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HTML
975 lines
62 KiB
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<title>dump command — LAMMPS documentation</title>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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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_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_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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<p class="caption"><span class="caption-text">Index</span></p>
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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="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="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 current"><a class="current reference internal" href="#">dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#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-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-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-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-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="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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<div class="section" id="dump-command">
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<span id="index-0"></span><h1>dump command</h1>
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</div>
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<div class="section" id="dump-custom-vtk-command">
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<h1><a class="reference internal" href="dump_custom_vtk.html"><span class="doc">dump custom/vtk</span></a> command</h1>
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</div>
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<div class="section" id="dump-h5md-command">
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<h1><a class="reference internal" href="dump_h5md.html"><span class="doc">dump h5md</span></a> command</h1>
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</div>
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<div class="section" id="dump-image-command">
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<h1><a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command</h1>
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</div>
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<div class="section" id="dump-movie-command">
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<h1><a class="reference internal" href="dump_image.html"><span class="doc">dump movie</span></a> command</h1>
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</div>
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<div class="section" id="dump-molfile-command">
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<h1><a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a> command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">N</span> <span class="n">file</span> <span class="n">args</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul>
|
|
<li><p class="first">ID = user-assigned name for the dump</p>
|
|
</li>
|
|
<li><p class="first">group-ID = ID of the group of atoms to be dumped</p>
|
|
</li>
|
|
<li><p class="first">style = <em>atom</em> or <em>atom/gz</em> or <em>atom/mpiio</em> or <em>cfg</em> or <em>cfg/gz</em> or <em>cfg/mpiio</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/gz</em> or <em>xyz/mpiio</em> or <em>h5md</em> or <em>image</em> or <em>movie</em> or <em>molfile</em> or <em>local</em> or <em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em></p>
|
|
</li>
|
|
<li><p class="first">N = dump every this many timesteps</p>
|
|
</li>
|
|
<li><p class="first">file = name of file to write dump info to</p>
|
|
</li>
|
|
<li><p class="first">args = list of arguments for a particular style</p>
|
|
<pre class="literal-block">
|
|
<em>atom</em> args = none
|
|
<em>atom/gz</em> args = none
|
|
<em>atom/mpiio</em> args = none
|
|
<em>cfg</em> args = same as <em>custom</em> args, see below
|
|
<em>cfg/gz</em> args = same as <em>custom</em> args, see below
|
|
<em>cfg/mpiio</em> args = same as <em>custom</em> args, see below
|
|
<em>dcd</em> args = none
|
|
<em>xtc</em> args = none
|
|
<em>xyz</em> args = none
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>xyz/gz</em> args = none
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>xyz/mpiio</em> args = none
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>custom/vtk</em> args = similar to custom args below, discussed on <a class="reference internal" href="dump_custom_vtk.html"><span class="doc">dump custom/vtk</span></a> doc page
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>h5md</em> args = discussed on <a class="reference internal" href="dump_h5md.html"><span class="doc">dump h5md</span></a> doc page
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>image</em> args = discussed on <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>movie</em> args = discussed on <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>molfile</em> args = discussed on <a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a> doc page
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>local</em> args = list of local attributes
|
|
possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I]
|
|
index = enumeration of local values
|
|
c_ID = local vector calculated by a compute with ID
|
|
c_ID[I] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
|
|
f_ID = local vector calculated by a fix with ID
|
|
f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below)
|
|
</pre>
|
|
<pre class="literal-block">
|
|
