681 lines
45 KiB
HTML
681 lines
45 KiB
HTML
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<title>fitpod command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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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 current"><a class="current reference internal" href="#">fitpod 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="#pod-potential">POD Potential</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#training">Training</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#validation">Validation</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="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>
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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="prd.html">prd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_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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</ul>
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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>
|
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<section id="fitpod-command">
|
|
<span id="index-0"></span><h1>fitpod command<a class="headerlink" href="#fitpod-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">fitpod</span><span class="w"> </span><span class="n">Ta_param.pod</span><span class="w"> </span><span class="n">Ta_data.pod</span><span class="w"> </span><span class="n">Ta_coefficients.pod</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li><p>fitpod = style name of this command</p></li>
|
|
<li><p>Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)</p></li>
|
|
<li><p>Ta_data.pod = an input file that specifies DFT data used to fit a POD potential</p></li>
|
|
<li><p>Ta_coefficients.pod (optional) = an input file that specifies trainable coefficients of a POD potential</p></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">fitpod</span><span class="w"> </span><span class="n">Ta_param.pod</span><span class="w"> </span><span class="n">Ta_data.pod</span>
|
|
<span class="k">fitpod</span><span class="w"> </span><span class="n">Ta_param.pod</span><span class="w"> </span><span class="n">Ta_data.pod</span><span class="w"> </span><span class="n">Ta_coefficients.pod</span>
|
|
</pre></div>
|
|
</div>
|
|
</section>
|
|
<section id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
|
<div class="versionadded">
|
|
<p><span class="versionmodified added">Added in version 22Dec2022.</span></p>
|
|
</div>
|
|
<p>Fit a machine-learning interatomic potential (ML-IAP) based on proper
|
|
orthogonal descriptors (POD); please see <a class="reference internal" href="#nguyen20222a"><span class="std std-ref">(Nguyen and Rohskopf)</span></a>, <a class="reference internal" href="#nguyen20232a"><span class="std std-ref">(Nguyen2023)</span></a>, <a class="reference internal" href="#nguyen20242a"><span class="std std-ref">(Nguyen2024)</span></a>, and <a class="reference internal" href="#nguyen20243a"><span class="std std-ref">(Nguyen and Sema)</span></a> for details.
|
|
The fitted POD potential can be used to run MD simulations via
|
|
<a class="reference internal" href="pair_pod.html"><span class="doc">pair_style pod</span></a>.</p>
|
|
<p>Two input files are required for this command. The first input file
|
|
describes a POD potential parameter settings, while the second input
|
|
file specifies the DFT data used for the fitting procedure. All keywords
|
|
except <em>species</em> have default values. If a keyword is not set in the
|
|
input file, its default value is used. The table below has one-line
|
|
descriptions of all the keywords that can be used in the first input
|
|
file (i.e. <code class="docutils literal notranslate"><span class="pre">Ta_param.pod</span></code>)</p>
|
|
<table class="docutils align-default">
|
|
<colgroup>
|
|
<col style="width: 40.0%" />
|
|
<col style="width: 9.0%" />
|
|
<col style="width: 10.0%" />
|
|
<col style="width: 41.0%" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr class="row-odd"><th class="head"><p>Keyword</p></th>
|
|
<th class="head"><p>Default</p></th>
|
|
<th class="head"><p>Type</p></th>
|
|
<th class="head"><p>Description</p></th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr class="row-even"><td><p>species</p></td>
|
|
<td><p>(none)</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>Chemical symbols for all elements in the system and have to match XYZ training files.</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>pbc</p></td>
|
|
<td><p>1 1 1</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>three integer constants specify boundary conditions</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>rin</p></td>
|
|
<td><p>0.5</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real number specifies the inner cut-off radius</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>rcut</p></td>
|
|
