895 lines
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HTML
895 lines
54 KiB
HTML
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<title>molecule command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="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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<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"><a class="reference internal" href="create_bonds.html">create_bonds command</a></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 current"><a class="current reference internal" href="#">molecule 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="#format-of-a-molecule-file">Format of a molecule file</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="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>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
|
||
</ul>
|
||
</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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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="molecule-command">
|
||
<span id="index-0"></span><h1>molecule command<a class="headerlink" href="#molecule-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">molecule</span><span class="w"> </span><span class="n">ID</span><span class="w"> </span><span class="n">file1</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">file2</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">fileN</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>ID = user-assigned name for the molecule template</p></li>
|
||
<li><p>file1,file2,… = names of files containing molecule descriptions</p></li>
|
||
<li><p>zero or more keyword/value pairs may be appended after each file</p></li>
|
||
<li><p>keyword = <em>offset</em> or <em>toff</em> or <em>boff</em> or <em>aoff</em> or <em>doff</em> or <em>ioff</em> or <em>scale</em></p>
|
||
<pre class="literal-block"><em>offset</em> values = Toff Boff Aoff Doff Ioff
|
||
Toff = offset to add to atom types
|
||
Boff = offset to add to bond types
|
||
Aoff = offset to add to angle types
|
||
Doff = offset to add to dihedral types
|
||
Ioff = offset to add to improper types
|
||
<em>toff</em> value = Toff
|
||
Toff = offset to add to atom types
|
||
<em>boff</em> value = Boff
|
||
Boff = offset to add to bond types
|
||
<em>aoff</em> value = Aoff
|
||
Aoff = offset to add to angle types
|
||
<em>doff</em> value = Doff
|
||
Doff = offset to add to dihedral types
|
||
<em>ioff</em> value = Ioff
|
||
Ioff = offset to add to improper types
|
||
<em>scale</em> value = sfactor
|
||
sfactor = scale factor to apply to the size and mass of the molecule</pre>
|
||
</li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">molecule</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">mymol.txt</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">co2.txt</span><span class="w"> </span><span class="n">h2o.txt</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">CO2</span><span class="w"> </span><span class="n">co2.txt</span><span class="w"> </span><span class="n">boff</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="n">aoff</span><span class="w"> </span><span class="m">2</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">mymol.txt</span><span class="w"> </span><span class="n">offset</span><span class="w"> </span><span class="m">6</span><span class="w"> </span><span class="m">9</span><span class="w"> </span><span class="m">18</span><span class="w"> </span><span class="m">23</span><span class="w"> </span><span class="m">14</span>
|
||
<span class="k">molecule</span><span class="w"> </span><span class="n">objects</span><span class="w"> </span><span class="n">file.1</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="m">1.5</span><span class="w"> </span><span class="n">file.1</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="n">file.2</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="m">1.3</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Define a molecule template that can be used as part of other LAMMPS
|
||
commands, typically to define a collection of particles as a bonded
|
||
molecule or a rigid body. Commands that currently use molecule
|
||
templates include:</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a></p></li>
|
||
<li><p><a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a></p></li>
|
||
<li><p><a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a></p></li>
|
||
<li><p><a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a></p></li>
|
||
<li><p><a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a></p></li>
|
||
<li><p><a class="reference internal" href="fix_bond_react.html"><span class="doc">fix bond/react</span></a></p></li>
|
||
<li><p><a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a></p></li>
|
||
<li><p><a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a></p></li>
|
||
</ul>
|
||
<p>The ID of a molecule template can only contain alphanumeric characters
|
||
and underscores.</p>
|
||
<p>A single template can contain multiple molecules, listed one per file.