<em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em> args = list of atom attributes
|
|
possible attributes = id, mol, proc, procp1, type, element, mass,
|
|
x, y, z, xs, ys, zs, xu, yu, zu,
|
|
xsu, ysu, zsu, ix, iy, iz,
|
|
vx, vy, vz, fx, fy, fz,
|
|
q, mux, muy, muz, mu,
|
|
radius, diameter, omegax, omegay, omegaz,
|
|
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
|
c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
|
</pre>
|
|
<pre class="literal-block">
|
|
id = atom ID
|
|
mol = molecule ID
|
|
proc = ID of processor that owns atom
|
|
procp1 = ID+1 of processor that owns atom
|
|
type = atom type
|
|
element = name of atom element, as defined by <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command
|
|
mass = atom mass
|
|
x,y,z = unscaled atom coordinates
|
|
xs,ys,zs = scaled atom coordinates
|
|
xu,yu,zu = unwrapped atom coordinates
|
|
xsu,ysu,zsu = scaled unwrapped atom coordinates
|
|
ix,iy,iz = box image that the atom is in
|
|
vx,vy,vz = atom velocities
|
|
fx,fy,fz = forces on atoms
|
|
q = atom charge
|
|
mux,muy,muz = orientation of dipole moment of atom
|
|
mu = magnitude of dipole moment of atom
|
|
radius,diameter = radius,diameter of spherical particle
|
|
omegax,omegay,omegaz = angular velocity of spherical particle
|
|
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
|
tqx,tqy,tqz = torque on finite-size particles
|
|
c_ID = per-atom vector calculated by a compute with ID
|
|
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
|
f_ID = per-atom vector calculated by a fix with ID
|
|
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
|
|
v_name = per-atom vector calculated by an atom-style variable with name
|
|
d_name = per-atom floating point vector with name, managed by fix property/atom
|
|
i_name = per-atom integer vector with name, managed by fix property/atom
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
dump myDump all atom 100 dump.atom
|
|
dump myDump all atom/mpiio 100 dump.atom.mpiio
|
|
dump myDump all atom/gz 100 dump.atom.gz
|
|
dump 2 subgroup atom 50 dump.run.bin
|
|
dump 2 subgroup atom 50 dump.run.mpiio.bin
|
|
dump 4a all custom 100 dump.myforce.* id type x y vx fx
|
|
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
|
|
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
|
|
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
|
|
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
|
|
dump 1 all xtc 1000 file.xtc
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Dump a snapshot of atom quantities to one or more files every N
|
|
timesteps in one of several styles. The <em>image</em> and <em>movie</em> styles are
|
|
the exception: the <em>image</em> style renders a JPG, PNG, or PPM image file
|
|
of the atom configuration every N timesteps while the <em>movie</em> style
|
|
combines and compresses them into a movie file; both are discussed in
|
|
detail on the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page. The timesteps on
|
|
which dump output is written can also be controlled by a variable.
|
|
See the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command.</p>
|
|
<p>Only information for atoms in the specified group is dumped. The
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify thresh and region</span></a> commands can also
|
|
alter what atoms are included. Not all styles support all these
|
|
options; see details below.</p>
|
|
<p>As described below, the filename determines the kind of output (text
|
|
or binary or gzipped, one big file or one per timestep, one big file
|
|
or multiple smaller files).</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Because periodic boundary conditions are enforced only on
|
|
timesteps when neighbor lists are rebuilt, the coordinates of an atom
|
|
written to a dump file may be slightly outside the simulation box.
|
|
Re-neighbor timesteps will not typically coincide with the timesteps
|
|
dump snapshots are written. See the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pbc</span></a> command if you with to force coordinates to be
|
|
strictly inside the simulation box.</p>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Unless the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a> option is
|
|
invoked, the lines of atom information written to dump files
|
|
(typically one line per atom) will be in an indeterminate order for
|
|
each snapshot. This is even true when running on a single processor,
|
|
if the <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify sort</span></a> option is on, which it is
|
|
by default. In this case atoms are re-ordered periodically during a
|
|
simulation, due to spatial sorting. It is also true when running in
|
|
parallel, because data for a single snapshot is collected from
|
|
multiple processors, each of which owns a subset of the atoms.</p>
|
|
</div>
|
|
<p>For the <em>atom</em>, <em>custom</em>, <em>cfg</em>, and <em>local</em> styles, sorting is off by
|
|
default. For the <em>dcd</em>, <em>xtc</em>, <em>xyz</em>, and <em>molfile</em> styles, sorting by
|
|
atom ID is on by default. See the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> doc
|
|
page for details.</p>
|
|
<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are identical
|
|
in command syntax to the corresponding styles without “gz”, however,
|
|
they generate compressed files using the zlib library. Thus the filename
|
|
suffix ”.gz” is mandatory. This is an alternative approach to writing
|
|
compressed files via a pipe, as done by the regular dump styles, which
|
|
may be required on clusters where the interface to the high-speed network
|
|
disallows using the fork() library call (which is needed for a pipe).
