forked from lijiext/lammps
497 lines
29 KiB
HTML
497 lines
29 KiB
HTML
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<title>atom_modify command — LAMMPS documentation</title>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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<p class="caption"><span class="caption-text">Index</span></p>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="commands.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 current"><a class="current reference internal" href="#">atom_modify 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="#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="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="box.html">box 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="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="dump.html">dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_h5md.html">dump h5md command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-movie-command">dump movie command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile 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="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="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="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="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="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style 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="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="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_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="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="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">Fixes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</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">Bonds</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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</ul>
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<li>atom_modify command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="atom_style.html" class="btn btn-neutral float-right" title="atom_style command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="angle_style.html" class="btn btn-neutral" title="angle_style command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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<div class="section" id="atom-modify-command">
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<span id="index-0"></span><h1>atom_modify command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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atom_modify keyword values ...
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</pre>
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<ul>
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<li><p class="first">one or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></p>
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<pre class="literal-block">
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<em>id</em> value = <em>yes</em> or <em>no</em>
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<em>map</em> value = <em>array</em> or <em>hash</em>
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<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
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<em>sort</em> values = Nfreq binsize
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Nfreq = sort atoms spatially every this many time steps
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binsize = bin size for spatial sorting (distance units)
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</pre>
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</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<pre class="literal-block">
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atom_modify map hash
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atom_modify map array sort 10000 2.0
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atom_modify first colloid
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</pre>
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</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Modify certain attributes of atoms defined and stored within LAMMPS,
|
|
in addition to what is specified by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>
|
|
command. The <em>id</em> and <em>map</em> keywords must be specified before a
|
|
simulation box is defined; other keywords can be specified any time.</p>
|
|
<p>The <em>id</em> keyword determines whether non-zero atom IDs can be assigned
|
|
to each atom. If the value is <em>yes</em>, which is the default, IDs are
|
|
assigned, whether you use the <a class="reference internal" href="create_atoms.html"><span class="doc">create atoms</span></a> or
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
|
commands to initialize atoms. If the value is <em>no</em> the IDs for all
|
|
atoms are assumed to be 0.</p>
|
|
<p>If atom IDs are used, they must all be positive integers. They should
|
|
also be unique, though LAMMPS does not check for this. Typically they
|
|
should also be consecutively numbered (from 1 to Natoms), though this
|
|
is not required. Molecular <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> are those
|
|
that store bond topology information (styles bond, angle, molecular,
|
|
full). These styles require atom IDs since the IDs are used to encode
|
|
the topology. Some other LAMMPS commands also require the use of atom
|
|
IDs. E.g. some many-body pair styles use them to avoid double
|
|
computation of the I-J interaction between two atoms.</p>
|
|
<p>The only reason not to use atom IDs is if you are running an atomic
|
|
simulation so large that IDs cannot be uniquely assigned. For a
|
|
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
|
|
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
|
|
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
|
|
switch. This is described in <a class="reference internal" href="Section_start.html#start-2"><span class="std std-ref">Section 2.2</span></a>
|
|
of the manual. If atom IDs are not used, they must be specified as 0
|
|
for all atoms, e.g. in a data or restart file.</p>
|
|
<p>The <em>map</em> keyword determines how atom ID lookup is done for molecular
|
|
atom styles. Lookups are performed by bond (angle, etc) routines in
|
|
LAMMPS to find the local atom index associated with a global atom ID.</p>
|
|
<p>When the <em>array</em> value is used, each processor stores a lookup table
|
|
of length N, where N is the largest atom ID in the system. This is a
|
|
fast, simple method for many simulations, but requires too much memory
|
|
