362 lines
27 KiB
HTML
362 lines
27 KiB
HTML
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<title>dynamical_matrix command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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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 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 current"><a class="current reference internal" href="#">dynamical_matrix 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 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="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="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="labelmap.html">labelmap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mdi.html">mdi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html">min_style spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-cg-command">min_style spin/cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_spin.html#min-style-spin-lbfgs-command">min_style spin/lbfgs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style cg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-hftn-command">min_style hftn command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-sd-command">min_style sd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-quickmin-command">min_style quickmin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-fire-command">min_style fire command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-command"><span class="xref std std-doc">min_style spin</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-cg-command"><span class="xref std std-doc">min_style spin/cg</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html#min-style-spin-lbfgs-command"><span class="xref std std-doc">min_style spin/lbfgs</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><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="neb_spin.html">neb/spin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="plugin.html">plugin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_atoms.html">reset_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper_grem.html">temper/grem command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper_npt.html">temper/npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="third_order.html">third_order command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="dynamical-matrix-command">
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<span id="index-1"></span><span id="index-0"></span><h1>dynamical_matrix command<a class="headerlink" href="#dynamical-matrix-command" title="Link to this heading"></a></h1>
|
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<p>Accelerator Variant: dynamical_matrix/kk</p>
|
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dynamical_matrix </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">gamma</span><span class="w"> </span><span class="n">args</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p>group-ID = ID of group of atoms to displace</p></li>
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<li><p>style = <em>regular</em> or <em>eskm</em></p></li>
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<li><p>gamma = finite different displacement length (distance units)</p></li>
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<li><p>one or more keyword/arg pairs may be appended</p>
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<pre class="literal-block">keyword = <em>file</em> or <em>binary</em>
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<em>file</em> name = name of output file for the dynamical matrix
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<em>binary</em> arg = <em>yes</em> or <em>no</em> or <em>gzip</em></pre>
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</li>
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</ul>
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</section>
|
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<section id="examples">
|
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<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">dynamical_matrix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">regular</span><span class="w"> </span><span class="m">0.000001</span>
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<span class="k">dynamical_matrix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">eskm</span><span class="w"> </span><span class="m">0.000001</span>
|
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<span class="k">dynamical_matrix </span><span class="nv nv-Identifier">3</span><span class="w"> </span><span class="n">regular</span><span class="w"> </span><span class="m">0.00004</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">dynmat.dat</span>
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||
<span class="k">dynamical_matrix </span><span class="nv nv-Identifier">5</span><span class="w"> </span><span class="n">eskm</span><span class="w"> </span><span class="m">0.00000001</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">dynamical.dat</span><span class="w"> </span><span class="n">binary</span><span class="w"> </span><span class="n">yes</span>
|
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</pre></div>
|
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</div>
|
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</section>
|
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<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Calculate the dynamical matrix by finite difference of the selected group,</p>
|
||
<div class="math notranslate nohighlight">
|
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\[D = \frac{\Phi_{ij}^{\alpha\beta}}{\sqrt{M_i M_j}}\]</div>
|
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<p>where D is the dynamical matrix and <span class="math notranslate nohighlight">\(\Phi\)</span> is the force constant
|
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matrix defined by</p>
|
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<div class="math notranslate nohighlight">
|
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\[\Phi_{ij}^{\alpha\beta} = \frac{\partial^2 U}{\partial x_{i,\alpha} \partial x_{j,\beta}}\]</div>
|
||
<p>The output for the dynamical matrix is printed three elements at a time.
|
||
The three elements are the three <span class="math notranslate nohighlight">\(\beta\)</span> elements for a respective
|
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i/<span class="math notranslate nohighlight">\(\alpha\)</span>/j combination. Each line is printed in order of j
|
||
increasing first, <span class="math notranslate nohighlight">\(\alpha\)</span> second, and i last.</p>
|
||
<p>If the style eskm is selected, the dynamical matrix will be in units of
|
||
inverse squared femtoseconds. These units will then conveniently leave
|
||
frequencies in THz.</p>
|
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<hr class="docutils" />
|
||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||
functionally the same as the corresponding style without the suffix.
|
||
They have been optimized to run faster, depending on your available
|
||
hardware, as discussed on the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a>
|
||
page. The accelerated styles take the same arguments and should
|
||
produce the same results, except for round-off and precision issues.</p>
|
||
<p>These accelerated styles are part of the GPU, INTEL, KOKKOS,
|
||
OPENMP, and OPT packages, respectively. They are only enabled if
|
||
LAMMPS was built with those packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
<p>You can specify the accelerated styles explicitly in your input script
|
||
by including their suffix, or you can use the <a class="reference internal" href="Run_options.html"><span class="doc">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can use the
|
||
<a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||
<p>See the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a> page for more
|
||
instructions on how to use the accelerated styles effectively.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>The command collects an array of nine times the number of atoms in a group
|
||
on every single MPI rank, so the memory requirements can be very significant
|
||
for large systems.</p>
|
||
<p>This command is part of the PHONON package. It is only enabled if
|
||
LAMMPS was built with that package.
|
||
See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="fix_phonon.html"><span class="doc">fix phonon</span></a>, <a class="reference internal" href="fix_numdiff.html"><span class="doc">fix numdiff</span></a>,</p>
|
||
<p><a class="reference internal" href="compute_hma.html"><span class="doc">compute hma</span></a> uses an analytic formulation of the
|
||
Hessian provided by a pair_style’s Pair::single_hessian() function,
|
||
if implemented.</p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The default settings are file = “dynmat.dyn”, binary = no</p>
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</section>
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