|
||
Some of the commands listed above currently use only the first
|
||
molecule in the template, and will issue a warning if the template
|
||
contains multiple molecules. The <a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a> command allows multiple-molecule templates to define a
|
||
system with more than one templated molecule.</p>
|
||
<p>Each filename can be followed by optional keywords which are applied
|
||
only to the molecule in the file as used in this template. This is to
|
||
make it easy to use the same molecule file in different molecule
|
||
templates or in different simulations. You can specify the same file
|
||
multiple times with different optional keywords.</p>
|
||
<p>The <em>offset</em>, <em>toff</em>, <em>boff</em>, <em>aoff</em>, <em>doff</em>, <em>ioff</em> keywords
|
||
add the specified offset values to the atom types, bond types, angle
|
||
types, dihedral types, and/or improper types as they are read from the
|
||
molecule file. E.g. if <em>toff</em> = 2, and the file uses atom types
|
||
1,2,3, then each created molecule will have atom types 3,4,5. For the
|
||
<em>offset</em> keyword, all five offset values must be specified, but
|
||
individual values will be ignored if the molecule template does not
|
||
use that attribute (e.g. no bonds).</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Offsets are <strong>ignored</strong> on lines using type labels, as the type
|
||
labels will determine the actual types directly depending on the
|
||
current <a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> settings.</p>
|
||
</div>
|
||
<p>The <em>scale</em> keyword scales the size of the molecule. This can be
|
||
useful for modeling polydisperse granular rigid bodies. The scale
|
||
factor is applied to each of these properties in the molecule file, if
|
||
they are defined: the individual particle coordinates (Coords
|
||
section), the individual mass of each particle (Masses section), the
|
||
individual diameters of each particle (Diameters section), the total
|
||
mass of the molecule (header keyword = mass), the center-of-mass of
|
||
the molecule (header keyword = com), and the moments of inertia of the
|
||
molecule (header keyword = inertia).</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>The molecule command can be used to define molecules with bonds,
|
||
angles, dihedrals, impropers, or special bond lists of neighbors
|
||
within a molecular topology, so that you can later add the molecules
|
||
to your simulation, via one or more of the commands listed above.
|
||
Since this topology-related information requires that suitable storage
|
||
is reserved when LAMMPS creates the simulation box (e.g. when using
|
||
the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command or the
|
||
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command) suitable space has to be reserved
|
||
so you do not overflow those pre-allocated data structures when adding
|
||
molecules later. Both the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command and
|
||
the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command have “extra” options which
|
||
ensure space is allocated for storing topology info for molecules that
|
||
are added later.</p>
|
||
</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="format-of-a-molecule-file">
|
||
<h2>Format of a molecule file<a class="headerlink" href="#format-of-a-molecule-file" title="Link to this heading"></a></h2>
|
||
<p>The format of an individual molecule file looks similar but is
|
||
different than that of a data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
||
commands. Here is a simple example for a TIP3P water molecule:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span># Water molecule. TIP3P geometry
|
||
# header section:
|
||
3 atoms
|
||
2 bonds
|
||
1 angles
|
||
|
||
# body section:
|
||
Coords
|
||
|
||
1 0.00000 -0.06556 0.00000
|
||
2 0.75695 0.52032 0.00000
|
||
3 -0.75695 0.52032 0.00000
|
||
|
||
Types
|
||
|
||
1 1 # O
|
||
2 2 # H
|
||
3 2 # H
|
||
|
||
Charges
|
||
|
||
1 -0.834
|
||
2 0.417
|
||
3 0.417
|
||
|
||
Bonds
|
||
|
||
1 1 1 2
|
||
2 1 1 3
|
||
|
||
Angles
|
||
|
||
1 1 2 1 3
|
||
</pre></div>
|
||
</div>
|
||
<p>A molecule file has a header and a body. The header appears first. The
|
||
first line of the header and thus of the molecule file is <em>always</em>
|
||
skipped; it typically contains a description of the file or a comment
|
||
from the software that created the file.</p>
|
||
<p>Then lines are read one line at a time. Lines can have a trailing
|
||
comment starting with ‘#’ that is ignored. There <em>must</em> be at least one
|
||
blank between any valid content and the comment. If the line is blank
|
||
(i.e. contains only white-space after comments are deleted), it is
|
||
skipped. If the line contains a header keyword, the corresponding
|
||
value(s) is/are read from the line. A line that is <em>not</em> blank and does
|
||
<em>not</em> contains a header keyword begins the body of the file.</p>
|
||
<p>The body of the file contains zero or more sections. The first line
