1839 lines
112 KiB
HTML
1839 lines
112 KiB
HTML
<!DOCTYPE html>
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<title>read_data command — LAMMPS documentation</title>
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1 current"><a class="reference internal" href="commands_list.html">Commands</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_write.html">angle_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_write.html">dihedral_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dynamical_matrix.html">dynamical_matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fitpod_command.html">fitpod command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="geturl.html">geturl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="hyper.html">hyper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kim_commands.html">kim command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="labelmap.html">labelmap command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="mdi.html">mdi command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_spin.html">min_style spin command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-cg-command">min_style spin/cg command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-lbfgs-command">min_style spin/lbfgs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style cg command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-hftn-command">min_style hftn command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-sd-command">min_style sd command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-quickmin-command">min_style quickmin command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-fire-command">min_style fire command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-command"><span class="xref std std-doc">min_style spin</span> command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-cg-command"><span class="xref std std-doc">min_style spin/cg</span> command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-lbfgs-command"><span class="xref std std-doc">min_style spin/lbfgs</span> command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="neb_spin.html">neb/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
|
||
<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>
|
||
<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="plugin.html">plugin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
|
||
<li class="toctree-l2 current"><a class="current reference internal" href="#">read_data 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="#reading-multiple-data-files">Reading multiple data files</a></li>
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||
<li class="toctree-l3"><a class="reference internal" href="#format-of-a-data-file">Format of a data file</a></li>
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||
<li class="toctree-l3"><a class="reference internal" href="#format-of-the-header-of-a-data-file">Format of the header of a data file</a></li>
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||
<li class="toctree-l3"><a class="reference internal" href="#header-specification-of-the-simulation-box-size-and-shape">Header specification of the simulation box size and shape</a></li>
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||
<li class="toctree-l3"><a class="reference internal" href="#meaning-of-other-header-keywords">Meaning of other header keywords</a></li>
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||
<li class="toctree-l3"><a class="reference internal" href="#format-of-the-body-of-a-data-file">Format of the body of a data file</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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||
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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||
</ul>
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||
</li>
|
||
<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="reset_atoms.html">reset_atoms command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="temper_grem.html">temper/grem command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="temper_npt.html">temper/npt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="third_order.html">third_order command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
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||
</ul>
|
||
|
||
</div>
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</div>
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</nav>
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<li class="breadcrumb-item active">read_data command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="read-data-command">
|
||
<span id="index-0"></span><h1>read_data command<a class="headerlink" href="#read-data-command" title="Link to this heading"></a></h1>
|
||
<section id="syntax">
|
||
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">read_data</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">args</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>file = name of data file to read in</p></li>
|
||
<li><p>zero or more keyword/arg pairs may be appended</p></li>
|
||
<li><p>keyword = <em>add</em> or <em>offset</em> or <em>shift</em> or <em>extra/atom/types</em> or <em>extra/bond/types</em> or <em>extra/angle/types</em> or <em>extra/dihedral/types</em> or <em>extra/improper/types</em> or <em>extra/bond/per/atom</em> or <em>extra/angle/per/atom</em> or <em>extra/dihedral/per/atom</em> or <em>extra/improper/per/atom</em> or <em>extra/special/per/atom</em> or <em>group</em> or <em>nocoeff</em> or <em>fix</em></p>
|
||
<pre class="literal-block"><em>add</em> arg = <em>append</em> or <em>IDoffset</em> or <em>IDoffset MOLoffset</em> or <em>merge</em>
|
||
append = add new atoms with atom IDs appended to current IDs
|
||
IDoffset = add new atoms with atom IDs having IDoffset added
|
||
MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled)
|
||
merge = add new atoms with their atom IDs (and molecule IDs) unchanged
|
||
<em>offset</em> args = toff boff aoff doff ioff
|
||
toff = offset to add to atom types
|
||
boff = offset to add to bond types
|
||
aoff = offset to add to angle types
|
||
doff = offset to add to dihedral types
|
||
ioff = offset to add to improper types
|
||
<em>shift</em> args = Sx Sy Sz
|
||
Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
|
||
<em>extra/atom/types</em> arg = # of extra atom types
|
||
<em>extra/bond/types</em> arg = # of extra bond types
|
||
<em>extra/angle/types</em> arg = # of extra angle types
|
||
<em>extra/dihedral/types</em> arg = # of extra dihedral types
|
||
<em>extra/improper/types</em> arg = # of extra improper types
|
||
<em>extra/bond/per/atom</em> arg = leave space for this many new bonds per atom
|
||
<em>extra/angle/per/atom</em> arg = leave space for this many new angles per atom
|
||
<em>extra/dihedral/per/atom</em> arg = leave space for this many new dihedrals per atom
|
||
<em>extra/improper/per/atom</em> arg = leave space for this many new impropers per atom
|
||
<em>extra/special/per/atom</em> arg = leave space for extra 1-2,1-3,1-4 interactions per atom
|
||
<em>group</em> args = groupID
|
||
groupID = add atoms in data file to this group
|
||
<em>nocoeff</em> = ignore force field parameters
|
||
<em>fix</em> args = fix-ID header-string section-string
|
||
fix-ID = ID of fix to process header lines and sections of data file
|
||
header-string = header lines containing this string will be passed to fix
|
||
section-string = section names with this string will be passed to fix</pre>
|
||
</li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">read_data</span><span class="w"> </span><span class="n">data.lj</span>
|
||
<span class="k">read_data</span><span class="w"> </span><span class="n">..</span><span class="o">/</span><span class="n">run7</span><span class="o">/</span><span class="n">data.polymer.gz</span>
|
||
<span class="k">read_data</span><span class="w"> </span><span class="n">data.protein</span><span class="w"> </span><span class="k">fix </span><span class="nv nv-Identifier">mycmap</span><span class="w"> </span><span class="nv nv-Identifier">crossterm</span><span class="w"> </span><span class="n">CMAP</span>
|
||
<span class="k">read_data</span><span class="w"> </span><span class="n">data.water</span><span class="w"> </span><span class="n">add</span><span class="w"> </span><span class="n">append</span><span class="w"> </span><span class="n">offset</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">shift</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">50.0</span>
|
||
<span class="k">read_data</span><span class="w"> </span><span class="n">data.water</span><span class="w"> </span><span class="n">add</span><span class="w"> </span><span class="n">merge</span><span class="w"> </span><span class="k">group </span><span class="nv nv-Identifier">solvent</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Read in a data file containing information LAMMPS needs to run a
|
||
simulation. The file can be ASCII text or a gzipped text file
|
||
(detected by a .gz suffix).</p>
|
||
<p>This is one of 3 ways to specify the simulation box: see the
|
||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> and <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
||
and commands for alternative methods. It is also one of 3 ways to
|
||
specify initial atom coordinates: see the <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> and <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> and commands
|
||
for alternative methods. Also see the explanation of the
|
||
<a class="reference internal" href="Run_options.html"><span class="doc">-restart command-line switch</span></a> which can convert a
|
||
restart file to a data file.</p>
|
||
<p>This command can be used multiple times to add new atoms and their
|
||
properties to an existing system by using the <em>add</em>, <em>offset</em>, and
|
||
<em>shift</em> keywords. However, it is important to understand that several
|
||
system parameters, like the number of types of different kinds and per
|
||
atom settings are <strong>locked in</strong> after the first <em>read_data</em> command,
|
||
which means that no type ID (including its offset) may have a larger
|
||
value when processing additional data files than what is set by the
|
||
first data file and the corresponding <em>read_data</em> command options. See
|
||
more details on this situation below, which includes the use case for
|
||
the <em>extra</em> keywords.</p>
|
||
<p>The <em>group</em> keyword adds all the atoms in the data file to the
|
||
specified group-ID. The group will be created if it does not already
|
||
exist. This is useful if you are reading multiple data files and wish
|
||
to put sets of atoms into different groups so they can be operated on
|
||
later. E.g. a group of added atoms can be moved to new positions via
|
||
the <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a> command. Note that atoms
|
||
read from the data file are also always added to the “all” group. The
|
||
<a class="reference internal" href="group.html"><span class="doc">group</span></a> command discusses atom groups, as used in LAMMPS.</p>
|
||
<p>The <em>nocoeff</em> keyword tells read_data to ignore force field parameters.