|
|
For the remainder of this doc page, you should thus consider the <em>atom</em>
|
|
and <em>atom/gz</em> styles (etc) to be inter-changeable, with the exception
|
|
of the required filename suffix.</p>
|
|
<p>As explained below, the <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and
|
|
<em>xyz/mpiio</em> styles are identical in command syntax and in the format
|
|
of the dump files they create, to the corresponding styles without
|
|
“mpiio”, except the single dump file they produce is written in
|
|
parallel via the MPI-IO library. For the remainder of this doc page,
|
|
you should thus consider the <em>atom</em> and <em>atom/mpiio</em> styles (etc) to
|
|
be inter-changeable. The one exception is how the filename is
|
|
specified for the MPI-IO styles, as explained below.</p>
|
|
<p>The precision of values output to text-based dump files can be
|
|
controlled by the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify format</span></a> command and
|
|
its options.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>style</em> keyword determines what atom quantities are written to the
|
|
file and in what format. Settings made via the
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command can also alter the format of
|
|
individual values and the file itself.</p>
|
|
<p>The <em>atom</em>, <em>local</em>, and <em>custom</em> styles create files in a simple text
|
|
format that is self-explanatory when viewing a dump file. Many of the
|
|
LAMMPS <a class="reference internal" href="Section_tools.html"><span class="doc">post-processing tools</span></a>, including
|
|
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a>, work with this
|
|
format, as does the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command.</p>
|
|
<p>For post-processing purposes the <em>atom</em>, <em>local</em>, and <em>custom</em> text
|
|
files are self-describing in the following sense.</p>
|
|
<p>The dimensions of the simulation box are included in each snapshot.
|
|
For an orthogonal simulation box this information is is formatted as:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xx</span> <span class="n">yy</span> <span class="n">zz</span>
|
|
<span class="n">xlo</span> <span class="n">xhi</span>
|
|
<span class="n">ylo</span> <span class="n">yhi</span>
|
|
<span class="n">zlo</span> <span class="n">zhi</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>where xlo,xhi are the maximum extents of the simulation box in the
|
|
x-dimension, and similarly for y and z. The “xx yy zz” represent 6
|
|
characters that encode the style of boundary for each of the 6
|
|
simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
|
|
the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
|
|
or m = shrink wrapped with a minimum value. See the
|
|
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command for details.</p>
|
|
<p>For triclinic simulation boxes (non-orthogonal), an orthogonal
|
|
bounding box which encloses the triclinic simulation box is output,
|
|
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
|
|
formatted as follows:</p>
|
|
<pre class="literal-block">
|
|
ITEM: BOX BOUNDS xy xz yz xx yy zz
|
|
xlo_bound xhi_bound xy
|
|
ylo_bound yhi_bound xz
|
|
zlo_bound zhi_bound yz
|
|
</pre>
|
|
<p>The presence of the text “xy xz yz” in the ITEM line indicates that
|
|
the 3 tilt factors will be included on each of the 3 following lines.
|
|
This bounding box is convenient for many visualization programs. The
|
|
meaning of the 6 character flags for “xx yy zz” is the same as above.</p>
|
|
<p>Note that the first two numbers on each line are now xlo_bound instead
|
|
of xlo, etc, since they repesent a bounding box. See <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">this section</span></a> of the doc pages for a geometric
|
|
description of triclinic boxes, as defined by LAMMPS, simple formulas
|
|
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
|
|
calculated from the triclinic parameters, and how to transform those
|
|
parameters to and from other commonly used triclinic representations.</p>
|
|
<p>The “ITEM: ATOMS” line in each snapshot lists column descriptors for
|
|
the per-atom lines that follow. For example, the descriptors would be
|
|
“id type xs ys zs” for the default <em>atom</em> style, and would be the atom
|
|
attributes you specify in the dump command for the <em>custom</em> style.</p>
|
|
<p>For style <em>atom</em>, atom coordinates are written to the file, along with
|
|
the atom ID and atom type. By default, atom coords are written in a
|
|
scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
|
|
is at a location 1/4 of the distance from xlo to xhi of the box
|
|
boundaries. The format can be changed to unscaled coords via the
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> settings. Image flags can also be
|
|
added for each atom via dump_modify.</p>
|
|
<p>Style <em>custom</em> allows you to specify a list of atom attributes to be
|
|
written to the dump file for each atom. Possible attributes are
|
|
listed above and will appear in the order specified. You cannot
|
|
specify a quantity that is not defined for a particular simulation -
|
|
such as <em>q</em> for atom style <em>bond</em>, since that atom style doesn’t
|
|
assign charges. Dumps occur at the very end of a timestep, so atom
|
|
attributes will include effects due to fixes that are applied during
|
|
the timestep. An explanation of the possible dump custom attributes
|
|
is given below.</p>
|
|
<p>For style <em>local</em>, local output generated by <a class="reference internal" href="compute.html"><span class="doc">computes</span></a>
|
|
and <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> is used to generate lines of output that is
|
|
written to the dump file. This local data is typically calculated by
|
|
each processor based on the atoms it owns, but there may be zero or
|
|
more entities per atom, e.g. a list of bond distances. An explanation
|
|
of the possible dump local attributes is given below. Note that by