|
||
of a section has only a keyword. The next line is skipped. The
|
||
remaining lines of the section contain values. The number of lines
|
||
depends on the section keyword as described below. Zero or more blank
|
||
lines can be used between sections. Sections can appear in any order,
|
||
with a few exceptions as noted below.</p>
|
||
<p>These are the recognized header keywords. Header lines can come in
|
||
any order. The numeric value(s) are read from the beginning of the
|
||
line. The keyword should appear at the end of the line. All these
|
||
settings have default values, as explained below. A line need only
|
||
appear if the value(s) are different than the default, except when
|
||
defining a <em>body</em> particle, which requires setting the number of
|
||
<em>atoms</em> to 1, and setting the <em>inertia</em> in a specific section (see below).</p>
|
||
<table class="docutils align-default">
|
||
<colgroup>
|
||
<col style="width: 22.2%" />
|
||
<col style="width: 14.4%" />
|
||
<col style="width: 46.7%" />
|
||
<col style="width: 16.7%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="row-odd"><th class="head"><p>Number(s)</p></th>
|
||
<th class="head"><p>Keyword</p></th>
|
||
<th class="head"><p>Meaning</p></th>
|
||
<th class="head"><p>Default Value</p></th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="row-even"><td><p>N</p></td>
|
||
<td><p>atoms</p></td>
|
||
<td><p># of atoms N in molecule</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Nb</p></td>
|
||
<td><p>bonds</p></td>
|
||
<td><p># of bonds Nb in molecule</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Na</p></td>
|
||
<td><p>angles</p></td>
|
||
<td><p># of angles Na in molecule</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Nd</p></td>
|
||
<td><p>dihedrals</p></td>
|
||
<td><p># of dihedrals Nd in molecule</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Ni</p></td>
|
||
<td><p>impropers</p></td>
|
||
<td><p># of impropers Ni in molecule</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Nf</p></td>
|
||
<td><p>fragments</p></td>
|
||
<td><p># of fragments Nf in molecule</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Ninteger Ndouble</p></td>
|
||
<td><p>body</p></td>
|
||
<td><p># of integer and floating-point values in body particle</p></td>
|
||
<td><p>0</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Mtotal</p></td>
|
||
<td><p>mass</p></td>
|
||
<td><p>total mass of molecule</p></td>
|
||
<td><p>computed</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Xc Yc Zc</p></td>
|
||
<td><p>com</p></td>
|
||
<td><p>coordinates of center-of-mass of molecule</p></td>
|
||
<td><p>computed</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Ixx Iyy Izz Ixy Ixz Iyz</p></td>
|
||
<td><p>inertia</p></td>
|
||
<td><p>6 components of inertia tensor of molecule</p></td>
|
||
<td><p>computed</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>For <em>mass</em>, <em>com</em>, and <em>inertia</em>, the default is for LAMMPS to calculate
|
||
this quantity itself if needed, assuming the molecules consist of a set
|
||
of point particles or finite-size particles (with a non-zero diameter)
|
||
that do <strong>not</strong> overlap. If finite-size particles in the molecule
|
||
<strong>do</strong> overlap, LAMMPS will not account for the overlap effects when
|
||
calculating any of these 3 quantities, so you should pre-compute them
|
||
yourself and list the values in the file.</p>
|
||
<p>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
|
||
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
|
||
should be the values consistent with the current orientation of the
|
||
rigid body around its center of mass. The values are with respect to
|
||
the simulation box XYZ axes, not with respect to the principal axes of
|
||
the rigid body itself. LAMMPS performs the latter calculation
|
||
internally.</p>
|
||
<p>These are the allowed section keywords for the body of the file.</p>
|
||
<ul class="simple">
|
||
<li><p><em>Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses</em> = atom-property sections</p></li>
|
||
<li><p><em>Bonds, Angles, Dihedrals, Impropers</em> = molecular topology sections</p></li>
|
||
<li><p><em>Special Bond Counts, Special Bonds</em> = special neighbor info</p></li>
|
||
<li><p><em>Shake Flags, Shake Atoms, Shake Bond Types</em> = SHAKE info</p></li>
|
||
<li><p><em>Body Integers, Body Doubles</em> = body-property sections</p></li>
|
||
</ul>
|
||
<p>For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
|
||
atom/bond/angle/etc type can be specified either as a number (numeric
|
||
type) or as an alphanumeric type label. The latter is only allowed if
|
||
type labels have been defined, either by the <a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or in data files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command which have sections for Atom Type Labels, Bond
|
||
Type Labels, Angle Type Labels, etc. See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed syntax of type labels
|
||
and a general discussion of how type labels can be used.