|
||
The various Coeff sections are still read and have to have the correct
|
||
number of lines, but they are not applied. This also allows to read a
|
||
data file without having any pair, bond, angle, dihedral or improper
|
||
styles defined, or to read a data file for a different force field.</p>
|
||
<p>The use of the <em>fix</em> keyword is discussed below.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="reading-multiple-data-files">
|
||
<h2>Reading multiple data files<a class="headerlink" href="#reading-multiple-data-files" title="Link to this heading"></a></h2>
|
||
<p>The read_data command can be used multiple times with the same or
|
||
different data files to build up a complex system from components
|
||
contained in individual data files. For example one data file could
|
||
contain fluid in a confined domain; a second could contain wall atoms,
|
||
and the second file could be read a third time to create a wall on the
|
||
other side of the fluid. The third set of atoms could be rotated to
|
||
an opposing direction using the <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a>
|
||
command, after the third read_data command is used.</p>
|
||
<p>The <em>add</em>, <em>offset</em>, <em>shift</em>, <em>extra</em>, and <em>group</em> keywords are
|
||
useful in this context.</p>
|
||
<p>If a simulation box does not yet exist, the <em>add</em> keyword cannot be
|
||
used; the read_data command is being used for the first time. If a
|
||
simulation box does exist, due to using the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command, or a previous read_data command, then the <em>add</em>
|
||
keyword must be used.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If the first read_data command defined an orthogonal or restricted
|
||
triclinic or general triclinic simulation box (see the sub-section
|
||
below on header keywords), then subsequent data files must define
|
||
the same kind of simulation box. For orthogonal boxes, the new box
|
||
can be a different size; see the next Note. For a restricted
|
||
triclinic box, the 3 new tilt factors (“xy xz yz” keyword) must
|
||
have the same values as in the original data file. For a general
|
||
triclinic box, the new avec, bvec, cvec, and “abc origin” keywords
|
||
must have the same values in the original data file. files. Also
|
||
the <em>shift</em> keyword cannot be used in subsequent read_data commands
|
||
for a general triclinic box.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>For orthogonal boxes, the simulation box size in the new data file
|
||
will be merged with the existing simulation box to create a large
|
||
enough box in each dimension to contain both the existing and new
|
||
atoms. Each box dimension never shrinks due to this merge
|
||
operation, it only stays the same or grows. Care must be used if
|
||
you are growing the existing simulation box in a periodic
|
||
dimension. If there are existing atoms with bonds that straddle
|
||
that periodic boundary, then the atoms may become far apart if the
|
||
box size grows. This will separate the atoms in the bond, which
|
||
can lead to “lost” bond atoms or bad dynamics.</p>
|
||
</div>
|
||
<p>The three choices for the <em>add</em> argument affect how the atom IDs and
|
||
molecule IDs of atoms in the data file are treated.</p>
|
||
<p>If <em>append</em> is specified, atoms in the data file are added to the
|
||
current system, with their atom IDs reset so that an atom-ID = M in
|
||
the data file becomes atom-ID = N+M, where N is the largest atom ID in
|
||
the current system. This rule is applied to all occurrences of atom
|
||
IDs in the data file, e.g. in the Velocity or Bonds section. This is
|
||
also done for molecule IDs, if the atom style does support molecule
|
||
IDs or they are enabled via fix property/atom.</p>
|
||
<p>If <em>IDoffset</em> is specified, then <em>IDoffset</em> is a numeric value is
|
||
given, e.g. 1000, so that an atom-ID = M in the data file becomes
|
||
atom-ID = 1000+M. For systems with enabled molecule IDs, another
|
||
numerical argument <em>MOLoffset</em> is required representing the equivalent
|
||
offset for molecule IDs.</p>
|
||
<p>If <em>merge</em> is specified, the data file atoms are added to the current
|
||
system without changing their IDs. They are assumed to merge (without
|
||
duplication) with the currently defined atoms. It is up to you to
|
||
ensure there are no multiply defined atom IDs, as LAMMPS only performs
|
||
an incomplete check that this is the case by ensuring the resulting
|
||
max atom-ID >= the number of atoms. For molecule IDs, there is no
|
||
check done at all.</p>
|
||
<p>The <em>offset</em> and <em>shift</em> keywords can only be used if the <em>add</em>
|
||
keyword is also specified.</p>
|
||
<p>The <em>offset</em> keyword adds the specified offset values to the atom
|
||
types, bond types, angle types, dihedral types, and improper types as
|
||
they are read from the data file. E.g. if <em>toff</em> = 2, and the file
|
||
uses atom types 1,2,3, then the added atoms will have atom types
|
||
3,4,5. These offsets apply to all occurrences of types in the data
|
||
file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
|
||
sections. This makes it easy to use atoms and molecules and their
|
||
attributes from a data file in different simulations, where you want
|
||
their types (atom, bond, angle, etc) to be different depending on what
|
||
other types already exist. All five offset values must be specified,
|
||
but individual values will be ignored if the data file does not use
|
||
that attribute (e.g. no bonds).</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Offsets are <strong>ignored</strong> on lines using type labels, as the type
|
||
labels will determine the actual types directly depending on the
|
||
current <a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> settings.</p>
|
||
</div>
|
||
<p>The <em>shift</em> keyword can be used to specify an (Sx, Sy, Sz)
|
||
displacement applied to the coordinates of each atom. Sz must be 0.0
|
||
for a 2d simulation. This is a mechanism for adding structured
|
||
collections of atoms at different locations within the simulation box,
|
||
to build up a complex geometry. It is up to you to ensure atoms do
|
||
not end up overlapping unphysically which would lead to bad dynamics.
|
||
Note that the <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a> command can be used
|
||
to move a subset of atoms after they have been read from a data file.
|
||
Likewise, the <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a> command can be used to
|
||
remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are
|
||
also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
|
||
zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo +
|
||
Sx, xhi_new = xhi + Sx.</p>
|
||
<p>The <em>extra</em> keywords can only be used the first time the read_data
|
||
command is used. They are useful if you intend to add new atom, bond,
|
||
angle, etc types later with additional read_data commands. This is
|
||
because the maximum number of allowed atom, bond, angle, etc types is
|
||
set by LAMMPS when the system is first initialized. If you do not use
|
||
the <em>extra</em> keywords, then the number of these types will be limited
|
||
to what appears in the first data file you read. For example, if the
|
||
first data file is a solid substrate of Si, it will likely specify a
|
||
single atom type. If you read a second data file with a different
|
||
material (water molecules) that sit on top of the substrate, you will
|
||
want to use different atom types for those atoms. You can only do
|
||
this if you set the <em>extra/atom/types</em> keyword to a sufficiently large
|
||
value when reading the substrate data file. Note that use of the
|
||
<em>extra</em> keywords also allows each data file to contain sections like
|
||
Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
|
||
the number of types in that data file. If the <em>offset</em> keyword is
|
||
used appropriately when each data file is read, the values in those
|
||
sections will be stored correctly in the larger data structures
|
||
allocated by the use of the <em>extra</em> keywords. E.g. the substrate file
|
||
can list mass and pair coefficients for type 1 silicon atoms. The
|
||
water file can list mass and pair coefficients for type 1 and type 2
|
||
hydrogen and oxygen atoms. Use of the <em>extra</em> and <em>offset</em> keywords
|
||
will store those mass and pair coefficient values appropriately in
|
||
data structures that allow for 3 atom types (Si, H, O). Of course,
|
||
you would still need to specify coefficients for H/Si and O/Si
|
||
interactions in your input script to have a complete pairwise
|
||
interaction model.</p>
|
||
<p>An alternative to using the <em>extra</em> keywords with the read_data
|
||
command, is to use the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command to
|
||
initialize the simulation box and all the various type limits you need
|
||
via its <em>extra</em> keywords. Then use the read_data command one or more
|
||
times to populate the system with atoms, bonds, angles, etc, using the
|
||
<em>offset</em> keyword if desired to alter types used in the various data
|
||
files you read.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="format-of-a-data-file">
|
||
<h2>Format of a data file<a class="headerlink" href="#format-of-a-data-file" title="Link to this heading"></a></h2>
|
||
<p>The structure of the data file is important, though many settings and
|
||
sections are optional or can come in any order. See the examples
|
||
directory for sample data files for different problems.</p>
|
||
<p>The file will be read line by line, but there is a limit of 254
|
||
characters per line and characters beyond that limit will be ignored.</p>
|
||
<p>A data file has a header and a body. The header appears first. The
|
||
first line of the header and thus of the data file is <em>always</em> skipped;
|
||
it typically contains a description of the file or a comment from the
|
||
software that created the file.</p>
|
||
<p>Then lines are read one line at a time. Lines can have a trailing
|
||
comment starting with ‘#’ that is ignored. There <em>must</em> be at least one
|
||
blank between any valid content and the comment. If a line is blank
|
||
(i.e. contains only white-space after comments are deleted), it is
|
||
skipped. If the line contains a header keyword, the corresponding
|
||
value(s) is/are read from the line. A line that is <em>not</em> blank and does
|
||
<em>not</em> contain a header keyword begins the body of the file.</p>
|
||
<p>The body of the file contains zero or more sections. The first line of
|
||
a section has only a keyword. This line can have a trailing comment
|
||
starting with ‘#’ that is either ignored or can be used to check for a
|
||
style match, as described below. There must be a blank between the
|
||
keyword and any comment. The <em>next</em> line is <em>always</em> skipped. The
|
||
remaining lines of the section contain values. The number of lines
|
||
depends on the section keyword as described below. Zero or more blank
|
||
lines can be used <em>between</em> sections. Sections can appear in any order,
|
||
with a few exceptions as noted below.</p>
|
||
<p>The keyword <em>fix</em> can be used one or more times. Each usage specifies
|
||
a fix that will be used to process a specific portion of the data
|
||
file. Any header line containing <em>header-string</em> and any section that
|
||
is an exact match to <em>section-string</em> will be passed to the specified
|
||
fix. See the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command for
|
||
an example of a fix that operates in this manner. The doc page for
|
||
the fix defines the syntax of the header line(s) and section that it
|
||
reads from the data file. Note that the <em>header-string</em> can be
|
||
specified as NULL, in which case no header lines are passed to the
|
||
fix. This means the fix can infer the length of its Section from
|
||
standard header settings, such as the number of atoms. Also the
|
||
<em>section-string</em> may be specified as NULL, and in that case the fix
|
||
ID is used as section name.</p>
|
||
<p>The formatting of individual lines in the data file (indentation,
|
||
spacing between words and numbers) is not important except that header
|
||
and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
|
||
be capitalized as shown and cannot have extra white-space between
|
||
their words - e.g. two spaces or a tab between the 2 words in “xlo
|
||
xhi” or the 2 words in “Bond Coeffs”, is not valid.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="format-of-the-header-of-a-data-file">
|
||
<h2>Format of the header of a data file<a class="headerlink" href="#format-of-the-header-of-a-data-file" title="Link to this heading"></a></h2>
|
||
<p>These are the recognized header keywords. Header lines can come in
|
||
any order. Each keyword takes a single value unless noted in this
|
||
list. The value(s) are read from the beginning of the line.
