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484 lines
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HTML
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<title>create_bonds command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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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="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<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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<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 current"><a class="reference internal" href="commands_list.html">Commands</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_write.html">angle_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">create_bonds 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="create_box.html">create_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_write.html">dihedral_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dynamical_matrix.html">dynamical_matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fitpod_command.html">fitpod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="geturl.html">geturl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="hyper.html">hyper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kim_commands.html">kim command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="labelmap.html">labelmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mdi.html">mdi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html">min_style spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-cg-command">min_style spin/cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-lbfgs-command">min_style spin/lbfgs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-hftn-command">min_style hftn command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-sd-command">min_style sd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-quickmin-command">min_style quickmin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-fire-command">min_style fire command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-command"><span class="xref std std-doc">min_style spin</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-cg-command"><span class="xref std std-doc">min_style spin/cg</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-lbfgs-command"><span class="xref std std-doc">min_style spin/lbfgs</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb_spin.html">neb/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="plugin.html">plugin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_atoms.html">reset_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper_grem.html">temper/grem command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper_npt.html">temper/npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="third_order.html">third_order command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</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 class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
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</ul>
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<li class="breadcrumb-item active">create_bonds command</li>
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<div itemprop="articleBody">
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|
||
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="create-bonds-command">
|
||
<span id="index-0"></span><h1>create_bonds command<a class="headerlink" href="#create-bonds-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">create_bonds</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">args</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul class="simple">
|
||
<li><p>style = <em>many</em> or <em>single/bond</em> or <em>single/angle</em> or <em>single/dihedral</em> or <em>single/improper</em></p></li>
|
||
</ul>
|
||
<pre class="literal-block"><em>many</em> args = group-ID group2-ID btype rmin rmax
|
||
group-ID = ID of first group
|
||
group2-ID = ID of second group, bonds will be between atoms in the 2 groups
|
||
btype = bond type of created bonds
|
||
rmin = minimum distance between pair of atoms to bond together
|
||
rmax = maximum distance between pair of atoms to bond together
|
||
<em>single/bond</em> args = btype batom1 batom2
|
||
btype = bond type of new bond
|
||
batom1,batom2 = atom IDs for two atoms in bond
|
||
<em>single/angle</em> args = atype aatom1 aatom2 aatom3
|
||
atype = angle type of new angle
|
||
aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
|
||
<em>single/dihedral</em> args = dtype datom1 datom2 datom3 datom4
|
||
dtype = dihedral type of new dihedral
|
||
datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral
|
||
<em>single/improper</em> args = itype iatom1 iatom2 iatom3 iatom4
|
||
itype = improper type of new improper
|
||
iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper</pre>
|
||
<ul class="simple">
|
||
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>special</em></p></li>
|
||
</ul>
|
||
<pre class="literal-block"><em>special</em> value = <em>yes</em> or <em>no</em></pre>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">create_bonds</span><span class="w"> </span><span class="n">many</span><span class="w"> </span><span class="n">all</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">1.0</span><span class="w"> </span><span class="m">1.2</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">many</span><span class="w"> </span><span class="n">surf</span><span class="w"> </span><span class="n">solvent</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="m">2.4</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">bond</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">angle</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">52</span><span class="w"> </span><span class="m">98</span><span class="w"> </span><span class="m">107</span><span class="w"> </span><span class="n">special</span><span class="w"> </span><span class="n">no</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">dihedral</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="m">19</span><span class="w"> </span><span class="m">27</span><span class="w"> </span><span class="m">101</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">improper</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">23</span><span class="w"> </span><span class="m">26</span><span class="w"> </span><span class="m">31</span><span class="w"> </span><span class="m">57</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Create bonds between pairs of atoms that meet a specified distance
|
||
criteria. Or create a single bond, angle, dihedral or improper between 2, 3,
|
||
or 4 specified atoms.</p>
|
||
<p>The new bond (angle, dihedral, improper) interactions will then be computed
|
||
during a simulation by the bond (angle, dihedral, improper) potential defined by
|
||