<td><p>5.0</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real number specifies the outer cut-off radius</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>bessel_polynomial_degree</p></td>
|
|
<td><p>4</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>the maximum degree of Bessel polynomials</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>inverse_polynomial_degree</p></td>
|
|
<td><p>8</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>the maximum degree of inverse radial basis functions</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>number_of_environment_clusters</p></td>
|
|
<td><p>1</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>the number of clusters for environment-adaptive potentials</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>number_of_principal_components</p></td>
|
|
<td><p>2</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>the number of principal components for dimensionality reduction</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>onebody</p></td>
|
|
<td><p>1</p></td>
|
|
<td><p>BOOL</p></td>
|
|
<td><p>turns on/off one-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>twobody_number_radial_basis_functions</p></td>
|
|
<td><p>8</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of radial basis functions for two-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>threebody_number_radial_basis_functions</p></td>
|
|
<td><p>6</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of radial basis functions for three-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>threebody_angular_degree</p></td>
|
|
<td><p>5</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>angular degree for three-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>fourbody_number_radial_basis_functions</p></td>
|
|
<td><p>4</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of radial basis functions for four-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>fourbody_angular_degree</p></td>
|
|
<td><p>3</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>angular degree for four-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>fivebody_number_radial_basis_functions</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of radial basis functions for five-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>fivebody_angular_degree</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>angular degree for five-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>sixbody_number_radial_basis_functions</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of radial basis functions for six-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>sixbody_angular_degree</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>angular degree for six-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>sevenbody_number_radial_basis_functions</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of radial basis functions for seven-body potential</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>sevenbody_angular_degree</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>angular degree for seven-body potential</p></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>Note that both the number of radial basis functions and angular degree
|
|
must decrease as the body order increases. The next table describes all
|
|
keywords that can be used in the second input file (i.e. <code class="docutils literal notranslate"><span class="pre">Ta_data.pod</span></code>
|
|
in the example above):</p>
|
|
<table class="docutils align-default">
|
|
<colgroup>
|
|
<col style="width: 38.0%" />
|
|
<col style="width: 9.0%" />
|
|
<col style="width: 10.0%" />
|
|
<col style="width: 43.0%" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr class="row-odd"><th class="head"><p>Keyword</p></th>
|
|
<th class="head"><p>Default</p></th>
|
|
<th class="head"><p>Type</p></th>
|
|
<th class="head"><p>Description</p></th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr class="row-even"><td><p>file_format</p></td>
|
|
<td><p>extxyz</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>only the extended xyz format (extxyz) is currently supported</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>file_extension</p></td>
|
|
<td><p>xyz</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>extension of the data files</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>path_to_training_data_set</p></td>
|
|
<td><p>(none)</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>specifies the path to training data files in double quotes</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>path_to_test_data_set</p></td>
|
|
<td><p>“”</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>specifies the path to test data files in double quotes</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>path_to_environment_configuration_set</p></td>
|
|
<td><p>“”</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>specifies the path to environment configuration files in double quotes</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>fraction_training_data_set</p></td>