|
||
Thus the keyword <em>atoms</em> should be in a line like “1000 atoms”; the
|
||
keyword <em>ylo yhi</em> should be in a line like “-10.0 10.0 ylo yhi”; the
|
||
keyword <em>xy xz yz</em> should be in a line like “0.0 5.0 6.0 xy xz yz”.</p>
|
||
<p>All these settings have a default value of 0, except for the
|
||
simulation box size settings; their defaults are explained below. A
|
||
keyword line need only appear if its value is different than the
|
||
default.</p>
|
||
<ul class="simple">
|
||
<li><p><em>atoms</em> = # of atoms in system</p></li>
|
||
<li><p><em>bonds</em> = # of bonds in system</p></li>
|
||
<li><p><em>angles</em> = # of angles in system</p></li>
|
||
<li><p><em>dihedrals</em> = # of dihedrals in system</p></li>
|
||
<li><p><em>impropers</em> = # of impropers in system</p></li>
|
||
<li><p><em>atom types</em> = # of atom types in system</p></li>
|
||
<li><p><em>bond types</em> = # of bond types in system</p></li>
|
||
<li><p><em>angle types</em> = # of angle types in system</p></li>
|
||
<li><p><em>dihedral types</em> = # of dihedral types in system</p></li>
|
||
<li><p><em>improper types</em> = # of improper types in system</p></li>
|
||
<li><p><em>extra bond per atom</em> = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword)</p></li>
|
||
<li><p><em>extra angle per atom</em> = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword)</p></li>
|
||
<li><p><em>extra dihedral per atom</em> = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword)</p></li>
|
||
<li><p><em>extra improper per atom</em> = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword)</p></li>
|
||
<li><p><em>extra special per atom</em> = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword)</p></li>
|
||
<li><p><em>ellipsoids</em> = # of ellipsoids in system</p></li>
|
||
<li><p><em>lines</em> = # of line segments in system</p></li>
|
||
<li><p><em>triangles</em> = # of triangles in system</p></li>
|
||
<li><p><em>bodies</em> = # of bodies in system</p></li>
|
||
<li><p><em>xlo xhi</em> = simulation box boundaries in x dimension (2 values)</p></li>
|
||
<li><p><em>ylo yhi</em> = simulation box boundaries in y dimension (2 values)</p></li>
|
||
<li><p><em>zlo zhi</em> = simulation box boundaries in z dimension (2 values)</p></li>
|
||
<li><p><em>xy xz yz</em> = simulation box tilt factors for triclinic system (3 values)</p></li>
|
||
<li><p><em>avec</em> = first edge vector of a general triclinic simulation box (3 values)</p></li>
|
||
<li><p><em>bvec</em> = second edge vector of a general triclinic simulation box (3 values)</p></li>
|
||
<li><p><em>cvec</em> = third edge vector of a general triclinic simulation box (3 values)</p></li>
|
||
<li><p><em>abc origin</em> = origin of a general triclinic simulation box (3 values)</p></li>
|
||
</ul>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="header-specification-of-the-simulation-box-size-and-shape">
|
||
<h2>Header specification of the simulation box size and shape<a class="headerlink" href="#header-specification-of-the-simulation-box-size-and-shape" title="Link to this heading"></a></h2>
|
||
<p>The last 8 keywords in the list of header keywords are for simulation
|
||
boxes of 3 kinds which LAMMPS supports:</p>
|
||
<ul class="simple">
|
||
<li><p>orthogonal box = faces are perpendicular to the xyz coordinate axes</p></li>
|
||
<li><p>restricted triclinic box = a parallelepiped defined by 3 edge vectors oriented in a constrained manner</p></li>
|
||
<li><p>general triclinic box = a parallelepiped defined by 3 arbitrary edge vectors</p></li>
|
||
</ul>
|
||
<p>For restricted and general triclinic boxes, see the
|
||
<a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page for a fuller
|
||
description than is given here.</p>
|
||
<p>The units of the values for all 8 keywords in in distance units; see
|
||
the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for details.</p>
|
||
<p>For all 3 kinds of simulation boxes, the system may be periodic or
|
||
non-periodic in any dimension; see the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>
|
||
command for details.</p>
|
||
<p>When the simulation box is created by the read_data command, it is
|
||
also partitioned into a regular 3d grid of subdomains, one per
|
||
processor, based on the number of processors being used and the
|
||
settings of the <a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command. For each kind
|
||
of simulation box the subdomains have the same shape as the simulation
|
||
box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller
|
||
parallelepipeds for triclinic boxes. The partitioning can later be
|
||
changed by the <a class="reference internal" href="balance.html"><span class="doc">balance</span></a> or <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a> commands.</p>
|
||
<p>For an orthogonal box, only the <em>xlo xhi</em>, <em>ylo yhi</em>, <em>zlo zhi</em>
|
||
keywords are used. They define the extent of the simulation box in
|
||
each dimension so that the resulting edge vectors of an orthogonal box
|
||
are:</p>
|
||
<ul class="simple">
|
||
<li><p><strong>A</strong> = (xhi-xlo,0,0)</p></li>
|
||
<li><p><strong>B</strong> = (0,yhi-ylo,0)</p></li>
|
||
<li><p><strong>C</strong> = (0,0,zhi-zlo)</p></li>
|
||
</ul>
|
||
<p>The origin (lower left corner) of the orthogonal box is at
|
||
(xlo,ylo,zlo). The default values for these 3 keywords are -0.5 and
|
||
0.5 for each lo/hi pair. For a 2d simulation, the zlo and zhi values
|
||
must straddle zero. The default zlo/zhi values do this, so that
|
||
keyword is not needed in 2d.</p>
|
||
<p>For a restricted triclinic box, the <em>xy xz yz</em> keyword is used in
|
||
addition to the <em>xlo xhi</em>, <em>ylo yhi</em>, <em>zlo zhi</em> keywords. The three
|
||
<em>xy,xz,yz</em> values can be 0.0 or positive or negative, and are called
|
||
“tilt factors” because they are the amount of displacement applied to
|
||
edges of faces of an orthogonal box to transform it into a restricted
|
||
triclinic parallelepiped.</p>
|
||
<p>The <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page discusses the
|
||
tilt factors in detail and explains that the resulting edge vectors of
|
||
a restricted triclinic box are:</p>
|
||
<ul class="simple">
|
||
<li><p><strong>A</strong> = (xhi-xlo,0,0)</p></li>
|
||
<li><p><strong>B</strong> = (xy,yhi-ylo,0)</p></li>
|
||
<li><p><strong>C</strong> = (xz,yz,zhi-zlo)</p></li>
|
||
</ul>
|
||
<p>This restricted form of edge vectors requires that <strong>A</strong> be in the
|
||
direction of the x-axis, <strong>B</strong> be in the xy plane with its y-component
|
||
in the +y direction, and <strong>C</strong> have its z-component in the +z
|
||
direction. The origin (lower left corner) of the restricted triclinic
|
||
box is at (xlo,ylo,zlo).</p>
|
||
<p>For a 2d simulation, the zlo and zhi values must straddle zero. The
|
||
default zlo/zhi values do this, so that keyword is not needed in 2d.
|
||
The xz and yz values must also be zero in 2d. The shape of the 2d
|
||
restricted triclinic simulation box is effectively a parallelogram.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When a restricted triclinic box is used, the simulation domain
|
||
should normally be periodic in any dimensions that tilt is applied
|
||
to, which is given by the second dimension of the tilt factor
|
||
(e.g. y for xy tilt). This is so that pairs of atoms interacting
|
||
across that boundary will have one of them shifted by the tilt
|
||
factor. Periodicity is set by the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>
|
||
command which also describes the shifting by the tilt factor. For
|
||
example, if the xy tilt factor is non-zero, then the y dimension
|
||
should be periodic. Similarly, the z dimension should be periodic
|
||
if xz or yz is non-zero. LAMMPS does not require this periodicity,
|
||
but you may lose atoms if this is not the case.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Normally, the specified tilt factors (xy,xz,yz) should not skew the
|
||
simulation box by more than half the distance of the corresponding
|
||
parallel box length for computational efficiency. For example, if
|
||
<span class="math notranslate nohighlight">\(x_\text{lo} = 2\)</span> and <span class="math notranslate nohighlight">\(x_\text{hi} = 12\)</span>, then the
|
||
<span class="math notranslate nohighlight">\(x\)</span> box length is 10 and the <span class="math notranslate nohighlight">\(xy\)</span> tilt factor should be
|
||
between <span class="math notranslate nohighlight">\(-5\)</span> and <span class="math notranslate nohighlight">\(5\)</span>. LAMMPS will issue a warning if
|
||
this is not the case. See the last sub-section of the
|
||
<a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page for more details.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If a simulation box is initially orthogonal, but will tilt during a
|
||
simulation, e.g. via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command,
|
||
then the box should be defined as restricted triclinic with all 3
|
||
tilt factors = 0.0. Alternatively, the <a class="reference internal" href="change_box.html"><span class="doc">change box</span></a> command can be used to convert an orthogonal box to a
|
||
restricted triclinic box.</p>
|
||
</div>
|
||
<p>For a general triclinic box, the <em>avec</em>, <em>bvec</em>, <em>cvec</em>, and <em>abc
|
||
origin</em> keywords are used. The <em>xlo xhi</em>, <em>ylo yhi</em>, <em>zlo zhi</em>, and
|
||
<em>xy xz yz</em> keywords are NOT used. The first 3 keywords define the 3
|
||
edge vectors <strong>A</strong>, <strong>B</strong>, <strong>C</strong> of the general triclinic box. They
|
||
can be arbitrary vectors so long as they are distinct, non-zero, and
|
||
not co-planar. They must also define a right-handed system such that
|
||
(<strong>A</strong> x <strong>B</strong>) points in the direction of <strong>C</strong>. Note that a
|
||
left-handed system can be converted to a right-handed system by simply
|
||
swapping the order of any pair of the <strong>A</strong>, <strong>B</strong>, <strong>C</strong> vectors.