the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>, <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>,
|
||
<a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>, <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>,
|
||
<a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>,
|
||
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>, <a class="reference internal" href="improper_style.html"><span class="doc">improper_style</span></a>,
|
||
<a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a> commands.</p>
|
||
<p>The <em>many</em> style is useful for adding bonds to a system (e.g., between
|
||
nearest neighbors in a lattice of atoms) without having to enumerate
|
||
all the bonds in the data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
||
command.</p>
|
||
<p>The <em>single</em> styles are useful for adding bonds, angles, dihedrals, and
|
||
impropers to a system incrementally, then continuing a simulation.</p>
|
||
<p>Note that this command does not auto-create any angle, dihedral, or improper
|
||
interactions when a bond is added, nor does it auto-create any bonds
|
||
when an angle, dihedral, or improper is added. It also will not auto-create
|
||
any angles when a dihedral or improper is added. Thus, the flexibility of this
|
||
command is limited. It can be used several times to create different types of
|
||
bond at different distances, but it cannot typically auto-create all the
|
||
bonds or angles or dihedrals or impropers that would normally be defined in a
|
||
data file for a complex system of molecules.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If the system has no bonds (angles, dihedrals, impropers) to begin
|
||
with, or if more bonds per atom are being added than currently exist,
|
||
then you must ensure that the number of bond types and the maximum
|
||
number of bonds per atom are set to large enough values, and
|
||
similarly for angles, dihedrals, impropers, and special neighbors,
|
||
otherwise an error may occur when too many bonds (angles, dihedrals,
|
||
impropers) are added to an atom. If the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
||
command is used to define the system, these parameters can be set via
|
||
its optional <em>extra/bond/types</em>, <em>extra/bond/per/atom</em>, and similar
|
||
keywords to the command. If the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>
|
||
command is used to define the system, these two parameters can be set
|
||
via its optional <em>bond/types</em> and <em>extra/bond/per/atom</em> arguments,
|
||
and similarly for angles, dihedrals, and impropers. See the
|
||
corresponding documentation pages for these two commands for details.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>many</em> style will create bonds between pairs of atoms <span class="math notranslate nohighlight">\(I,J\)</span>,
|
||
where <span class="math notranslate nohighlight">\(I\)</span> is in one of the two specified groups and <span class="math notranslate nohighlight">\(J\)</span> is in the
|
||
other. The two groups can be the same (e.g., group “all”). The created bonds
|
||
will be of bond type <em>btype</em>, where <em>btype</em> must be a value between 1 and the
|
||
number of bond types defined.</p>
|
||
<p>For a bond to be created, an <span class="math notranslate nohighlight">\(I,J\)</span> pair of atoms must be a distance
|
||
<span class="math notranslate nohighlight">\(D\)</span> apart such that <span class="math notranslate nohighlight">\(r_\text{min} \le D \le r_\text{max}\)</span>.</p>
|
||
<p>The following settings must have been made in an input script before
|
||
the <em>many</em> style is used:</p>
|
||
<ul class="simple">
|
||
<li><p>special_bonds weight for 1–2 interactions must be 0.0</p></li>
|
||
<li><p>a <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> must be defined</p></li>
|
||
<li><p>no <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> defined</p></li>
|
||
<li><p>minimum <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> cutoff + <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a>
|
||
skin <span class="math notranslate nohighlight">\(\ge r_\text{max}\)</span></p></li>
|
||
</ul>
|
||
<p>These settings are required so that a neighbor list can be created to
|
||
search for nearby atoms. Pairs of atoms that are already bonded cannot
|
||
appear in the neighbor list, to avoid creation of duplicate bonds. The
|
||
neighbor list for all atom type pairs must also extend to a distance
|
||
that encompasses the <em>rmax</em> for new bonds to create. When using
|
||
periodic boundary conditions, the box length in each periodic dimension
|
||
must be larger than <em>rmax</em>, so that no bonds are created between the
|
||
system and its own periodic image.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you want to create bonds between pairs of 1–3 or 1–4 atoms in
|
||
the current bond topology, then you need to use <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds
|
||
lj 0 1 1</span></a> to ensure those pairs appear in the
|
||
neighbor list. They will not appear with the default special_bonds
|
||
settings, which are zero for 1–2, 1–3, and 1–4 atoms. 1–3 or 1–4
|
||
atoms are those which are two hops or three hops apart in the bond
|
||
topology.</p>
|
||
</div>
|
||
<p>An additional requirement for this style is that your system must be
|
||
ready to perform a simulation. This means, for example, that all
|
||
<a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> coefficients be set via the
|
||
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command. A <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>
|
||
command and all bond coefficients must also be set, even if no bonds
|
||
exist before this command is invoked. This is because the building of
|
||
neighbor list requires initialization and setup of a simulation,
|
||
similar to what a <a class="reference internal" href="run.html"><span class="doc">run</span></a> command would require.</p>
|
||
<p>Note that you can change any of these settings after this command
|
||
executes (e.g., if you wish to use long-range Coulombic interactions)
|
||
via the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command for your subsequent
|
||
simulation.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>single/bond</em> style creates a single bond of type <em>btype</em> between
|
||
two atoms with IDs <em>batom1</em> and <em>batom2</em>. <em>Btype</em> must be a value
|
||
between 1 and the number of bond types defined.</p>
|
||
<p>The <em>single/angle</em> style creates a single angle of type <em>atype</em>
|
||
between three atoms with IDs <em>aatom1</em>, <em>aatom2</em>, and <em>aatom3</em>. The
|
||
ordering of the atoms is the same as in the <em>Angles</em> section of a data
|
||
file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command (i.e., the three atoms
|
||
are ordered linearly within the angle; the central atom is <em>aatom2</em>).