|
|
using input from the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command with dump local,
|
|
it is possible to generate information on bonds, angles, etc that can
|
|
be cut and pasted directly into a data file read by the
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command.</p>
|
|
<p>Style <em>cfg</em> has the same command syntax as style <em>custom</em> and writes
|
|
extended CFG format files, as used by the
|
|
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualization
|
|
package. Since the extended CFG format uses a single snapshot of the
|
|
system per file, a wildcard “*” must be included in the filename, as
|
|
discussed below. The list of atom attributes for style <em>cfg</em> must
|
|
begin with either “mass type xs ys zs” or “mass type xsu ysu zsu”
|
|
since these quantities are needed to write the CFG files in the
|
|
appropriate format (though the “mass” and “type” fields do not appear
|
|
explicitly in the file). Any remaining attributes will be stored as
|
|
“auxiliary properties” in the CFG files. Note that you will typically
|
|
want to use the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> command with
|
|
CFG-formatted files, to associate element names with atom types, so
|
|
that AtomEye can render atoms appropriately. When unwrapped
|
|
coordinates <em>xsu</em>, <em>ysu</em>, and <em>zsu</em> are requested, the nominal AtomEye
|
|
periodic cell dimensions are expanded by a large factor UNWRAPEXPAND =
|
|
10.0, which ensures atoms that are displayed correctly for up to
|
|
UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond
|
|
this, AtomEye will rewrap the unwrapped coordinates. The expansion
|
|
causes the atoms to be drawn farther away from the viewer, but it is
|
|
easy to zoom the atoms closer, and the interatomic distances are
|
|
unaffected.</p>
|
|
<p>The <em>dcd</em> style writes DCD files, a standard atomic trajectory format
|
|
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
|
|
files are binary and thus may not be portable to different machines.
|
|
The number of atoms per snapshot cannot change with the <em>dcd</em> style.
|
|
The <em>unwrap</em> option of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command
|
|
allows DCD coordinates to be written “unwrapped” by the image flags
|
|
for each atom. Unwrapped means that if the atom has passed through
|
|
a periodic boundary one or more times, the value is printed for what
|
|
the coordinate would be if it had not been wrapped back into the
|
|
periodic box. Note that these coordinates may thus be far outside
|
|
the box size stored with the snapshot.</p>
|
|
<p>The <em>xtc</em> style writes XTC files, a compressed trajectory format used
|
|
by the GROMACS molecular dynamics package, and described
|
|
<a class="reference external" href="http://manual.gromacs.org/current/online/xtc.html">here</a>.
|
|
The precision used in XTC files can be adjusted via the
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command. The default value of 1000
|
|
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
|
|
files are portable binary files written in the NFS XDR data format,
|
|
so that any machine which supports XDR should be able to read them.
|
|
The number of atoms per snapshot cannot change with the <em>xtc</em> style.
|
|
The <em>unwrap</em> option of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command allows
|
|
XTC coordinates to be written “unwrapped” by the image flags for each
|
|
atom. Unwrapped means that if the atom has passed thru a periodic
|
|
boundary one or more times, the value is printed for what the
|
|
coordinate would be if it had not been wrapped back into the periodic
|
|
box. Note that these coordinates may thus be far outside the box size
|
|
stored with the snapshot.</p>
|
|
<p>The <em>xyz</em> style writes XYZ files, which is a simple text-based
|
|
coordinate format that many codes can read. Specifically it has
|
|
a line with the number of atoms, then a comment line that is
|
|
usually ignored followed by one line per atom with the atom type
|
|
and the x-, y-, and z-coordinate of that atom. You can use the
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> option to change the output
|
|
from using the (numerical) atom type to an element name (or some
|
|
other label). This will help many visualization programs to guess
|
|
bonds and colors.</p>
|
|
<p>Note that <em>atom</em>, <em>custom</em>, <em>dcd</em>, <em>xtc</em>, and <em>xyz</em> style dump files
|
|
can be read directly by <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a>, a
|
|
popular molecular viewing program. See <a class="reference internal" href="Section_tools.html#vmd"><span class="std std-ref">Section tools</span></a> of the manual and the
|
|
tools/lmp2vmd/README.txt file for more information about support in
|
|
VMD for reading and visualizing LAMMPS dump files.</p>
|
|
<hr class="docutils" />
|
|
<p>Dumps are performed on timesteps that are a multiple of N (including
|
|
timestep 0) and on the last timestep of a minimization if the
|
|
minimization converges. Note that this means a dump will not be
|
|
performed on the initial timestep after the dump command is invoked,
|
|
if the current timestep is not a multiple of N. This behavior can be
|
|
changed via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command, which
|
|
can also be useful if the dump command is invoked after a minimization
|
|
ended on an arbitrary timestep. N can be changed between runs by
|
|
using the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command (not allowed
|
|
for <em>dcd</em> style). The <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command
|
|
also allows a variable to be used to determine the sequence of
|
|
timesteps on which dump files are written. In this mode a dump on the
|
|
first timestep of a run will also not be written unless the
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command is used.</p>
|
|
<p>The specified filename determines how the dump file(s) is written.