|
|
<td><p>1.0</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real number (<= 1.0) specifies the fraction of the training set used to fit POD</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>randomize_training_data_set</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>BOOL</p></td>
|
|
<td><p>turns on/off randomization of the training set</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>fraction_test_data_set</p></td>
|
|
<td><p>1.0</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real number (<= 1.0) specifies the fraction of the test set used to validate POD</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>randomize_test_data_set</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>BOOL</p></td>
|
|
<td><p>turns on/off randomization of the test set</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>fitting_weight_energy</p></td>
|
|
<td><p>100.0</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real constant specifies the weight for energy in the least-squares fit</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>fitting_weight_force</p></td>
|
|
<td><p>1.0</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real constant specifies the weight for force in the least-squares fit</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>fitting_regularization_parameter</p></td>
|
|
<td><p>1.0e-10</p></td>
|
|
<td><p>REAL</p></td>
|
|
<td><p>a real constant specifies the regularization parameter in the least-squares fit</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>error_analysis_for_training_data_set</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>BOOL</p></td>
|
|
<td><p>turns on/off error analysis for the training data set</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>error_analysis_for_test_data_set</p></td>
|
|
<td><p>0</p></td>
|
|
<td><p>BOOL</p></td>
|
|
<td><p>turns on/off error analysis for the test data set</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>basename_for_output_files</p></td>
|
|
<td><p>pod</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p>a basename string added to the output files</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>precision_for_pod_coefficients</p></td>
|
|
<td><p>8</p></td>
|
|
<td><p>INT</p></td>
|
|
<td><p>number of digits after the decimal points for numbers in the coefficient file</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>group_weights</p></td>
|
|
<td><p>global</p></td>
|
|
<td><p>STRING</p></td>
|
|
<td><p><code class="docutils literal notranslate"><span class="pre">table</span></code> uses group weights defined for each group named by filename</p></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>All keywords except <em>path_to_training_data_set</em> have default values. If
|
|
a keyword is not set in the input file, its default value is used. After
|
|
successful training, a number of output files are produced, if enabled:</p>
|
|
<ul class="simple">
|
|
<li><p><code class="docutils literal notranslate"><span class="pre"><basename>_training_errors.pod</span></code> reports the errors in energy and forces for the training data set</p></li>
|
|
<li><p><code class="docutils literal notranslate"><span class="pre"><basename>_training_analysis.pod</span></code> reports detailed errors for all training configurations</p></li>
|
|
<li><p><code class="docutils literal notranslate"><span class="pre"><basename>_test_errors.pod</span></code> reports errors for the test data set</p></li>
|
|
<li><p><code class="docutils literal notranslate"><span class="pre"><basename>_test_analysis.pod</span></code> reports detailed errors for all test configurations</p></li>
|
|
<li><p><code class="docutils literal notranslate"><span class="pre"><basename>_coefficients.pod</span></code> contains the coefficients of the POD potential</p></li>
|
|
</ul>
|
|
<p>After training the POD potential, <code class="docutils literal notranslate"><span class="pre">Ta_param.pod</span></code> and
|
|
<code class="docutils literal notranslate"><span class="pre"><basename>_coefficients.pod</span></code> are the two files needed to use the POD
|
|
potential in LAMMPS. See <a class="reference internal" href="pair_pod.html"><span class="doc">pair_style pod</span></a> for using the
|
|
POD potential. Examples about training and using POD potentials are
|
|
found in the directory lammps/examples/PACKAGES/pod and the Github repo
|
|
<a class="reference external" href="https://github.com/cesmix-mit/pod-examples">https://github.com/cesmix-mit/pod-examples</a>.</p>
|
|
<section id="loss-function-group-weights">
|
|
<h3>Loss Function Group Weights<a class="headerlink" href="#loss-function-group-weights" title="Link to this heading"></a></h3>
|
|
<p>The <em>group_weights</em> keyword in the <code class="docutils literal notranslate"><span class="pre">data.pod</span></code> file is responsible for
|
|
weighting certain groups of configurations in the loss function. For
|
|
