a new 1st neighbor
|
|
but may also induce *many* new 2nd and 3rd neighbors, depending on the
|
|
molecular topology of your system. The “extra special per atom”
|
|
parameter must typically be set to allow for the new maximum total
|
|
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
|
|
ways to do this. See the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
|
|
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or “special_bonds extra” commands for
|
|
details.</p>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Even if you do not use the <em>atype</em>, <em>dtype</em>, or <em>itype</em>
|
|
keywords, the list of topological neighbors is updated for atoms
|
|
affected by the new bond. This in turn affects which neighbors are
|
|
considered for pairwise interactions, using the weighting rules set by
|
|
the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command. Consider a new bond
|
|
created between atoms I,J. If J has a bonded neighbor K, then K
|
|
becomes a 2nd neighbor of I. Even if the <em>atype</em> keyword is not used
|
|
to create angle I-J-K, the pairwise interaction between I and K will
|
|
be potentially turned off or weighted by the 1-3 weighting specified
|
|
by the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command. This is the case
|
|
even if the “angle yes” option was used with that command. The same
|
|
is true for 3rd neighbors (1-4 interactions), the <em>dtype</em> keyword, and
|
|
the “dihedral yes” option used with the
|
|
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command.</p>
|
|
</div>
|
|
<p>Note that even if your simulation starts with no bonds, you must
|
|
define a <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> and use the
|
|
<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command to specify coefficients for the
|
|
<em>bondtype</em>. Similarly, if new atom types are specified by the
|
|
<em>iparam</em> or <em>jparam</em> keywords, they must be within the range of atom
|
|
types allowed by the simulation and pairwise coefficients must be
|
|
specified for the new types.</p>
|
|
<p>Computationally, each timestep this fix operates, it loops over
|
|
neighbor lists and computes distances between pairs of atoms in the
|
|
list. It also communicates between neighboring processors to
|
|
coordinate which bonds are created. Moreover, if any bonds are
|
|
created, neighbor lists must be immediately updated on the same
|
|
timestep. This is to insure that any pairwise interactions that
|
|
should be turned “off” due to a bond creation, because they are now
|
|
excluded by the presence of the bond and the settings of the
|
|
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command, will be immediately
|
|
recognized. All of these operations increase the cost of a timestep.
|
|
Thus you should be cautious about invoking this fix too frequently.</p>
|
|
<p>You can dump out snapshots of the current bond topology via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Creating a bond typically alters the energy of a system. You
|
|
should be careful not to choose bond creation criteria that induce a
|
|
dramatic change in energy. For example, if you define a very stiff
|
|
harmonic bond and create it when 2 atoms are separated by a distance
|
|
far from the equilibribum bond length, then the 2 atoms will oscillate
|
|
dramatically when the bond is formed. More generally, you may need to
|
|
thermostat your system to compensate for energy changes resulting from
|
|
created bonds (and angles, dihedrals, impropers).</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
|
are relevant to this fix.</p>
|
|
<p>This fix computes two statistics which it stores in a global vector of
|
|
length 2, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The vector values calculated
|
|
by this fix are “intensive”.</p>
|
|
<p>These are the 2 quantities:</p>
|
|
<ul class="simple">
|
|
<li><ol class="first arabic">
|
|
<li># of bonds created on the most recent creation timestep</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="2">
|
|
<li>cummulative # of bonds created</li>
|
|
</ol>
|
|
</li>
|
|
</ul>
|
|
<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>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
|
|
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>, <a class="reference internal" href="fix_bond_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>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are iparam = (0,itype), jparam = (0,jtype), and
|
|
prob = 1.0.</p>
|
|
</div>
|
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