|
|
The default is to write one large text file, which is opened when the
|
|
dump command is invoked and closed when an <a class="reference internal" href="undump.html"><span class="doc">undump</span></a>
|
|
command is used or when LAMMPS exits. For the <em>dcd</em> and <em>xtc</em> styles,
|
|
this is a single large binary file.</p>
|
|
<p>Dump filenames can contain two wildcard characters. If a “*”
|
|
character appears in the filename, then one file per snapshot is
|
|
written and the “*” character is replaced with the timestep value.
|
|
For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
|
|
tmp.dump.20000, etc. This option is not available for the <em>dcd</em> and
|
|
<em>xtc</em> styles. Note that the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pad</span></a>
|
|
command can be used to insure all timestep numbers are the same length
|
|
(e.g. 00010), which can make it easier to read a series of dump files
|
|
in order with some post-processing tools.</p>
|
|
<p>If a “%” character appears in the filename, then each of P processors
|
|
writes a portion of the dump file, and the “%” character is replaced
|
|
with the processor ID from 0 to P-1. For example, tmp.dump.% becomes
|
|
tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller
|
|
files and can be a fast mode of output on parallel machines that
|
|
support parallel I/O for output. This option is not available for the
|
|
<em>dcd</em>, <em>xtc</em>, and <em>xyz</em> styles.</p>
|
|
<p>By default, P = the number of processors meaning one file per
|
|
processor, but P can be set to a smaller value via the <em>nfile</em> or
|
|
<em>fileper</em> keywords of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.
|
|
These options can be the most efficient way of writing out dump files
|
|
when running on large numbers of processors.</p>
|
|
<p>Note that using the “*” and “%” characters together can produce a
|
|
large number of small dump files!</p>
|
|
<p>For the <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and <em>xyz/mpiio</em>
|
|
styles, a single dump file is written in parallel via the MPI-IO
|
|
library, which is part of the MPI standard for versions 2.0 and above.
|
|
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
|
|
package installed, e.g.</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">mpiio</span> <span class="c1"># installs the MPIIO package</span>
|
|
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="c1"># build LAMMPS for your platform</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>Second, use a dump filename which contains ”.mpiio”. Note that it
|
|
does not have to end in ”.mpiio”, just contain those characters.