example:</p>
|
|
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="n">group_weights</span><span class="w"> </span><span class="n">table</span>
|
|
<span class="n">Displaced_A15</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Displaced_BCC</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Displaced_FCC</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Elastic_BCC</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Elastic_FCC</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">GSF_110</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">GSF_112</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Liquid</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Surface</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Volume_A15</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Volume_BCC</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
<span class="n">Volume_FCC</span><span class="w"> </span><span class="m">100.0</span><span class="w"> </span><span class="m">1.0</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>This will apply an energy weight of <code class="docutils literal notranslate"><span class="pre">100.0</span></code> and a force weight of
|
|
<code class="docutils literal notranslate"><span class="pre">1.0</span></code> for all groups in the <code class="docutils literal notranslate"><span class="pre">Ta</span></code> example. The groups are named by
|
|
their respective filename. If certain groups are left out of this table,
|
|
then the globally defined weights from the <code class="docutils literal notranslate"><span class="pre">fitting_weight_energy</span></code> and
|
|
<code class="docutils literal notranslate"><span class="pre">fitting_weight_force</span></code> keywords will be used.</p>
|
|
</section>
|
|
</section>
|
|
<section id="pod-potential">
|
|
<h2>POD Potential<a class="headerlink" href="#pod-potential" title="Link to this heading"></a></h2>
|
|
<p>We consider a multi-element system of <em>N</em> atoms with <span class="math notranslate nohighlight">\(N_{\rm e}\)</span>
|
|
unique elements. We denote by <span class="math notranslate nohighlight">\(\boldsymbol r_n\)</span> and <span class="math notranslate nohighlight">\(Z_n\)</span>
|
|
position vector and type of an atom <em>n</em> in the system,
|
|
respectively. Note that we have <span class="math notranslate nohighlight">\(Z_n \in \{1, \ldots, N_{\rm e}
|
|
\}\)</span>, <span class="math notranslate nohighlight">\(\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
|
|
\boldsymbol r_N) \in \mathbb{R}^{3N}\)</span>, and <span class="math notranslate nohighlight">\(\boldsymbol Z = (Z_1,
|
|
Z_2, \ldots, Z_N) \in \mathbb{N}^{N}\)</span>. The total energy of the
|
|
POD potential is expressed as <span class="math notranslate nohighlight">\(E(\boldsymbol R, \boldsymbol Z) =
|
|
\sum_{i=1}^N E_i(\boldsymbol R_i, \boldsymbol Z_i)\)</span>, where</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[E_i(\boldsymbol R_i, \boldsymbol Z_i) \ = \ \sum_{m=1}^M c_m \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)\]</div>
|
|
<p>Here <span class="math notranslate nohighlight">\(c_m\)</span> are trainable coefficients and
|
|
<span class="math notranslate nohighlight">\(\mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)\)</span> are per-atom
|
|
POD descriptors. Summing the per-atom descriptors over <span class="math notranslate nohighlight">\(i\)</span> yields
|
|
the global descriptors <span class="math notranslate nohighlight">\(d_m(\boldsymbol R, \boldsymbol Z) =
|
|
\sum_{i=1}^N \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)\)</span>. It
|
|
thus follows that <span class="math notranslate nohighlight">\(E(\boldsymbol R, \boldsymbol Z) = \sum_{m=1}^M
|
|
c_m d_m(\boldsymbol R, \boldsymbol Z)\)</span>.</p>
|
|
<p>The per-atom POD descriptors include one, two, three, four, five, six,
|
|
and seven-body descriptors, which can be specified in the first input
|
|
file. Furthermore, the per-atom POD descriptors also depend on the
|
|
number of environment clusters specified in the first input file.
|
|
Please see <a class="reference internal" href="#nguyen20242a"><span class="std std-ref">(Nguyen2024)</span></a> and <a class="reference internal" href="#nguyen20243a"><span class="std std-ref">(Nguyen and Sema)</span></a> for the detailed description of the per-atom POD
|
|
descriptors.</p>
|
|
</section>
|
|
<section id="training">
|
|
<h2>Training<a class="headerlink" href="#training" title="Link to this heading"></a></h2>
|
|
<p>A POD potential is trained using the least-squares regression against
|
|
density functional theory (DFT) data. Let <span class="math notranslate nohighlight">\(J\)</span> be the number of
|
|
training configurations, with <span class="math notranslate nohighlight">\(N_j\)</span> being the number of atoms in
|
|
the j-th configuration. The training configurations are extracted from
|
|
the extended XYZ files located in a directory (i.e.,
|
|