|
||
When using type labels, any values specified as <em>offset</em> are ignored.</p>
|
||
<p>If a Bonds section is specified then the Special Bond Counts and
|
||
Special Bonds sections can also be used, if desired, to explicitly
|
||
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
|
||
details below). This is optional since if these sections are not
|
||
included, LAMMPS will auto-generate this information. Note that
|
||
LAMMPS uses this info to properly exclude or weight bonded pairwise
|
||
interactions between bonded atoms. See the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command for more details. One reason to list the
|
||
special bond info explicitly is for the <a class="reference internal" href="Howto_drude.html"><span class="doc">thermalized Drude
|
||
oscillator model</span></a> which treats the bonds between nuclear
|
||
cores and Drude electrons in a different manner.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Whether a section is required depends on how the molecule template
|
||
is used by other LAMMPS commands. For example, to add a molecule
|
||
via the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> command, the Coords and
|
||
Types sections are required. To add a rigid body via the <a class="reference internal" href="fix_pour.html"><span class="doc">fix
|
||
pour</span></a> command, the Bonds (Angles, etc) sections are not
|
||
required, since the molecule will be treated as a rigid body. Some
|
||
sections are optional. For example, the <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>
|
||
command can be used to add “molecules” which are clusters of
|
||
finite-size granular particles. If the Diameters section is not
|
||
specified, each particle in the molecule will have a default
|
||
diameter of 1.0. See the doc pages for LAMMPS commands that use
|
||
molecule templates for more details.</p>
|
||
</div>
|
||
<p>Each section is listed below in alphabetic order. The format of each
|
||
section is described including the number of lines it must contain and
|
||
rules (if any) for whether it can appear in the data file. For per-
|
||
atom sections, entries should be numbered from 1 to Natoms (where
|
||
Natoms is the number of atoms in the template), indicating which atom
|
||
(or bond, etc) the entry applies to. Per-atom sections need to
|
||
include a setting for every atom, but the atoms can be listed in any
|
||
order.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Coords</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID x y z</p></li>
|
||
<li><p>x,y,z = coordinate of atom</p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Types</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID type</p></li>
|
||
<li><p>type = atom type of atom (1-Natomtype, or type label)</p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Molecules</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID molecule-ID</p></li>
|
||
<li><p>molecule-ID = molecule ID of atom</p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Fragments</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per fragment</p></li>
|
||
<li><p>line syntax: ID a b c d …</p></li>
|
||
<li><p>a,b,c,d,… = IDs of atoms in fragment</p></li>
|
||
</ul>
|
||
<p>The ID of a fragment can only contain alphanumeric characters and
|
||
underscores. The atom IDs should be values from 1 to Natoms, where
|
||
Natoms = # of atoms in the molecule.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Charges</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID q</p></li>
|
||
<li><p>q = charge on atom</p></li>
|
||
</ul>
|
||
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> that
|
||
support charge. If this section is not included, the default charge
|
||
on each atom in the molecule is 0.0.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Diameters</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID diam</p></li>
|
||
<li><p>diam = diameter of atom</p></li>
|
||
</ul>
|
||
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> that
|
||
support finite-size spherical particles, e.g. atom_style sphere. If
|
||
not listed, the default diameter of each atom in the molecule is 1.0.</p>
|
||
<hr class="docutils" />
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 7Feb2024.</span></p>
|
||
</div>
|
||
<p><em>Dipoles</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID mux muy muz</p></li>
|
||
<li><p>mux,muy,muz = x-, y-, and z-component of point dipole vector of atom</p></li>