|
|
Unlike MPI-IO restart files, which must be both written and read using
|
|
MPI-IO, the dump files produced by these MPI-IO styles are identical
|
|
in format to the files produced by their non-MPI-IO style
|
|
counterparts. This means you can write a dump file using MPI-IO and
|
|
use the <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a> command or perform other
|
|
post-processing, just as if the dump file was not written using
|
|
MPI-IO.</p>
|
|
<p>Note that MPI-IO dump files are one large file which all processors
|
|
write to. You thus cannot use the “%” wildcard character described
|
|
above in the filename since that specifies generation of multiple
|
|
files. You can use the ”.bin” suffix described below in an MPI-IO
|
|
dump file; again this file will be written in parallel and have the
|
|
same binary format as if it were written without MPI-IO.</p>
|
|
<p>If the filename ends with ”.bin”, the dump file (or files, if “*” or
|
|
“%” is also used) is written in binary format. A binary dump file
|
|
will be about the same size as a text version, but will typically
|
|
write out much faster. Of course, when post-processing, you will need
|
|
to convert it back to text format (see the <a class="reference internal" href="Section_tools.html#binary"><span class="std std-ref">binary2txt tool</span></a>) or write your own code to read the
|
|
binary file. The format of the binary file can be understood by
|
|
looking at the tools/binary2txt.cpp file. This option is only
|
|
available for the <em>atom</em> and <em>custom</em> styles.</p>
|
|
<p>If the filename ends with ”.gz”, the dump file (or files, if “*” or “%”
|
|
is also used) is written in gzipped format. A gzipped dump file will
|
|
be about 3x smaller than the text version, but will also take longer
|
|
to write. This option is not available for the <em>dcd</em> and <em>xtc</em>
|
|
styles.</p>
|
|
<hr class="docutils" />
|
|
<p>Note that in the discussion which follows, for styles which can
|
|
reference values from a compute or fix, like the <em>custom</em>, <em>cfg</em>, or
|
|
<em>local</em> styles, the bracketed index I can be specified using a
|
|
wildcard asterisk with the index to effectively specify multiple
|
|
values. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
|
|
size of the vector (for <em>mode</em> = scalar) or the number of columns in
|
|
the array (for <em>mode</em> = vector), then an asterisk with no numeric
|
|
values means all indices from 1 to N. A leading asterisk means all
|
|
indices from 1 to n (inclusive). A trailing asterisk means all
|
|
indices from n to N (inclusive). A middle asterisk means all indices
|
|
from m to n (inclusive).</p>
|
|
<p>Using a wildcard is the same as if the individual columns of the array
|
|
had been listed one by one. E.g. these 2 dump commands are
|
|
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
|
|
command creates a per-atom array with 6 columns:</p>
|
|
<pre class="literal-block">
|
|
compute myPress all stress/atom NULL
|
|
dump 2 all custom 100 tmp.dump id myPress[*]
|
|
dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
|
|
myPress[4] myPress[5] myPress[6]
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p>This section explains the local attributes that can be specified as
|
|
part of the <em>local</em> style.</p>
|
|
<p>The <em>index</em> attribute can be used to generate an index number from 1
|
|
to N for each line written into the dump file, where N is the total
|
|
number of local datums from all processors, or lines of output that
|
|
will appear in the snapshot. Note that because data from different
|
|
processors depend on what atoms they currently own, and atoms migrate
|
|
between processor, there is no guarantee that the same index will be
|
|
used for the same info (e.g. a particular bond) in successive
|
|
snapshots.</p>
|
|
<p>The <em>c_ID</em> and <em>c_ID[I]</em> attributes allow local vectors or arrays
|
|
calculated by a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to be output. The ID in the
|
|
attribute should be replaced by the actual ID of the compute that has
|
|
been defined previously in the input script. See the
|
|
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command for details. There are computes for
|
|
calculating local information such as indices, types, and energies for
|
|
bonds and angles.</p>
|
|
<p>Note that computes which calculate global or per-atom quantities, as
|
|
opposed to local quantities, cannot be output in a dump local command.
|
|
Instead, global quantities can be output by the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command, and per-atom quantities can be
|
|
output by the dump custom command.</p>
|
|
<p>If <em>c_ID</em> is used as a attribute, then the local vector calculated by
|
|
the compute is printed. If <em>c_ID[I]</em> is used, then I must be in the
|
|
range from 1-M, which will print the Ith column of the local array
|
|
with M columns calculated by the compute. See the discussion above
|
|
for how I can be specified with a wildcard asterisk to effectively
|
|
specify multiple values.</p>
|
|
<p>The <em>f_ID</em> and <em>f_ID[I]</em> attributes allow local vectors or arrays
|
|
calculated by a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> to be output. The ID in the attribute
|
|
should be replaced by the actual ID of the fix that has been defined
