forked from lijiext/lammps
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HTML
520 lines
30 KiB
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<title>thermo_modify command — LAMMPS documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<p class="caption"><span class="caption-text">Index</span></p>
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<li class="toctree-l1 current"><a class="reference internal" href="commands.html">Commands</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="box.html">box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html">dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_h5md.html">dump h5md command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-movie-command">dump movie command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">thermo_modify command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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</ul>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li>thermo_modify command</li>
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<div class="section" id="thermo-modify-command">
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<span id="index-0"></span><h1>thermo_modify command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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thermo_modify keyword value ...
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</pre>
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<ul>
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<li><p class="first">one or more keyword/value pairs may be listed</p>
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<pre class="literal-block">
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keyword = <em>lost</em> or <em>lost/bond</em> or <em>norm</em> or <em>flush</em> or <em>line</em> or <em>format</em> or <em>temp</em> or <em>press</em>:l
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<em>lost</em> value = <em>error</em> or <em>warn</em> or <em>ignore</em>
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<em>lost/bond</em> value = <em>error</em> or <em>warn</em> or <em>ignore</em>
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<em>norm</em> value = <em>yes</em> or <em>no</em>
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<em>flush</em> value = <em>yes</em> or <em>no</em>
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<em>line</em> value = <em>one</em> or <em>multi</em>
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<em>format</em> values = <em>line</em> string, <em>int</em> string, <em>float</em> string, M string, or <em>none</em>
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string = C-style format string
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M = integer from 1 to N, where N = # of quantities being output
|
|
<em>temp</em> value = compute ID that calculates a temperature
|
|
<em>press</em> value = compute ID that calculates a pressure
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
thermo_modify lost ignore flush yes
|
|
thermo_modify temp myTemp format 3 %15.8g
|
|
thermo_modify temp myTemp format line "%ld %g %g %15.8g"
|
|
thermo_modify line multi format float %g
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Set options for how thermodynamic information is computed and printed
|
|
by LAMMPS.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">These options apply to the currently defined thermo style. When
|
|
you specify a <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command, all
|
|
thermodynamic settings are restored to their default values, including
|
|
those previously reset by a thermo_modify command. Thus if your input
|
|
script specifies a thermo_style command, you should use the
|
|
thermo_modify command after it.</p>
|
|
</div>
|
|
<p>The <em>lost</em> keyword determines whether LAMMPS checks for lost atoms
|
|
each time it computes thermodynamics and what it does if atoms are
|
|
lost. An atom can be “lost” if it moves across a non-periodic
|
|
simulation box <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> or if it moves more than a box
|
|
length outside the simulation domain (or more than a processor
|
|
sub-domain length) before reneighboring occurs. The latter case is
|
|
typically due to bad dynamics, e.g. too large a timestep or huge
|
|
forces and velocities. If the value is <em>ignore</em>, LAMMPS does not
|
|
check for lost atoms. If the value is <em>error</em> or <em>warn</em>, LAMMPS
|
|
checks and either issues an error or warning. The code will exit with
|
|
an error and continue with a warning. A warning will only be issued
|
|
once, the first time an atom is lost. This can be a useful debugging
|
|
option.</p>
|
|
<p>The <em>lost/bond</em> keyword determines whether LAMMPS throws an error or
|
|
not if an atom in a bonded interaction (bond, angle, etc) cannot be
|
|
found when it creates bonded neighbor lists. By default this is a
|
|
fatal error. However in some scenarios it may be desirable to only
|
|
issue a warning or ignore it and skip the computation of the missing
|
|
bond, angle, etc. An example would be when gas molecules in a vapor
|
|
are drifting out of the box through a fixed boundary condition (see
|
|
the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command). In this case one atom may be
|
|
deleted before the rest of the molecule is, on a later timestep.</p>
|
|
<p>The <em>norm</em> keyword determines whether various thermodynamic output
|
|
values are normalized by the number of atoms or not, depending on
|
|
whether it is set to <em>yes</em> or <em>no</em>. Different unit styles have
|
|
different defaults for this setting (see below). Even if <em>norm</em> is
|
|
set to <em>yes</em>, a value is only normalized if it is an “extensive”
|
|
quantity, meaning that it scales with the number of atoms in the
|
|
system. For the thermo keywords described by the doc page for the
|
|
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command, all energy-related keywords
|
|
are extensive, such as <em>pe</em> or <em>ebond</em> or <em>enthalpy</em>. Other keywords
|
|
such as <em>temp</em> or <em>press</em> are “intensive” meaning their value is
|
|
independent (in a statistical sense) of the number of atoms in the
|
|
system and thus are never normalized. For thermodynamic output values
|
|
extracted from fixes and computes in a <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command, the doc page for the individual
|
|
<a class="reference internal" href="fix.html"><span class="doc">fix</span></a> or <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> lists whether the value is
|
|
“extensive” or “intensive” and thus whether it is normalized.