|
||
</ul>
|
||
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> that
|
||
support particles with point dipoles, e.g. atom_style dipole. If not
|
||
listed, the default dipole component of each atom in the molecule is set
|
||
to 0.0.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Masses</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID mass</p></li>
|
||
<li><p>mass = mass of atom</p></li>
|
||
</ul>
|
||
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> that
|
||
support per-atom mass, as opposed to per-type mass. See the
|
||
<a class="reference internal" href="mass.html"><span class="doc">mass</span></a> command for details. If this section is not
|
||
included, the default mass for each atom is derived from its volume
|
||
(see Diameters section) and a default density of 1.0, in
|
||
<a class="reference internal" href="units.html"><span class="doc">units</span></a> of mass/volume.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Bonds</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per bond</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2</p></li>
|
||
<li><p>type = bond type (1-Nbondtype, or type label)</p></li>
|
||
<li><p>atom1,atom2 = IDs of atoms in bond</p></li>
|
||
</ul>
|
||
<p>The IDs for the two atoms in each bond should be values
|
||
from 1 to Natoms, where Natoms = # of atoms in the molecule.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Angles</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per angle</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2 atom3</p></li>
|
||
<li><p>type = angle type (1-Nangletype, or type label)</p></li>
|
||
<li><p>atom1,atom2,atom3 = IDs of atoms in angle</p></li>
|
||
</ul>
|
||
<p>The IDs for the three atoms in each angle should be values from 1 to
|
||
Natoms, where Natoms = # of atoms in the molecule. The three atoms are
|
||
ordered linearly within the angle. Thus the central atom (around
|
||
which the angle is computed) is the atom2 in the list.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Dihedrals</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per dihedral</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2 atom3 atom4</p></li>
|
||
<li><p>type = dihedral type (1-Ndihedraltype, or type label)</p></li>
|
||
<li><p>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral</p></li>
|
||
</ul>
|
||
<p>The IDs for the four atoms in each dihedral should be values from 1 to
|
||
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
|
||
ordered linearly within the dihedral.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Impropers</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per improper</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2 atom3 atom4</p></li>
|
||
<li><p>type = improper type (1-Nimpropertype, or type label)</p></li>
|
||
<li><p>atom1,atom2,atom3,atom4 = IDs of atoms in improper</p></li>
|
||
</ul>
|
||
<p>The IDs for the four atoms in each improper should be values from 1 to
|
||
Natoms, where Natoms = # of atoms in the molecule. The ordering of
|
||
the 4 atoms determines the definition of the improper angle used in
|
||
the formula for the defined <a class="reference internal" href="improper_style.html"><span class="doc">improper style</span></a>. See
|
||
the doc pages for individual styles for details.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Special Bond Counts</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID N1 N2 N3</p></li>
|
||
<li><p>N1 = # of 1-2 bonds</p></li>
|
||
<li><p>N2 = # of 1-3 bonds</p></li>
|
||
<li><p>N3 = # of 1-4 bonds</p></li>
|
||
</ul>
|
||
<p>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
|
||
this atom within the topology of the molecule. See the
|
||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> page for more discussion of
|
||
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
|
||
section must also appear.</p>
|
||
<p>As explained above, LAMMPS will auto-generate this information if this
|
||
section is not specified. If specified, this section will
|
||
override what would be auto-generated.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Special Bonds</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID a b c d …</p></li>
|
||
<li><p>a,b,c,d,… = IDs of atoms in N1+N2+N3 special bonds</p></li>
|
||
</ul>
|
||
<p>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
|
||
1-4 neighbors of this atom. The IDs should be values from 1 to
|
||