|
|
previously in the input script.</p>
|
|
<p>If <em>f_ID</em> is used as a attribute, then the local vector calculated by
|
|
the fix is printed. If <em>f_ID[I]</em> is used, then I must be in the
|
|
range from 1-M, which will print the Ith column of the local with M
|
|
columns calculated by the fix. See the discussion above for how I can
|
|
be specified with a wildcard asterisk to effectively specify multiple
|
|
values.</p>
|
|
<p>Here is an example of how to dump bond info for a system, including
|
|
the distance and energy of each bond:</p>
|
|
<pre class="literal-block">
|
|
compute 1 all property/local batom1 batom2 btype
|
|
compute 2 all bond/local dist eng
|
|
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p>This section explains the atom attributes that can be specified as
|
|
part of the <em>custom</em> and <em>cfg</em> styles.</p>
|
|
<p>The <em>id</em>, <em>mol</em>, <em>proc</em>, <em>procp1</em>, <em>type</em>, <em>element</em>, <em>mass</em>, <em>vx</em>,
|
|
<em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</em>, <em>q</em> attributes are self-explanatory.</p>
|
|
<p><em>Id</em> is the atom ID. <em>Mol</em> is the molecule ID, included in the data
|
|
file for molecular systems. <em>Proc</em> is the ID of the processor (0 to
|
|
Nprocs-1) that currently owns the atom. <em>Procp1</em> is the proc ID+1,
|
|
which can be convenient in place of a <em>type</em> attribute (1 to Ntypes)
|
|
for coloring atoms in a visualization program. <em>Type</em> is the atom
|
|
type (1 to Ntypes). <em>Element</em> is typically the chemical name of an
|
|
element, which you must assign to each type via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> command. More generally, it can be any
|
|
string you wish to associated with an atom type. <em>Mass</em> is the atom
|
|
mass. <em>Vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</em>, and <em>q</em> are components of
|
|
atom velocity and force and atomic charge.</p>
|
|
<p>There are several options for outputting atom coordinates. The <em>x</em>,
|
|
<em>y</em>, <em>z</em> attributes write atom coordinates “unscaled”, in the
|
|
appropriate distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> (Angstroms, sigma, etc). Use
|
|
<em>xs</em>, <em>ys</em>, <em>zs</em> if you want the coordinates “scaled” to the box size,
|
|
so that each value is 0.0 to 1.0. If the simulation box is triclinic
|
|
(tilted), then all atom coords will still be between 0.0 and 1.0.
|
|
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
|
|
the non-orthogonal vectors of the simulation box edges, as discussed
|
|
in <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">Section howto 6.12</span></a>.</p>
|
|
<p>Use <em>xu</em>, <em>yu</em>, <em>zu</em> if you want the coordinates “unwrapped” by the
|
|
image flags for each atom. Unwrapped means that if the atom has
|
|
passed thru a periodic boundary one or more times, the value is
|
|
printed for what the coordinate would be if it had not been wrapped
|
|
back into the periodic box. Note that using <em>xu</em>, <em>yu</em>, <em>zu</em> means
|
|
that the coordinate values may be far outside the box bounds printed
|
|
with the snapshot. Using <em>xsu</em>, <em>ysu</em>, <em>zsu</em> is similar to using
|
|
<em>xu</em>, <em>yu</em>, <em>zu</em>, except that the unwrapped coordinates are scaled by
|
|
the box size. Atoms that have passed through a periodic boundary will
|
|
have the corresponding cooordinate increased or decreased by 1.0.</p>
|
|
<p>The image flags can be printed directly using the <em>ix</em>, <em>iy</em>, <em>iz</em>
|
|
attributes. For periodic dimensions, they specify which image of the
|
|
simulation box the atom is considered to be in. An image of 0 means
|
|
it is inside the box as defined. A value of 2 means add 2 box lengths
|
|
to get the true value. A value of -1 means subtract 1 box length to
|
|
get the true value. LAMMPS updates these flags as atoms cross
|
|
periodic boundaries during the simulation.</p>
|
|
<p>The <em>mux</em>, <em>muy</em>, <em>muz</em> attributes are specific to dipolar systems
|
|
defined with an atom style of <em>dipole</em>. They give the orientation of
|
|
the atom’s point dipole moment. The <em>mu</em> attribute gives the
|
|
magnitude of the atom’s dipole moment.</p>
|
|
<p>The <em>radius</em> and <em>diameter</em> attributes are specific to spherical
|
|
particles that have a finite size, such as those defined with an atom
|
|
style of <em>sphere</em>.</p>
|
|
<p>The <em>omegax</em>, <em>omegay</em>, and <em>omegaz</em> attributes are specific to
|
|
finite-size spherical particles that have an angular velocity. Only
|
|
certain atom styles, such as <em>sphere</em> define this quantity.</p>
|
|
<p>The <em>angmomx</em>, <em>angmomy</em>, and <em>angmomz</em> attributes are specific to
|
|
finite-size aspherical particles that have an angular momentum. Only
|
|
the <em>ellipsoid</em> atom style defines this quantity.</p>
|
|
<p>The <em>tqx</em>, <em>tqy</em>, <em>tqz</em> attributes are for finite-size particles that
|
|
can sustain a rotational torque due to interactions with other
|
|
particles.</p>
|
|
<p>The <em>c_ID</em> and <em>c_ID[I]</em> attributes allow per-atom vectors or arrays
|
|
calculated by a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to be output. The ID in the
|
|