|
|
Thermodynamic output values calculated by a variable formula are
|
|
assumed to be “intensive” and thus are never normalized. You can
|
|
always include a divide by the number of atoms in the variable formula
|
|
if this is not the case.</p>
|
|
<p>The <em>flush</em> keyword invokes a flush operation after thermodynamic info
|
|
is written to the log file. This insures the output in that file is
|
|
current (no buffering by the OS), even if LAMMPS halts before the
|
|
simulation completes.</p>
|
|
<p>The <em>line</em> keyword determines whether thermodynamics will be output as
|
|
a series of numeric values on one line or in a multi-line format with
|
|
3 quantities with text strings per line and a dashed-line header
|
|
containing the timestep and CPU time. This modify option overrides
|
|
the <em>one</em> and <em>multi</em> thermo_style settings.</p>
|
|
<p>The <em>format</em> keyword can be used to change the default numeric format
|
|
of any of quantities the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
|
|
outputs. All the specified format strings are C-style formats,
|
|
e.g. as used by the C/C++ printf() command. The <em>line</em> keyword takes
|
|
a single argument which is the format string for the entire line of
|
|
thermo output, with N fields, which you must enclose in quotes if it
|
|
is more than one field. The <em>int</em> and <em>float</em> keywords take a single
|
|
format argument and are applied to all integer or floating-point
|
|
quantities output. The setting for <em>M string</em> also takes a single
|
|
format argument which is used for the Mth value output in each line,
|
|
e.g. the 5th column is output in high precision for “format 5
|
|
%20.15g”.</p>
|
|
<p>The <em>format</em> keyword can be used multiple times. The precedence is
|
|
that for each value in a line of output, the <em>M</em> format (if specified)
|
|
is used, else the <em>int</em> or <em>float</em> setting (if specified) is used,
|
|
else the <em>line</em> setting (if specified) for that value is used, else
|
|
the default setting is used. A setting of <em>none</em> clears all previous
|
|
settings, reverting all values to their default format.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The thermo output values <em>step</em> and <em>atoms</em> are stored
|
|
internally as 8-byte signed integers, rather than the usual 4-byte
|
|
signed integers. When specifying the <em>format int</em> option you can use
|
|
a “%d”-style format identifier in the format string and LAMMPS will
|
|
convert this to the corresponding 8-byte form when it is applied to
|
|
those keywords. However, when specifying the <em>line</em> option or <em>format
|
|
M string</em> option for <em>step</em> and <em>natoms</em>, you should specify a format
|
|
string appropriate for an 8-byte signed integer, e.g. one with “%ld”.</p>
|
|
</div>
|
|
<p>The <em>temp</em> keyword is used to determine how thermodynamic temperature
|
|
is calculated, which is used by all thermo quantities that require a
|
|
temperature (“temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc).
|
|
The specified compute ID must have been previously defined by the user
|
|
via the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command and it must be a style of
|
|
compute that calculates a temperature. As described in the
|
|
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command, thermo output uses a default
|
|
compute for temperature with ID = <em>thermo_temp</em>. This option allows
|
|
the user to override the default.</p>
|
|
<p>The <em>press</em> keyword is used to determine how thermodynamic pressure is
|
|
calculated, which is used by all thermo quantities that require a
|
|
pressure (“press”, “enthalpy”, “pxx”, etc). The specified compute ID
|
|
must have been previously defined by the user via the
|
|
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command and it must be a style of compute that
|
|
calculates a pressure. As described in the
|
|
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command, thermo output uses a default
|
|
compute for pressure with ID = <em>thermo_press</em>. This option allows the
|
|
user to override the default.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If both the <em>temp</em> and <em>press</em> keywords are used in a single
|
|
thermo_modify command (or in two separate commands), then the order in
|
|
which the keywords are specified is important. Note that a <a class="reference internal" href="compute_pressure.html"><span class="doc">pressure compute</span></a> defines its own temperature compute as
|
|
an argument when it is specified. The <em>temp</em> keyword will override
|
|
this (for the pressure compute being used by thermodynamics), but only
|
|
if the <em>temp</em> keyword comes after the <em>press</em> keyword. If the <em>temp</em>
|
|
keyword comes before the <em>press</em> keyword, then the new pressure
|
|
compute specified by the <em>press</em> keyword will be unaffected by the
|
|
<em>temp</em> setting.</p>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="thermo.html"><span class="doc">thermo</span></a>, <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are lost = error, norm = yes for unit style of
|
|
<em>lj</em>, norm = no for unit style of <em>real</em> and <em>metal</em>, flush = no,
|
|
and temp/press = compute IDs defined by thermo_style.</p>
|
|
<p>The defaults for the line and format options depend on the thermo
|
|
style. For styles “one” and “custom”, the line and format defaults
|
|
are “one”, “%8d”, and “%12.8g”. For style “multi”, the line and
|
|
format defaults are “multi”, “%8d”, and “%14.4f”.</p>
|
|
</div>
|
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