|
||
The origin of the box (origin of the 3 edge vectors) is set by the
|
||
<em>abc origin</em> keyword.</p>
|
||
<p>The default values for these 4 keywords are as follows:</p>
|
||
<ul class="simple">
|
||
<li><p>avec = (1,0,0)</p></li>
|
||
<li><p>bvec = (0,1,0)</p></li>
|
||
<li><p>cvec = (0,0,1)</p></li>
|
||
<li><p>abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d</p></li>
|
||
</ul>
|
||
<p>For 2d simulations, <em>cvec</em> = (0,0,1) is required, and the 3rd value of
|
||
<em>abc origin</em> must be -0.5. These are the default values, so the
|
||
<em>cvec</em> keyword is not needed in 2d.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>LAMMPS allows specification of general triclinic simulation boxes
|
||
as a convenience for users who may be converting data from
|
||
solid-state crystallographic representations or from DFT codes for
|
||
input to LAMMPS. However, as explained on the
|
||
<a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page, internally,
|
||
LAMMPS only uses restricted triclinic simulation boxes. This means
|
||
the box and per-atom information (e.g. coordinates, velocities) in
|
||
the data file are converted (rotated) from general to restricted
|
||
triclinic form when the file is read. Other sections of the data
|
||
file must also list their per-atom data appropriately if vector
|
||
quantities are specified. This requirement is explained below for
|
||
the relevant sections. The <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page also discusses other LAMMPS commands
|
||
which can input/output general triclinic representations of the
|
||
simulation box and per-atom data.</p>
|
||
</div>
|
||
<p>The following explanations apply to all 3 kinds of simulation boxes:
|
||
orthogonal, restricted triclinic, and general triclinic.</p>
|
||
<p>If the system is periodic (in a dimension), then atom coordinates can
|
||
be outside the bounds (in that dimension); they will be remapped (in a
|
||
periodic sense) back inside the box. For triclinic boxes, periodicity
|
||
in x,y,z refers to the faces of the parallelepiped defined by the
|
||
<strong>A</strong>,**B**,**C** edge vectors of the simulation box. See the
|
||
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command doc page for a fuller discussion.</p>
|
||
<p>Note that if the <em>add</em> option is being used to add atoms to a
|
||
simulation box that already exists, this periodic remapping will be
|
||
performed using simulation box bounds that are the union of the
|
||
existing box and the box boundaries in the new data file.</p>
|
||
<p>If the system is non-periodic (in a dimension), then an image flag for
|
||
that direction has no meaning, since there cannot be periodic images
|
||
without periodicity and the data file is therefore - technically speaking
|
||
- invalid. This situation would happen when a data file was written
|
||
with periodic boundaries and then read back for non-periodic boundaries.
|
||
Accepting a non-zero image flag can lead to unexpected results for any
|
||
operations and computations in LAMMPS that internally use unwrapped
|
||
coordinates (for example computing the center of mass of a group of
|
||
atoms). Thus all non-zero image flags for non-periodic dimensions will
|
||
be be reset to zero on reading the data file and LAMMPS will print a
|
||
warning message, if that happens. This is equivalent to wrapping atoms
|
||
individually back into the principal unit cell in that direction. This
|
||
operation is equivalent to the behavior of the <a class="reference internal" href="change_box.html"><span class="doc">change_box command</span></a> when used to change periodicity.</p>
|
||
<p>If those atoms with non-zero image flags are involved in bonded
|
||
interactions, this reset can lead to undesired changes, when the image
|
||
flag values differ between the atoms, i.e. the bonded interaction
|
||
straddles domain boundaries. For example a bond can become stretched
|
||
across the unit cell if one of its atoms is wrapped to one side of the
|
||
cell and the second atom to the other. In those cases the data file
|
||
needs to be pre-processed externally to become valid again. This can be
|
||
done by first unwrapping coordinates and then wrapping entire molecules
|
||
instead of individual atoms back into the principal simulation cell and
|
||
finally expanding the cell dimensions in the non-periodic direction as
|
||
needed, so that the image flag would be zero.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If the system is non-periodic (in a dimension), then all atoms in
|
||
the data file must have coordinates (in that dimension) that are
|
||
“greater than or equal to” the lo value and “less than or equal to”
|
||
the hi value. If the non-periodic dimension is of style “fixed”
|
||
(see the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command), then the atom coords
|
||
must be strictly “less than” the hi value, due to the way LAMMPS
|
||
assign atoms to processors. Note that you should not make the
|
||
lo/hi values radically smaller/larger than the extent of the atoms.
|
||
For example, if atoms extend from 0 to 50, you should not specify
|
||
the box bounds as -10000 and 10000 unless you also use the
|
||
<a class="reference internal" href="processors.html"><span class="doc">processors command</span></a>. This is because LAMMPS
|
||
uses the specified box size to layout the 3d grid of processors. A
|
||
huge (mostly empty) box will be sub-optimal for performance when
|
||
using “fixed” boundary conditions (see the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command). When using “shrink-wrap” boundary conditions
|
||
(see the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command), a huge (mostly empty)
|
||
box may cause a parallel simulation to lose atoms when LAMMPS
|
||
shrink-wraps the box around the atoms. The read_data command will
|
||
generate an error in this case.</p>
|
||
</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="meaning-of-other-header-keywords">
|
||
<h2>Meaning of other header keywords<a class="headerlink" href="#meaning-of-other-header-keywords" title="Link to this heading"></a></h2>
|
||
<p>The “extra bond per atom” setting (angle, dihedral, improper) is only
|
||
needed if new bonds (angles, dihedrals, impropers) will be added to
|
||
the system when a simulation runs, e.g. by using the <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix
|
||
bond/create</span></a> command. Using this header flag is
|
||
deprecated; please use the <em>extra/bond/per/atom</em> keyword (and
|
||
correspondingly for angles, dihedrals and impropers) in the read_data
|
||
command instead. Either will pre-allocate space in LAMMPS data
|
||
structures for storing the new bonds (angles, dihedrals, impropers).</p>
|
||
<p>The “extra special per atom” setting is typically only needed if new
|
||
bonds/angles/etc will be added to the system, e.g. by using the
|
||
<a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a> command. Or if entire new
|
||
molecules will be added to the system, e.g. by using the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix
|
||
deposit</span></a> or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a> commands, which
|
||
will have more special 1-2,1-3,1-4 neighbors than any other molecules
|
||
defined in the data file. Using this header flag is deprecated;
|
||
please use the <em>extra/special/per/atom</em> keyword instead. Using this
|
||
setting will pre-allocate space in the LAMMPS data structures for
|
||
storing these neighbors. See the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
|
||
and <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> doc pages for more discussion of
|
||
1-2,1-3,1-4 neighbors.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>All of the “extra” settings are only applied in the first data file
|
||
read and when no simulation box has yet been created; as soon as
|
||
the simulation box is created (and read_data implies that), these
|
||
settings are <em>locked</em> and cannot be changed anymore. Please see the
|
||
description of the <em>add</em> keyword above for reading multiple data
|
||
files. If they appear in later data files, they are ignored.</p>
|
||
</div>
|
||
<p>The “ellipsoids” and “lines” and “triangles” and “bodies” settings are
|
||
only used with <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid or line or tri or body</span></a> and specify how many of the atoms are finite-size
|
||
ellipsoids or lines or triangles or bodies; the remainder are point
|
||
particles. See the discussion of ellipsoidflag and the <em>Ellipsoids</em>
|
||
section below. See the discussion of lineflag and the <em>Lines</em> section
|
||
below. See the discussion of triangleflag and the <em>Triangles</em> section
|
||
below. See the discussion of bodyflag and the <em>Bodies</em> section below.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>For <a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a>, the molecular topology
|
||
(bonds,angles,etc) is contained in the molecule templates read-in
|
||
by the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command. This means you cannot
|
||
set the <em>bonds</em>, <em>angles</em>, etc header keywords in the data file,
|
||
nor can you define <em>Bonds</em>, <em>Angles</em>, etc sections as discussed
|
||
below. You can set the <em>bond types</em>, <em>angle types</em>, etc header
|
||
keywords, though it is not necessary. If specified, they must
|
||
match the maximum values defined in any of the template molecules.</p>
|
||
</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="format-of-the-body-of-a-data-file">
|
||
<h2>Format of the body of a data file<a class="headerlink" href="#format-of-the-body-of-a-data-file" title="Link to this heading"></a></h2>
|
||
<p>These are the section keywords for the body of the file.</p>
|
||
<ul class="simple">
|
||
<li><p><em>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies</em> = atom-property sections</p></li>
|
||
<li><p><em>Bonds, Angles, Dihedrals, Impropers</em> = molecular topology sections</p></li>
|
||
<li><p><em>Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels</em> = type label maps</p></li>
|
||
<li><p><em>Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</em> = force field sections</p></li>
|
||
<li><p><em>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</em> = class 2 force field sections</p></li>
|
||
</ul>
|
||
<p>These keywords will check an appended comment for a match with the
|
||
currently defined style:</p>
|
||
<ul class="simple">
|
||
<li><p><em>Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</em></p></li>
|
||
</ul>
|
||
<p>For example, these lines:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>Atoms # sphere
|
||
Pair Coeffs # lj/cut
|
||
</pre></div>
|
||
</div>
|
||
<p>will check if the currently-defined <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> is
|
||
<em>sphere</em>, and the current <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> is <em>lj/cut</em>.