path_to_training_data_set in the second input file). Let
|
|
<span class="math notranslate nohighlight">\(\{E^{\star}_j\}_{j=1}^{J}\)</span> and <span class="math notranslate nohighlight">\(\{\boldsymbol
|
|
F^{\star}_j\}_{j=1}^{J}\)</span> be the DFT energies and forces for <span class="math notranslate nohighlight">\(J\)</span>
|
|
configurations. Next, we calculate the global descriptors and their
|
|
derivatives for all training configurations. Let <span class="math notranslate nohighlight">\(d_{jm}, 1 \le m
|
|
\le M\)</span>, be the global descriptors associated with the j-th
|
|
configuration, where <span class="math notranslate nohighlight">\(M\)</span> is the number of global descriptors. We
|
|
then form a matrix <span class="math notranslate nohighlight">\(\boldsymbol A \in \mathbb{R}^{J \times M}\)</span>
|
|
with entries <span class="math notranslate nohighlight">\(A_{jm} = d_{jm}/ N_j\)</span> for <span class="math notranslate nohighlight">\(j=1,\ldots,J\)</span> and
|
|
<span class="math notranslate nohighlight">\(m=1,\ldots,M\)</span>. Moreover, we form a matrix <span class="math notranslate nohighlight">\(\boldsymbol B
|
|
\in \mathbb{R}^{\mathcal{N} \times M}\)</span> by stacking the derivatives of
|
|
the global descriptors for all training configurations from top to
|
|
bottom, where <span class="math notranslate nohighlight">\(\mathcal{N} = 3\sum_{j=1}^{J} N_j\)</span>.</p>
|
|
<p>The coefficient vector <span class="math notranslate nohighlight">\(\boldsymbol c\)</span> of the POD potential is
|
|
found by solving the following least-squares problem</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[{\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,\]</div>
|
|
<p>where <span class="math notranslate nohighlight">\(w_E\)</span> and <span class="math notranslate nohighlight">\(w_F\)</span> are weights for the energy
|
|
(<em>fitting_weight_energy</em>) and force (<em>fitting_weight_force</em>),
|
|
respectively; and <span class="math notranslate nohighlight">\(w_R\)</span> is the regularization parameter
|
|
(<em>fitting_regularization_parameter</em>). Here <span class="math notranslate nohighlight">\(\bar{\boldsymbol
|
|
E}^{\star} \in \mathbb{R}^{J}\)</span> is a vector of with entries
|
|
<span class="math notranslate nohighlight">\(\bar{E}^{\star}_j = E^{\star}_j/N_j\)</span> and <span class="math notranslate nohighlight">\(\boldsymbol
|
|
F^{\star}\)</span> is a vector of <span class="math notranslate nohighlight">\(\mathcal{N}\)</span> entries obtained by
|
|
stacking <span class="math notranslate nohighlight">\(\{\boldsymbol F^{\star}_j\}_{j=1}^{J}\)</span> from top to
|
|
bottom.</p>
|
|
</section>
|
|
<section id="validation">
|
|
<h2>Validation<a class="headerlink" href="#validation" title="Link to this heading"></a></h2>
|
|
<p>POD potential can be validated on a test dataset in a directory
|
|
specified by setting path_to_test_data_set in the second input file. It
|
|
is possible to validate the POD potential after the training is
|
|
complete. This is done by providing the coefficient file as an input to
|
|
<a class="reference internal" href="#"><span class="doc">fitpod</span></a>, for example,</p>
|
|
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fitpod</span><span class="w"> </span><span class="n">Ta_param.pod</span><span class="w"> </span><span class="n">Ta_data.pod</span><span class="w"> </span><span class="n">Ta_coefficients.pod</span>
|
|
</pre></div>
|
|
</div>
|
|
</section>
|
|
<section id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
|
<p>This command is part of the ML-POD 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="pair_pod.html"><span class="doc">pair_style pod</span></a>,
|
|
<a class="reference internal" href="compute_pod_atom.html"><span class="doc">compute pod/atom</span></a>,
|
|
<a class="reference internal" href="compute_pod_atom.html"><span class="doc">compute podd/atom</span></a>,
|
|
<a class="reference internal" href="compute_pod_atom.html"><span class="doc">compute pod/local</span></a>,
|
|
<a class="reference internal" href="compute_pod_atom.html"><span class="doc">compute pod/global</span></a></p>
|
|
</section>
|
|
<section id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
|
<p>The keyword defaults are also given in the description of the input files.</p>
|
|
<hr class="docutils" />
|
|
<p id="nguyen20222a"><strong>(Nguyen and Rohskopf)</strong> Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).</p>
|
|
<p id="nguyen20232a"><strong>(Nguyen2023)</strong> Nguyen, Physical Review B, 107(14), 144103, (2023).</p>
|
|
<p id="nguyen20242a"><strong>(Nguyen2024)</strong> Nguyen, Journal of Computational Physics, 113102, (2024).</p>
|
|
<p id="nguyen20243a"><strong>(Nguyen and Sema)</strong> Nguyen and Sema, <a class="reference external" href="https://arxiv.org/abs/2405.00306">https://arxiv.org/abs/2405.00306</a>, (2024).</p>
|
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</section>
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