Natoms, where Natoms = # of atoms in the molecule. The first N1
|
||
values should be the 1-2 neighbors, the next N2 should be the 1-3
|
||
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
|
||
appear more than once. See the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> doc
|
||
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
|
||
appears, the Special Bond Counts section must also appear.</p>
|
||
<p>As explained above, LAMMPS will auto-generate this information if this
|
||
section is not specified. If specified, this section will override
|
||
what would be auto-generated.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Shake Flags</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID flag</p></li>
|
||
<li><p>flag = 0,1,2,3,4</p></li>
|
||
</ul>
|
||
<p>This section is only needed when molecules created using the template
|
||
will be constrained by SHAKE via the “fix shake” command. The other
|
||
two Shake sections must also appear in the file, following this one.</p>
|
||
<p>The meaning of the flag for each atom is as follows. See the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> page for a further description of SHAKE
|
||
clusters.</p>
|
||
<ul class="simple">
|
||
<li><p>0 = not part of a SHAKE cluster</p></li>
|
||
<li><p>1 = part of a SHAKE angle cluster (two bonds and the angle they form)</p></li>
|
||
<li><p>2 = part of a 2-atom SHAKE cluster with a single bond</p></li>
|
||
<li><p>3 = part of a 3-atom SHAKE cluster with two bonds</p></li>
|
||
<li><p>4 = part of a 4-atom SHAKE cluster with three bonds</p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Shake Atoms</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID a b c d</p></li>
|
||
<li><p>a,b,c,d = IDs of atoms in cluster</p></li>
|
||
</ul>
|
||
<p>This section is only needed when molecules created using the template
|
||
will be constrained by SHAKE via the “fix shake” command. The other
|
||
two Shake sections must also appear in the file.</p>
|
||
<p>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
|
||
in the SHAKE cluster that this atom belongs to. The number of values
|
||
that must appear is determined by the shake flag for the atom (see the
|
||
Shake Flags section above). All atoms in a particular cluster should
|
||
list their a,b,c,d values identically.</p>
|
||
<p>If flag = 0, no a,b,c,d values are listed on the line, just the
|
||
(ignored) ID.</p>
|
||
<p>If flag = 1, a,b,c are listed, where a = ID of central atom in the
|
||
angle, and b,c the other two atoms in the angle.</p>
|
||
<p>If flag = 2, a,b are listed, where a = ID of atom in bond with the
|
||
lowest ID, and b = ID of atom in bond with the highest ID.</p>
|
||
<p>If flag = 3, a,b,c are listed, where a = ID of central atom,
|
||
and b,c = IDs of other two atoms bonded to the central atom.</p>
|
||
<p>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
|
||
and b,c,d = IDs of other three atoms bonded to the central atom.</p>
|
||
<p>See the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> page for a further description
|
||
of SHAKE clusters.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Shake Bond Types</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: ID a b c</p></li>
|
||
<li><p>a,b,c = bond types (or angle type) of bonds (or angle) in cluster</p></li>
|
||
</ul>
|
||
<p>This section is only needed when molecules created using the template
|
||
will be constrained by SHAKE via the “fix shake” command. The other
|
||
two Shake sections must also appear in the file.</p>
|
||
<p>The a,b,c values are bond types for all bonds in the SHAKE cluster that
|
||
this atom belongs to. Bond types may be either numbers (from 1 to Nbondtypes)
|
||
or bond type labels as defined by the <a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command
|
||
or a “Bond Type Labels” section of a data file.</p>
|
||
<p>The number of values that must appear is determined by the shake flag
|
||
for the atom (see the Shake Flags section above). All atoms in a
|
||
particular cluster should list their a,b,c values identically.</p>
|
||
<p>If flag = 0, no a,b,c values are listed on the line, just the
|
||
(ignored) ID.</p>
|
||
<p>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
|
||
the central atom and the first non-central atom (value b in the Shake
|
||
Atoms section), b = bondtype of the bond between the central atom and
|
||
the second non-central atom (value c in the Shake Atoms section), and c
|
||
= the angle type (1 to Nangletypes, or angle type label) of the angle