|
||
If not, LAMMPS will issue a warning to indicate that the data file
|
||
section likely does not contain the correct number or type of
|
||
parameters expected for the currently-defined style.</p>
|
||
<p>Each section is listed below in alphabetic order. The format of each
|
||
section is described including the number of lines it must contain and
|
||
rules (if any) for where it can appear in the data file.</p>
|
||
<p>Any individual line in the various sections can have a trailing
|
||
comment starting with “#” for annotation purposes. There must be at least
|
||
one blank between valid content and the comment. E.g. in the
|
||
Atoms section:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>10 1 17 -1.0 10.0 5.0 6.0 # salt ion
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p><em>Angle Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per angle type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = angle type (1-N)
|
||
coeffs = list of coeffs
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>6 70 108.5 0 0
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The number and meaning of the coefficients are specific to the defined
|
||
angle style. See the <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a> and
|
||
<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> commands for details. Coefficients can
|
||
also be set via the <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command in the
|
||
input script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Angle Type Labels</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per angle type</p></li>
|
||
<li><p>line syntax: ID label</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = angle type (1-N)
|
||
label = alphanumeric type label
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>Define alphanumeric type labels for each numeric angle type. These
|
||
can be used in the Angles section in place of a numeric type, but only
|
||
if the this section appears before the Angles section.</p>
|
||
<p>See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the
|
||
allowed syntax of type labels and a general discussion of how type
|
||
labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>AngleAngle Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per improper type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = improper type (1-N)
|
||
coeffs = list of coeffs (see <a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>AngleAngleTorsion Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = dihedral type (1-N)
|
||
coeffs = list of coeffs (see <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Angles</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per angle</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2 atom3</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = number of angle (1-Nangles)
|
||
type = angle type (1-Nangletype, or type label)
|
||
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>example:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>2 2 17 29 430
|
||
</pre></div>
|
||
</div>
|
||
</div></blockquote>
|
||
<p>The three atoms are ordered linearly within the angle. Thus the central
|
||
atom (around which the angle is computed) is the atom2 in the list.
|
||
E.g. H,O,H for a water molecule. The <em>Angles</em> section must appear
|
||
after the <em>Atoms</em> section.</p>
|
||
<p>All values in this section must be integers (1, not 1.0). However,
|
||
the type can be a numeric value or an alphanumeric label. The latter
|
||
is only allowed if the type label has been defined by the
|
||
<a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or an Angle Type Labels section
|
||
earlier in the data file. See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed syntax of type labels
|
||
and a general discussion of how type labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>AngleTorsion Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = dihedral type (1-N)
|
||
coeffs = list of coeffs (see <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Atom Type Labels</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per atom type</p></li>
|
||
<li><p>line syntax: ID label</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = numeric atom type (1-N)
|
||
label = alphanumeric type label
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>Define alphanumeric type labels for each numeric atom type. These
|
||
can be used in the Atoms section in place of a numeric type, but only
|
||
if the Atom Type Labels section appears before the Atoms section.</p>
|
||
<p>See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the
|
||
allowed syntax of type labels and a general discussion of how type
|
||
labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Atoms</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: depends on atom style</p></li>
|
||
</ul>
|
||
<p>An <em>Atoms</em> section must appear in the data file if natoms > 0 in the
|
||
header section. The atoms can be listed in any order. These are the
|
||
line formats for each <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> in LAMMPS. As
|
||
discussed below, each line can optionally have 3 flags (nx,ny,nz)
|
||
appended to it, which indicate which image of a periodic simulation
|
||
box the atom is in. These may be important to include for some kinds
|
||
of analysis.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>For orthogonal and restricted and general triclinic simulation
|
||
boxes, the atom coordinates (x,y,z) listed in this section should
|
||
be inside the corresponding simulation box. For restricted
|
||
triclinic boxes that means the parallelepiped defined by the <em>xlo
|
||
xhi</em>, <em>ylo yhi</em>, <em>zlo zhi</em>, and <em>xy xz yz</em>, keywords. For general
|
||
triclinic boxes that means the parallelepiped defined by the 3 edge
|
||
vectors and origin specified by the <em>avec</em>, <em>bvec</em>, <em>cvec</em>, and
|
||
<em>abc origin</em> header keywords. See the discussion in the header
|
||
section above about how atom coordinates outside the simulation box
|
||
are (or are not) remapped to be inside the box.</p>
|
||
</div>
|
||
<table class="docutils align-default">
|
||
<tbody>
|
||
<tr class="row-odd"><td><p>angle</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>atomic</p></td>
|
||
<td><p>atom-ID atom-type x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>body</p></td>
|
||
<td><p>atom-ID atom-type bodyflag mass x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>bond</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>bpm/sphere</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type diameter density x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>charge</p></td>
|
||
<td><p>atom-ID atom-type q x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>dielectric</p></td>
|
||
<td><p>atom-ID atom-type q x y z mux muy muz area ed em epsilon curvature</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>dipole</p></td>
|
||
<td><p>atom-ID atom-type q x y z mux muy muz</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>dpd</p></td>
|
||
<td><p>atom-ID atom-type theta x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>edpd</p></td>
|
||
<td><p>atom-ID atom-type edpd_temp edpd_cv x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>electron</p></td>
|
||
<td><p>atom-ID atom-type q espin eradius x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>ellipsoid</p></td>
|
||
<td><p>atom-ID atom-type ellipsoidflag density x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>full</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type q x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>line</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type lineflag density x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>mdpd</p></td>
|
||
<td><p>atom-ID atom-type rho x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>molecular</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>peri</p></td>
|
||
<td><p>atom-ID atom-type volume density x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>rheo</p></td>
|
||
<td><p>atom-ID atom-type status rho x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>rheo/thermal</p></td>
|
||
<td><p>atom-ID atom-type status rho energy x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>smd</p></td>
|
||
<td><p>atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>sph</p></td>
|
||
<td><p>atom-ID atom-type rho esph cv x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>sphere</p></td>
|
||
<td><p>atom-ID atom-type diameter density x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>spin</p></td>
|
||
<td><p>atom-ID atom-type x y z spx spy spz sp</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>tdpd</p></td>
|
||
<td><p>atom-ID atom-type x y z cc1 cc2 … ccNspecies</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>template</p></td>
|
||
<td><p>atom-ID atom-type molecule-ID template-index template-atom x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>tri</p></td>
|
||
<td><p>atom-ID molecule-ID atom-type triangleflag density x y z</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>wavepacket</p></td>
|
||
<td><p>atom-ID atom-type charge espin eradius etag cs_re cs_im x y z</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>hybrid</p></td>
|
||
<td><p>atom-ID atom-type x y z sub-style1 sub-style2 …</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>The per-atom values have these meanings and units, listed alphabetically:</p>
|
||
<ul class="simple">
|
||
<li><p>atom-ID = integer ID of atom</p></li>
|
||
<li><p>atom-type = type of atom (1-Ntype, or type label)</p></li>
|
||
<li><p>bodyflag = 1 for body particles, 0 for point particles</p></li>
|
||
<li><p>ccN = chemical concentration for tDPD particles for each species (mole/volume units)</p></li>
|
||
<li><p>cradius = contact radius for SMD particles (distance units)</p></li>
|
||
<li><p>cs_re,cs_im = real/imaginary parts of wave packet coefficients</p></li>
|
||
<li><p>cv = heat capacity (need units) for SPH particles</p></li>
|
||
<li><p>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)</p></li>
|
||
<li><p>diameter = diameter of spherical atom (distance units)</p></li>
|
||
<li><p>edpd_temp = temperature for eDPD particles (temperature units)</p></li>
|
||
<li><p>edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units)</p></li>
|
||
<li><p>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles</p></li>
|
||
<li><p>eradius = electron radius (or fixed-core radius)</p></li>
|
||
<li><p>esph = energy (need units) for SPH particles</p></li>
|
||
<li><p>espin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)</p></li>
|
||
<li><p>etag = integer ID of electron that each wave packet belongs to</p></li>
|
||
<li><p>kradius = kernel radius for SMD particles (distance units)</p></li>
|
||
<li><p>lineflag = 1 for line segment particles, 0 for point or spherical particles</p></li>
|
||
<li><p>mass = mass of particle (mass units)</p></li>
|
||
<li><p>molecule-ID = integer ID of molecule the atom belongs to</p></li>
|
||
<li><p>mux,muy,muz = components of dipole moment of atom (dipole units) (see general triclinic note below)</p></li>
|
||
<li><p>q = charge on atom (charge units)</p></li>
|
||
<li><p>rho = density (need units) for SPH particles</p></li>
|
||
<li><p>sp = magnitude of magnetic spin of atom (Bohr magnetons)</p></li>
|
||
<li><p>spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic note below)</p></li>
|
||
<li><p>template-atom = which atom within a template molecule the atom is</p></li>
|
||
<li><p>template-index = which molecule within the molecule template the atom is part of</p></li>
|
||
<li><p>theta = internal temperature of a DPD particle</p></li>
|
||
<li><p>triangleflag = 1 for triangular particles, 0 for point or spherical particles</p></li>
|
||
<li><p>volume = volume of Peridynamic particle (distance^3 units)</p></li>
|
||
<li><p>x,y,z = coordinates of atom (distance units)</p></li>
|
||
<li><p>x0,y0,z0 = original (strain-free) coordinates of atom (distance
|
||
units) (see general triclinic note below)</p></li>
|
||
</ul>
|
||
<p>The units for these quantities depend on the unit style; see the
|
||
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command for details.</p>
|
||
<p>For 2d simulations, the atom coordinate z must be specified as 0.0.