for large simulations. The <em>hash</em> value uses a hash table to perform
|
|
the lookups. This can be slightly slower than the <em>array</em> method, but
|
|
its memory cost is proportional to the number of atoms owned by a
|
|
processor, i.e. N/P when N is the total number of atoms in the system
|
|
and P is the number of processors.</p>
|
|
<p>When this setting is not specified in your input script, LAMMPS
|
|
creates a map, if one is needed, as an array or hash. See the
|
|
discussion of default values below for how LAMMPS chooses which kind
|
|
of map to build. Note that atomic systems do not normally need to
|
|
create a map. However, even in this case some LAMMPS commands will
|
|
create a map to find atoms (and then destroy it), or require a
|
|
permanent map. An example of the former is the <a class="reference internal" href="velocity.html"><span class="doc">velocity loop all</span></a> command, which uses a map when looping over all
|
|
atoms and insuring the same velocity values are assigned to an atom
|
|
ID, no matter which processor owns it.</p>
|
|
<p>The <em>first</em> keyword allows a <a class="reference internal" href="group.html"><span class="doc">group</span></a> to be specified whose
|
|
atoms will be maintained as the first atoms in each processor’s list
|
|
of owned atoms. This in only useful when the specified group is a
|
|
small fraction of all the atoms, and there are other operations LAMMPS
|
|
is performing that will be sped-up significantly by being able to loop
|
|
over the smaller set of atoms. Otherwise the reordering required by
|
|
this option will be a net slow-down. The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify include</span></a> and <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify group</span></a>
|
|
commands are two examples of commands that require this setting to
|
|
work efficiently. Several <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, most notably time
|
|
integration fixes like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, also take advantage of
|
|
this setting if the group they operate on is the group specified by
|
|
this command. Note that specifying “all” as the group-ID effectively
|
|
turns off the <em>first</em> option.</p>
|
|
<p>It is OK to use the <em>first</em> keyword with a group that has not yet been
|
|
defined, e.g. to use the atom_modify first command at the beginning of
|
|
your input script. LAMMPS does not use the group until a simullation
|
|
is run.</p>
|
|
<p>The <em>sort</em> keyword turns on a spatial sorting or reordering of atoms
|
|
within each processor’s sub-domain every <em>Nfreq</em> timesteps. If
|
|
<em>Nfreq</em> is set to 0, then sorting is turned off. Sorting can improve
|
|
cache performance and thus speed-up a LAMMPS simulation, as discussed
|
|
in a paper by <a class="reference internal" href="#meloni"><span class="std std-ref">(Meloni)</span></a>. Its efficacy depends on the problem
|
|
size (atoms/processor), how quickly the system becomes disordered, and
|
|
various other factors. As a general rule, sorting is typically more
|
|
effective at speeding up simulations of liquids as opposed to solids.
|
|
In tests we have done, the speed-up can range from zero to 3-4x.</p>
|
|
<p>Reordering is peformed every <em>Nfreq</em> timesteps during a dynamics run
|
|
or iterations during a minimization. More precisely, reordering
|
|
occurs at the first reneighboring that occurs after the target
|
|
timestep. The reordering is performed locally by each processor,
|
|
using bins of the specified <em>binsize</em>. If <em>binsize</em> is set to 0.0,
|
|
then a binsize equal to half the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a> cutoff
|
|
distance (force cutoff plus skin distance) is used, which is a
|
|
reasonable value. After the atoms have been binned, they are
|
|
reordered so that atoms in the same bin are adjacent to each other in
|
|
the processor’s 1d list of atoms.</p>
|
|
<p>The goal of this procedure is for atoms to put atoms close to each
|
|
other in the processor’s one-dimensional list of atoms that are also
|
|
near to each other spatially. This can improve cache performance when
|
|
pairwise intereractions and neighbor lists are computed. Note that if
|
|
bins are too small, there will be few atoms/bin. Likewise if bins are
|
|
too large, there will be many atoms/bin. In both cases, the goal of
|
|
cache locality will be undermined.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Running a simulation with sorting on versus off should not
|
|
change the simulation results in a statistical sense. However, a
|
|
different ordering will induce round-off differences, which will lead
|
|
to diverging trajectories over time when comparing two simluations.
|
|
Various commands, particularly those which use random numbers
|
|
(e.g. <a class="reference internal" href="velocity.html"><span class="doc">velocity create</span></a>, and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>), may generate (statistically identical)
|
|
results which depend on the order in which atoms are processed. The
|
|
order of atoms in a <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> file will also typically change
|
|
if sorting is enabled.</p>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>The <em>first</em> and <em>sort</em> options cannot be used together. Since sorting
|
|
is on by default, it will be turned off if the <em>first</em> keyword is
|
|
used with a group-ID that is not “all”.</p>
|
|
<p><strong>Related commands:</strong> none</p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>By default, <em>id</em> is yes. By default, atomic systems (no bond topology
|
|
info) do not use a map. For molecular systems (with bond topology
|
|
info), a map is used. The default map style is array if no atom ID is
|
|
larger than 1 million, otherwise the default is hash. By default, a
|
|
“first” group is not defined. By default, sorting is enabled with a
|
|
frequency of 1000 and a binsize of 0.0, which means the neighbor
|
|
cutoff will be used to set the bin size.</p>
|
|
<hr class="docutils" />
|
|
<p id="meloni"><strong>(Meloni)</strong> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).</p>
|
|
</div>
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</div>
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<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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<a href="atom_style.html" class="btn btn-neutral float-right" title="atom_style command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="angle_style.html" class="btn btn-neutral" title="angle_style command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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