|
||
<em>Atype</em> must be a value between 1 and the number of angle types
|
||
defined.</p>
|
||
<p>The <em>single/dihedral</em> style creates a single dihedral of type <em>dtype</em>
|
||
between four atoms with IDs <em>datom1</em>, <em>datom2</em>, <em>datom3</em>, and <em>datom4</em>. The
|
||
ordering of the atoms is the same as in the <em>Dihedrals</em> section of a data file
|
||
read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. I.e. the 4 atoms are ordered
|
||
linearly within the dihedral. <em>dtype</em> must be a value between 1 and
|
||
the number of dihedral types defined.</p>
|
||
<p>The <em>single/improper</em> style creates a single improper of type <em>itype</em>
|
||
between four atoms with IDs <em>iatom1</em>, <em>iatom2</em>, <em>iatom3</em>, and <em>iatom4</em>. The
|
||
ordering of the atoms is the same as in the <em>Impropers</em> section of a data file
|
||
read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. I.e. the 4 atoms are ordered
|
||
linearly within the improper. <em>itype</em> must be a value between 1 and
|
||
the number of improper types defined.</p>
|
||
<hr class="docutils" />
|
||
<p>The keyword <em>special</em> controls whether an internal list of special
|
||
bonds is created after one or more bonds, or a single angle, dihedral, or
|
||
improper is added to the system.</p>
|
||
<p>The default value is <em>yes</em>. A value of <em>no</em> cannot be used
|
||
with the <em>many</em> style.</p>
|
||
<p>This is an expensive operation since the bond topology for the system
|
||
must be walked to find all 1–2, 1–3, and 1–4 interactions to store in an
|
||
internal list, which is used when pairwise interactions are weighted;
|
||
see the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command for details.</p>
|
||
<p>Thus if you are adding a few bonds or a large list of angles all at
|
||
the same time, by using this command repeatedly, it is more efficient
|
||
to only trigger the internal list to be created once, after the last
|
||
bond (or angle, or dihedral, or improper) is added:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">bond</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">52</span><span class="w"> </span><span class="m">98</span><span class="w"> </span><span class="n">special</span><span class="w"> </span><span class="n">no</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">bond</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">73</span><span class="w"> </span><span class="m">74</span><span class="w"> </span><span class="n">special</span><span class="w"> </span><span class="n">no</span>
|
||
<span class="n">...</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">bond</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">17</span><span class="w"> </span><span class="m">386</span><span class="w"> </span><span class="n">special</span><span class="w"> </span><span class="n">no</span>
|
||
<span class="k">create_bonds</span><span class="w"> </span><span class="n">single</span><span class="o">/</span><span class="n">bond</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="m">112</span><span class="w"> </span><span class="m">183</span><span class="w"> </span><span class="n">special</span><span class="w"> </span><span class="n">yes</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Note that you <strong>must</strong> ensure the internal list is rebuilt after the last
|
||
bond (angle, dihedral, improper) is added, <em>before</em> performing a simulation.
|
||
Otherwise, pairwise interactions will not be properly excluded or
|
||
weighted. LAMMPS does <strong>not</strong> check that you have done this correctly.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This command cannot be used with molecular systems defined using
|
||
molecule template files via the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> and
|
||
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a> commands.</p>
|
||
<p>For style <em>many</em>, no <a class="reference internal" href="kspace_style.html"><span class="doc">kspace style</span></a> must be
|
||
defined. Also, the <em>rmax</em> value must be smaller than any periodic box
|
||
length and the neighbor list cutoff (largest pair cutoff plus neighbor
|
||
skin).</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="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The keyword default is special = yes.</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
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|
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