|
||
If the data file is created by another program, then z values for a 2d
|
||
simulation can be within epsilon of 0.0, and LAMMPS will force them to
|
||
zero.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If the data file defines a general triclinic box, then the
|
||
following per-atom values in the list above are per-atom vectors
|
||
which imply an orientation: (mux,muy,muz) and (spx,spy,spz). This
|
||
means they should be specified consistent with the general
|
||
triclinic box and its orientation relative to the standard x,y,z
|
||
coordinate axes. For example a dipole moment vector which will be
|
||
in the +x direction once LAMMPS converts from a general to
|
||
restricted triclinic box, should be specified in the data file in
|
||
the direction of the <strong>A</strong> edge vector. Likewise the (x0,y0,z0)
|
||
per-atom strain-free coordinates should be inside the general
|
||
triclinic simulation box as explained in the note above. See the
|
||
<a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto triclinic</span></a> doc page for more details.</p>
|
||
</div>
|
||
<p>The atom-ID is used to identify the atom throughout the simulation and
|
||
in dump files. Normally, it is a unique value from 1 to Natoms for
|
||
each atom. Unique values larger than Natoms can be used, but they
|
||
will cause extra memory to be allocated on each processor, if an atom
|
||
map array is used, but not if an atom map hash is used; see the
|
||
<a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a> command for details. If an atom map is
|
||
not used (e.g. an atomic system with no bonds), and you don’t care if
|
||
unique atom IDs appear in dump files, then the atom-IDs can all be set
|
||
to 0.</p>
|
||
<p>The atom-type can be a numeric value or an alphanumeric label. The
|
||
latter is only allowed if the type label has been defined by the
|
||
<a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or an Atom Type Labels section
|
||
earlier in the data file. See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed syntax of type labels
|
||
and a general discussion of how type labels can be used.</p>
|
||
<p>The molecule ID is a second identifier attached to an atom. Normally, it
|
||
is a number from 1 to N, identifying which molecule the atom belongs
|
||
to. It can be 0 if it is a non-bonded atom or if you don’t care to
|
||
keep track of molecule assignments.</p>
|
||
<p>The diameter specifies the size of a finite-size spherical particle.
|
||
It can be set to 0.0, which means that atom is a point particle.</p>
|
||
<p>The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
|
||
whether the particle is a finite-size ellipsoid or line or triangle or
|
||
body of finite size, or whether the particle is a point particle.
|
||
Additional attributes must be defined for each ellipsoid, line,
|
||
triangle, or body in the corresponding <em>Ellipsoids</em>, <em>Lines</em>,
|
||
<em>Triangles</em>, or <em>Bodies</em> section.</p>
|
||
<p>The <em>template-index</em> and <em>template-atom</em> are only defined used by
|
||
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a>. In this case the
|
||
<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command is used to define a molecule template
|
||
which contains one or more molecules (as separate files). If an atom
|
||
belongs to one of those molecules, its <em>template-index</em> and <em>template-atom</em>
|
||
are both set to positive integers; if not the values are both 0. The
|
||
<em>template-index</em> is which molecule (1 to Nmols) the atom belongs to.
|
||
The <em>template-atom</em> is which atom (1 to Natoms) within the molecule
|
||
the atom is.</p>
|
||
<p>Some pair styles and fixes and computes that operate on finite-size
|
||
particles allow for a mixture of finite-size and point particles. See
|
||
the doc pages of individual commands for details.</p>
|
||
<p>For finite-size particles, the density is used in conjunction with the
|
||
particle volume to set the mass of each particle as mass = density *
|
||
volume. In this context, volume can be a 3d quantity (for spheres or
|
||
ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
|
||
segments). If the volume is 0.0, meaning a point particle, then the
|
||
density value is used as the mass. One exception is for the body atom
|
||
style, in which case the mass of each particle (body or point
|
||
particle) is specified explicitly. This is because the volume of the
|
||
body is unknown.</p>
|
||
<p>Note that for 2d simulations of spheres, this command will treat them
|
||
as spheres when converting density to mass. However, they can also be
|
||
modeled as 2d discs (circles) if the <a class="reference internal" href="set.html"><span class="doc">set density/disc</span></a>
|
||
command is used to reset their mass after the read_data command is
|
||
used. A <em>disc</em> keyword can also be used with time integration fixes,
|
||
such as <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a> and <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix
|
||
nvt/sphere</span></a> to time integrate their motion as 2d
|
||
discs (not 3d spheres), by changing their moment of inertia.</p>
|
||
<p>For atom_style hybrid, following the 5 initial values
|
||
(ID,type,x,y,z), specific values for each sub-style must be listed.
|
||
The order of the sub-styles is the same as they were listed in the
|
||
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command. The specific values for each
|
||
sub-style are those that are not the 5 standard ones (ID,type,x,y,z).
|
||
For example, for the “charge” sub-style, a “q” value would appear.
|
||
For the “full” sub-style, a “molecule-ID” and “q” would appear. These
|
||
are listed in the same order they appear as listed above. Thus if</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom_style hybrid charge sphere
|
||
</pre></div>
|
||
</div>
|
||
<p>were used in the input script, each atom line would have these fields:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom-ID atom-type x y z q diameter density
|
||
</pre></div>
|
||
</div>
|
||
<p>Note that if a non-standard value is defined by multiple sub-styles,
|
||
it only appears once in the atom line. E.g. the atom line for
|
||
atom_style hybrid dipole full would list “q” only once, with the
|
||
dipole sub-style fields; “q” does not appear with the full sub-style
|
||
fields.</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom-ID atom-type x y z q mux muy myz molecule-ID
|
||
</pre></div>
|
||
</div>
|
||
<p>Atom lines specify the (x,y,z) coordinates of atoms. These can be
|
||
inside or outside the simulation box. When the data file is read,
|
||
LAMMPS wraps coordinates outside the box back into the box for
|
||
dimensions that are periodic. As discussed above, if an atom is
|
||
outside the box in a non-periodic dimension, it will be lost.</p>
|
||
<p>LAMMPS always stores atom coordinates as values which are inside the
|
||
simulation box. It also stores 3 flags which indicate which image of
|
||
the simulation box (in each dimension) the atom would be in if its
|
||
coordinates were unwrapped across periodic boundaries. An image flag
|
||
of 0 means the atom is still inside the box when unwrapped. A value
|
||
of 2 means add 2 box lengths to get the unwrapped coordinate. A value
|
||
of -1 means subtract 1 box length to get the unwrapped coordinate.