|
||
between the three atoms.</p>
|
||
<p>If flag = 2, only a is listed, where a = bondtype of the bond between
|
||
the two atoms in the cluster.</p>
|
||
<p>If flag = 3, a,b are listed, where a = bondtype of the bond between
|
||
the central atom and the first non-central atom (value b in the Shake
|
||
Atoms section), and b = bondtype of the bond between the central atom
|
||
and the second non-central atom (value c in the Shake Atoms section).</p>
|
||
<p>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
|
||
the central atom and the first non-central atom (value b in the Shake
|
||
Atoms section), b = bondtype of the bond between the central atom and
|
||
the second non-central atom (value c in the Shake Atoms section), and c
|
||
= bondtype of the bond between the central atom and the third
|
||
non-central atom (value d in the Shake Atoms section).</p>
|
||
<p>See the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> page for a further description
|
||
of SHAKE clusters.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Body Integers</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line</p></li>
|
||
<li><p>line syntax: N E F</p></li>
|
||
<li><p>N = number of sub-particles or number or vertices</p></li>
|
||
<li><p>E,F = number of edges and faces</p></li>
|
||
</ul>
|
||
<p>This section is only needed when the molecule is a body particle. the other
|
||
Body section must also appear in the file.</p>
|
||
<p>The total number of values that must appear is determined by the body style, and
|
||
must be equal to the Ninteger value given in the <em>body</em> header.</p>
|
||
<p>For <em>nparticle</em> and <em>rounded/polygon</em>, only the number of sub-particles or
|
||
vertices N is required, and Ninteger should have a value of 1.</p>
|
||
<p>For <em>rounded/polyhedron</em>, the number of edges E and faces F is required, and
|
||
Ninteger should have a value of 3.</p>
|
||
<p>See the <a class="reference internal" href="Howto_body.html"><span class="doc">Howto body</span></a> page for a further description of
|
||
the file format.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Body Doubles</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>first line</p></li>
|
||
<li><p>line syntax: Ixx Iyy Izz Ixy Ixz Iyz</p></li>
|
||
<li><p>Ixx Iyy Izz Ixy Ixz Iyz = 6 components of inertia tensor of body particle</p></li>
|
||
<li><p>one line per sub-particle or vertex</p></li>
|
||
<li><p>line syntax: x y z</p></li>
|
||
<li><p>x, y, z = coordinates of sub-particle or vertex</p></li>
|
||
<li><p>one line per edge</p></li>
|
||
<li><p>line syntax: N1 N2</p></li>
|
||
<li><p>N1, N2 = vertex indices</p></li>
|
||
<li><p>one line per face</p></li>
|
||
<li><p>line syntax: N1 N2 N3 N4</p></li>
|
||
<li><p>N1, N2, N3, N4 = vertex indices</p></li>
|
||
<li><p>last line</p></li>
|
||
<li><p>line syntax: diam</p></li>
|
||
<li><p>diam = rounded diameter that surrounds each vertex</p></li>
|
||
</ul>
|
||
<p>This section is only needed when the molecule is a body particle. the other
|
||
Body section must also appear in the file.</p>
|
||
<p>The total number of values that must appear is determined by the body style, and
|
||
must be equal to the Ndouble value given in the <em>body</em> header. The 6 moments of
|
||
inertia and the 3N coordinates of the sub-particles or vertices are required
|
||
for all body styles.</p>
|
||
<p>For <em>rounded/polygon</em>, the E = 6 + 3*N + 1 edges are automatically determined
|
||
from the vertices.</p>
|
||
<p>For <em>rounded/polyhedron</em>, the 2E vertex indices for the end points of the edges
|
||
and 4F vertex indices defining the faces are required.</p>
|
||
<p>See the <a class="reference internal" href="Howto_body.html"><span class="doc">Howto body</span></a> page for a further description of
|
||
the file format.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>None</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>, <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>,
|
||
<a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The default keywords values are offset 0 0 0 0 0 and scale = 1.0.</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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||
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||
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||
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|
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