attribute should be replaced by the actual ID of the compute that has
|
|
been defined previously in the input script. See the
|
|
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command for details. There are computes for
|
|
calculating the per-atom energy, stress, centro-symmetry parameter,
|
|
and coordination number of individual atoms.</p>
|
|
<p>Note that computes which calculate global or local quantities, as
|
|
opposed to per-atom quantities, cannot be output in a dump custom
|
|
command. Instead, global quantities can be output by the
|
|
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command, and local quantities
|
|
can be output by the dump local command.</p>
|
|
<p>If <em>c_ID</em> is used as a attribute, then the per-atom vector calculated
|
|
by the compute is printed. If <em>c_ID[I]</em> is used, then I must be in
|
|
the range from 1-M, which will print the Ith column of the per-atom
|
|
array with M columns calculated by the compute. See the discussion
|
|
above for how I can be specified with a wildcard asterisk to
|
|
effectively specify multiple values.</p>
|
|
<p>The <em>f_ID</em> and <em>f_ID[I]</em> attributes allow vector or array per-atom
|
|
quantities calculated by a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> to be output. The ID in the
|
|
attribute should be replaced by the actual ID of the fix that has been
|
|
defined previously in the input script. The <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command is one that calculates per-atom
|
|
quantities. Since it can time-average per-atom quantities produced by
|
|
any <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or atom-style
|
|
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, this allows those time-averaged results to
|
|
be written to a dump file.</p>
|
|
<p>If <em>f_ID</em> is used as a attribute, then the per-atom vector calculated
|
|
by the fix is printed. If <em>f_ID[I]</em> is used, then I must be in the
|
|
range from 1-M, which will print the Ith column of the per-atom array
|
|
with M columns calculated by the fix. See the discussion above for
|
|
how I can be specified with a wildcard asterisk to effectively specify
|
|
multiple values.</p>
|
|
<p>The <em>v_name</em> attribute allows per-atom vectors calculated by a
|
|
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a> to be output. The name in the attribute
|
|
should be replaced by the actual name of the variable that has been
|
|
defined previously in the input script. Only an atom-style variable
|
|
can be referenced, since it is the only style that generates per-atom
|
|
values. Variables of style <em>atom</em> can reference individual atom
|
|
attributes, per-atom atom attributes, thermodynamic keywords, or
|
|
invoke other computes, fixes, or variables when they are evaluated, so
|
|
this is a very general means of creating quantities to output to a
|
|
dump file.</p>
|
|
<p>The <em>d_name</em> and <em>i_name</em> attributes allow to output custom per atom
|
|
floating point or integer properties that are managed by
|
|
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a>.</p>
|
|
<p>See <a class="reference internal" href="Section_modify.html"><span class="doc">Section 10</span></a> of the manual for information
|
|
on how to add new compute and fix styles to LAMMPS to calculate
|
|
per-atom quantities which could then be output into dump files.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>To write gzipped dump files, you must either compile LAMMPS with the
|
|
-DLAMMPS_GZIP option or use the styles from the COMPRESS package
|
|
- see the <a class="reference internal" href="Section_start.html#start-2"><span class="std std-ref">Making LAMMPS</span></a> section of
|
|
the documentation.</p>
|
|
<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are part
|
|
of the COMPRESS package. They are only enabled if LAMMPS was built
|
|
with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>The <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and <em>xyz/mpiio</em> styles
|
|
are part of the MPIIO package. They are only enabled if LAMMPS was
|
|
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>The <em>xtc</em> style is part of the MISC package. It is only enabled if
|
|
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info. This is
|
|
because some machines may not support the low-level XDR data format
|
|
that XTC files are written with, which will result in a compile-time
|
|
error when a low-level include file is not found. Putting this style
|
|
in a package makes it easy to exclude from a LAMMPS build for those
|
|
machines. However, the MISC package also includes two compatibility
|
|
header files and associated functions, which should be a suitable
|
|
substitute on machines that do not have the appropriate native header
|
|
files. This option can be invoked at build time by adding
|
|
-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
|
|
Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
|
|
been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
|
|
machines and should also work on IBM BG/P, and Windows XP/Vista/7
|
|
machines.</p>
|
|
</div>
|
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="dump_h5md.html"><span class="doc">dump h5md</span></a>, <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>,
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