|
||
LAMMPS updates these flags as atoms cross periodic boundaries during
|
||
the simulation. The <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command can output atom
|
||
coordinates in wrapped or unwrapped form, as well as the 3 image
|
||
flags.</p>
|
||
<p>In the data file, atom lines (all lines or none of them) can
|
||
optionally list 3 trailing integer values (nx,ny,nz), which are used
|
||
to initialize the atom’s image flags. If nx,ny,nz values are not
|
||
listed in the data file, LAMMPS initializes them to 0. Note that the
|
||
image flags are immediately updated if an atom’s coordinates need to
|
||
wrapped back into the simulation box.</p>
|
||
<p>It is only important to set image flags correctly in a data file if a
|
||
simulation model relies on unwrapped coordinates for some calculation;
|
||
otherwise they can be left unspecified. Examples of LAMMPS commands
|
||
that use unwrapped coordinates internally are as follows:</p>
|
||
<ul class="simple">
|
||
<li><p>Atoms in a rigid body (see <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a>) must have consistent image flags, so that
|
||
when the atoms are unwrapped, they are near each other, i.e. as a
|
||
single body.</p></li>
|
||
<li><p>If the <a class="reference internal" href="replicate.html"><span class="doc">replicate</span></a> command is used to generate a larger
|
||
system, image flags must be consistent for bonded atoms when the bond
|
||
crosses a periodic boundary. I.e. the values of the image flags
|
||
should be different by 1 (in the appropriate dimension) for the two
|
||
atoms in such a bond.</p></li>
|
||
<li><p>If you plan to <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> image flags and perform post-analysis
|
||
that will unwrap atom coordinates, it may be important that a
|
||
continued run (restarted from a data file) begins with image flags
|
||
that are consistent with the previous run.</p></li>
|
||
</ul>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If your system is an infinite periodic crystal with bonds then
|
||
it is impossible to have fully consistent image flags. This is because
|
||
some bonds will cross periodic boundaries and connect two atoms with the
|
||
same image flag.</p>
|
||
</div>
|
||
<p>Atom velocities and other atom quantities not defined above are set to
|
||
0.0 when the <em>Atoms</em> section is read. Velocities can be set later by
|
||
a <em>Velocities</em> section in the data file or by a <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> or <a class="reference internal" href="set.html"><span class="doc">set</span></a> command in the input script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Bodies</em> section:</p>
|
||
<ul>
|
||
<li><p>one or more lines per body</p></li>
|
||
<li><p>first line syntax: atom-ID Ninteger Ndouble</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>Ninteger = # of integer quantities for this particle
|
||
Ndouble = # of floating-point quantities for this particle
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>0 or more integer lines with total of Ninteger values</p></li>
|
||
<li><p>0 or more double lines with total of Ndouble values</p></li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 3 6
|
||
2 3 2
|
||
1.0 2.0 3.0 1.0 2.0 4.0
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 0 14
|
||
1.0 2.0 3.0 1.0 2.0 4.0 1.0
|
||
2.0 3.0 1.0 2.0 4.0 4.0 2.0
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The <em>Bodies</em> section must appear if <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>
|
||
is used and any atoms listed in the <em>Atoms</em> section have a bodyflag =
|
||
1. The number of bodies should be specified in the header section via
|
||
the “bodies” keyword.</p>
|
||
<p>Each body can have a variable number of integer and/or floating-point
|
||
values. The number and meaning of the values is defined by the body
|
||
style, as described in the <a class="reference internal" href="Howto_body.html"><span class="doc">Howto body</span></a> doc page.
|
||
The body style is given as an argument to the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a> command.</p>
|
||
<p>The Ninteger and Ndouble values determine how many integer and
|
||
floating-point values are specified for this particle. Ninteger and
|
||
Ndouble can be as large as needed and can be different for every body.
|
||
Integer values are then listed next on subsequent lines. Lines are
|
||
read one at a time until Ninteger values are read. Floating-point
|
||
values follow on subsequent lines, Again lines are read one at a time
|
||
until Ndouble values are read. Note that if there are no values of a
|
||
particular type, no lines appear for that type.</p>
|
||
<p>The <em>Bodies</em> section must appear after the <em>Atoms</em> section.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Bond Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per bond type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = bond type (1-N)
|
||
coeffs = list of coeffs
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>4 250 1.49
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The number and meaning of the coefficients are specific to the defined
|
||
bond style. See the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> and
|
||
<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> commands for details. Coefficients can
|
||
also be set via the <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command in the input
|
||
script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Bond Type Labels</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per bond type</p></li>
|
||
<li><p>line syntax: ID label</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = bond type (1-N)
|
||
label = alphanumeric type label
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>Define alphanumeric type labels for each numeric bond type. These can
|
||
be used in the Bonds section in place of a numeric type, but only if
|
||
the this section appears before the Angles section.</p>
|
||
<p>See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the
|
||
allowed syntax of type labels and a general discussion of how type
|
||
labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>BondAngle Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per angle type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = angle type (1-N)
|
||
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>BondBond Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per angle type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = angle type (1-N)
|
||
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>BondBond13 Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = dihedral type (1-N)
|
||
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Bonds</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per bond</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = bond number (1-Nbonds)
|
||
type = bond type (1-Nbondtype, or type label)
|
||
atom1,atom2 = IDs of 1st,2nd atom in bond
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 3 17 29
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The <em>Bonds</em> section must appear after the <em>Atoms</em> section.</p>
|
||
<p>All values in this section must be integers (1, not 1.0). However,
|
||
the type can be a numeric value or an alphanumeric label. The latter
|
||
is only allowed if the type label has been defined by the
|
||
<a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or a Bond Type Labels section
|
||
earlier in the data file. See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed syntax of type labels
|
||
and a general discussion of how type labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Dihedral Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = dihedral type (1-N)
|
||
coeffs = list of coeffs
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>3 0.6 1 0 1
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The number and meaning of the coefficients are specific to the defined
|
||
dihedral style. See the <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a> and
|
||
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> commands for details.
|
||
Coefficients can also be set via the
|
||
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command in the input script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Dihedral Type Labels</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID label</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = dihedral type (1-N)
|
||
label = alphanumeric type label
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>Define alphanumeric type labels for each numeric dihedral type. These
|
||
can be used in the Dihedrals section in place of a numeric type, but
|
||
only if the this section appears before the Dihedrals section.</p>
|
||
<p>See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the
|
||
allowed syntax of type labels and a general discussion of how type
|
||
labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Dihedrals</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2 atom3 atom4</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = number of dihedral (1-Ndihedrals)
|
||
type = dihedral type (1-Ndihedraltype, or type label)
|
||
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 4 17 29 30 21
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The 4 atoms are ordered linearly within the dihedral. The <em>Dihedrals</em>
|
||
section must appear after the <em>Atoms</em> section.</p>
|
||
<p>All values in this section must be integers (1, not 1.0). However,
|
||
the type can be a numeric value or an alphanumeric label. The latter
|
||
is only allowed if the type label has been defined by the
|
||
<a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or a Dihedral Type Labels section
|
||
earlier in the data file. See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed syntax of type labels
|
||
and a general discussion of how type labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Ellipsoids</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per ellipsoid</p></li>
|
||
<li><p>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom-ID = ID of atom which is an ellipsoid
|
||
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
|
||
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 1 2 1 1 0 0 0
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The <em>Ellipsoids</em> section must appear if <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> is used and any atoms are listed in the <em>Atoms</em> section
|
||
with an ellipsoidflag = 1. The number of ellipsoids should be
|
||
specified in the header section via the “ellipsoids” keyword.</p>
|
||
<p>The 3 shape values specify the 3 diameters or aspect ratios of a
|
||
finite-size ellipsoidal particle, when it is oriented along the 3
|
||
coordinate axes. They must all be non-zero values.</p>
|
||
<p>The values <em>quatw</em>, <em>quati</em>, <em>quatj</em>, and <em>quatk</em> set the orientation
|
||
of the atom as a quaternion (4-vector). Note that the shape
|
||
attributes specify the aspect ratios of an ellipsoidal particle, which
|
||
is oriented by default with its x-axis along the simulation box’s
|
||
x-axis, and similarly for y and z. If this body is rotated (via the
|
||
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
||
the quaternion that represents its new orientation is given by
|
||
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
||
4 components are quatw, quati, quatj, and quatk as specified above.
|
||
LAMMPS normalizes each atom’s quaternion in case (a,b,c) is not
|
||
specified as a unit vector.</p>
|
||
<p>If the data file defines a general triclinic box, then the quaternion
|
||
for each ellipsoid should be specified for its orientation relative to
|
||
the standard x,y,z coordinate axes. When the system is converted to a
|
||
restricted triclinic box, the ellipsoid quaternions will be altered to
|
||
reflect the new orientation of the ellipsoid.</p>
|
||
<p>The <em>Ellipsoids</em> section must appear after the <em>Atoms</em> section.</p>
|
||
<hr class="docutils" />
|
||
<p><em>EndBondTorsion Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = dihedral type (1-N)
|
||
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Improper Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per improper type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = improper type (1-N)
|
||
coeffs = list of coeffs
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>2 20 0.0548311
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The number and meaning of the coefficients are specific to the defined
|
||
improper style. See the <a class="reference internal" href="improper_style.html"><span class="doc">improper_style</span></a> and
|
||
<a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a> commands for details.
|
||
Coefficients can also be set via the
|
||
<a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a> command in the input script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Improper Type Labels</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per improper type</p></li>
|
||
<li><p>line syntax: ID label</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = improper type (1-N)
|
||
label = alphanumeric type label
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>Define alphanumeric type labels for each numeric improper type. These
|
||
can be used in the Impropers section in place of a numeric type, but
|
||
only if the this section appears before the Impropers section.</p>
|
||
<p>See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the
|
||
allowed syntax of type labels and a general discussion of how type
|
||
labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Impropers</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per improper</p></li>
|
||
<li><p>line syntax: ID type atom1 atom2 atom3 atom4</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = number of improper (1-Nimpropers)
|
||
type = improper type (1-Nimpropertype, or type label)
|
||
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 3 17 29 13 100
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The ordering of the 4 atoms determines the definition of the improper
|
||
angle used in the formula for each <a class="reference internal" href="improper_style.html"><span class="doc">improper style</span></a>. See the doc pages for individual styles for
|
||
details.</p>
|
||
<p>The <em>Impropers</em> section must appear after the <em>Atoms</em> section.</p>
|
||
<p>All values in this section must be integers (1, not 1.0). However,
|
||
the type can be a numeric value or an alphanumeric label. The latter
|
||
is only allowed if the type label has been defined by the
|
||
<a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or a Improper Type Labels section
|
||
earlier in the data file. See the <a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed syntax of type labels
|
||
and a general discussion of how type labels can be used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Lines</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per line segment</p></li>
|
||
<li><p>line syntax: atom-ID x1 y1 x2 y2</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom-ID = ID of atom which is a line segment
|
||
x1,y1 = 1st end point
|
||
x2,y2 = 2nd end point
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 1.0 0.0 2.0 0.0
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The <em>Lines</em> section must appear if <a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a>
|
||
is used and any atoms are listed in the <em>Atoms</em> section with a
|
||
lineflag = 1. The number of lines should be specified in the header
|
||
section via the “lines” keyword.</p>
|
||
<p>The 2 end points are the end points of the line segment. They should
|
||
be values close to the center point of the line segment specified in
|
||
the Atoms section of the data file, even if individual end points are
|
||
outside the simulation box.</p>
|
||
<p>The ordering of the 2 points should be such that using a right-hand
|
||
rule to cross the line segment with a unit vector in the +z direction,
|
||
gives an “outward” normal vector perpendicular to the line segment.
|
||
I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
|
||
for defining some interactions.</p>
|
||
<p>If the data file defines a general triclinic box, then the x1,y1 and
|
||
x2,y2 values for each line segment should be specified for its
|
||
orientation relative to the standard x,y,z coordinate axes. When the
|
||
system is converted to a restricted triclinic box, the x1,y1,x2,y2
|
||
values will be altered to reflect the new orientation of the line
|
||
segment.</p>
|
||
<p>The <em>Lines</em> section must appear after the <em>Atoms</em> section.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Masses</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per atom type</p></li>
|
||
<li><p>line syntax: ID mass</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = atom type (1-N or atom type label)
|
||
mass = mass value
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>3 1.01
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>This defines the mass of each atom type. This can also be set via the
|
||
<a class="reference internal" href="mass.html"><span class="doc">mass</span></a> command in the input script. This section cannot be
|
||
used for atom styles that define a mass for individual atoms -
|
||
e.g. <a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere</span></a>.</p>
|
||
<p>Using type labels instead of atom type numbers is only allowed if the
|
||
type label has been defined by the <a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a> command or
|
||
a Atom Type Labels section earlier in the data file. See the
|
||
<a class="reference internal" href="Howto_type_labels.html"><span class="doc">Howto type labels</span></a> doc page for the allowed
|
||
syntax of type labels and a general discussion of how type labels can be
|
||
used.</p>
|
||
<hr class="docutils" />
|
||
<p><em>MiddleBondTorsion Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per dihedral type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<pre class="literal-block">ID = dihedral type (1-N)
|
||
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>)</pre>
|
||
</li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p><em>Pair Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per atom type</p></li>
|
||
<li><p>line syntax: ID coeffs</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID = atom type (1-N)
|
||
coeffs = list of coeffs
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>3 0.022 2.35197 0.022 2.35197
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The number and meaning of the coefficients are specific to the defined
|
||
pair style. See the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and
|
||
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands for details. Since pair
|
||
coefficients for types I != J are not specified, these will be
|
||
generated automatically by the pair style’s mixing rule. See the
|
||
individual pair_style doc pages and the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify mix</span></a> command for details. Pair coefficients can also be set
|
||
via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command in the input script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>PairIJ Coeffs</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per pair of atom types for all I,J with I <= J</p></li>
|
||
<li><p>line syntax: ID1 ID2 coeffs</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ID1 = atom type I = 1-N
|
||
ID2 = atom type J = I-N, with I <= J
|
||
coeffs = list of coeffs
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>examples:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>3 3 0.022 2.35197 0.022 2.35197
|
||
3 5 0.022 2.35197 0.022 2.35197
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>This section must have N*(N+1)/2 lines where N = # of atom types.
|
||
The number and meaning of the coefficients are specific to the defined
|
||
pair style. See the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and
|
||
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands for details. Since pair
|
||
coefficients for types I != J are all specified, these values will
|
||
turn off the default mixing rule defined by the pair style. See the
|
||
individual pair_style doc pages and the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify mix</span></a> command for details. Pair coefficients can also be set
|
||
via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command in the input script.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Triangles</em> section:</p>
|
||
<ul>
|
||
<li><p>one line per triangle</p></li>
|
||
<li><p>line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom-ID = ID of atom which is a line segment
|
||
x1,y1,z1 = 1st corner point
|
||
x2,y2,z2 = 2nd corner point
|
||
x3,y3,z3 = 3rd corner point
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p>example:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>The <em>Triangles</em> section must appear if <a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a> is used and any atoms are listed in the <em>Atoms</em> section
|
||
with a triangleflag = 1. The number of lines should be specified in
|
||
the header section via the “triangles” keyword.</p>
|
||
<p>The 3 corner points are the corner points of the triangle. They
|
||
should be values close to the center point of the triangle specified
|
||
in the Atoms section of the data file, even if individual corner
|
||
points are outside the simulation box.</p>
|
||
<p>The ordering of the 3 points should be such that using a right-hand
|
||
rule to go from point1 to point2 to point3 gives an “outward” normal
|
||
vector to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1).
|
||
This orientation may be important for defining some interactions.</p>
|
||
<p>If the data file defines a general triclinic box, then the x1,y1,z1
|
||
and x2,y2,z2 and x3,y3,z3 values for each triangle should be specified
|
||
for its orientation relative to the standard x,y,z coordinate axes.
|
||
When the system is converted to a restricted triclinic box, the
|
||
x1,y1,z1,x2,y2,z2,x3,y3,z3 values will be altered to reflect the new
|
||
orientation of the triangle.</p>
|
||
<p>The <em>Triangles</em> section must appear after the <em>Atoms</em> section.</p>
|
||
<hr class="docutils" />
|
||
<p><em>Velocities</em> section:</p>
|
||
<ul class="simple">
|
||
<li><p>one line per atom</p></li>
|
||
<li><p>line syntax: depends on atom style</p></li>
|
||
</ul>
|
||
<table class="docutils align-default">
|
||
<tbody>
|
||
<tr class="row-odd"><td><p>all styles except those listed</p></td>
|
||
<td><p>atom-ID vx vy vz</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>electron</p></td>
|
||
<td><p>atom-ID vx vy vz ervel</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>ellipsoid</p></td>
|
||
<td><p>atom-ID vx vy vz lx ly lz</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>sphere</p></td>
|
||
<td><p>atom-ID vx vy vz wx wy wz</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>hybrid</p></td>
|
||
<td><p>atom-ID vx vy vz sub-style1 sub-style2 …</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>where the keywords have these meanings:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>vx,vy,vz = translational velocity of atom
|
||
lx,ly,lz = angular momentum of aspherical atom
|
||
wx,wy,wz = angular velocity of spherical atom
|
||
ervel = electron radial velocity (0 for fixed-core)
|
||
</pre></div>
|
||
</div>
|
||
</div></blockquote>
|
||
<p>The velocity lines can appear in any order. This section can only be
|
||
used after an <em>Atoms</em> section. This is because the <em>Atoms</em> section
|
||
must have assigned a unique atom ID to each atom so that velocities
|
||
can be assigned to them.</p>
|
||
<p>Vx, vy, vz, and ervel are in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of velocity. Lx, ly,
|
||
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
|
||
Wz are in units of angular velocity (radians/time).</p>
|
||
<p>If the data file defines a general triclinic box, then each of the 3
|
||
vectors (translational velocity, angular momentum, angular velocity)
|
||
should be specified for the rotated coordinate axes of the general
|
||
triclinic box. See the <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto triclinic</span></a> doc
|
||
page for more details.</p>
|
||
<p>For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz),
|
||
specific values for each sub-style must be listed. The order of the
|
||
sub-styles is the same as they were listed in the
|
||
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command. The sub-style specific values
|
||
are those that are not the 5 standard ones (ID,vx,vy,vz). For
|
||
example, for the “sphere” sub-style, “wx”, “wy”, “wz” values would
|
||
appear. These are listed in the same order they appear as listed
|
||
above. Thus if</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">atom_style</span><span class="w"> </span><span class="n">hybrid</span><span class="w"> </span><span class="n">electron</span><span class="w"> </span><span class="n">sphere</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>were used in the input script, each velocity line would have these
|
||
fields:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>atom-ID vx vy vz ervel wx wy wz
|
||
</pre></div>
|
||
</div>
|
||
<p>Translational velocities can also be (re)set by the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command in the input script.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>To read gzipped data files, you must compile LAMMPS with the
|
||
-DLAMMPS_GZIP option. See the <a class="reference internal" href="Build_settings.html"><span class="doc">Build settings</span></a>
|
||
doc page for details.</p>
|
||
<p>Label maps are currently not supported when using the KOKKOS package.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>,
|
||
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="write_data.html"><span class="doc">write_data</span></a>,
|
||
<a class="reference internal" href="labelmap.html"><span class="doc">labelmap</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The default for all the <em>extra</em> keywords is 0.</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="quit.html" class="btn btn-neutral float-left" title="quit command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="read_dump.html" class="btn btn-neutral float-right" title="read_dump command" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
|
||
<hr/>
|
||
|
||
<div role="contentinfo">
|
||
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