554 lines
48 KiB
HTML
554 lines
48 KiB
HTML
<!DOCTYPE html>
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<title>compute pace command — LAMMPS documentation</title>
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<link rel="next" title="compute pair command" href="compute_pair.html" />
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<ul>
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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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</ul>
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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"><a class="reference internal" href="commands_list.html">Commands</a></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 current"><a class="reference internal" href="computes.html">Compute Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_adf.html">compute adf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ave_sphere_atom.html">compute ave/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_spread_atom.html">compute chunk/spread/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-fragment-atom-command">compute fragment/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-aggregate-atom-command">compute aggregate/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cnp_atom.html">compute cnp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_composition_atom.html">compute composition/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_count_type.html">compute count/type command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html">compute dipole command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html#compute-dipole-tip4p-command">compute dipole/tip4p command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html#compute-dipole-tip4p-chunk-command">compute dipole/tip4p/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_edpd_temp_atom.html">compute edpd/temp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_efield_atom.html">compute efield/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_efield_wolf_atom.html">compute efield/wolf/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_entropy_atom.html">compute entropy/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_fabric.html">compute fabric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_fep_ta.html">compute fep/ta command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_global_atom.html">compute global/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape.html">compute gyration/shape command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape_chunk.html">compute gyration/shape/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_hma.html">compute hma command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_mliap.html">compute mliap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_momentum.html">compute momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd.html">compute msd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_nbond_atom.html">compute nbond/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">compute pace 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="#output-info">Output info</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="compute_pair.html">compute pair command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html">compute pod/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-podd-atom-command">compute podd/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-local-command">compute pod/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-global-command">compute pod/global command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure_alchemy.html">compute pressure/alchemy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure_uef.html">compute pressure/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_grid.html">compute property/grid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ptm_atom.html">compute ptm/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rattlers_atom.html">compute rattlers/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reaxff_atom.html">compute reaxff/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce_chunk.html">compute reduce/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rheo_property_atom.html">compute rheo/property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_saed.html">compute saed command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_slcsa_atom.html">compute slcsa/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_slice.html">compute slice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_contact_radius.html">compute smd/contact/radius command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_damage.html">compute smd/damage command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_hourglass_error.html">compute smd/hourglass/error command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_internal_energy.html">compute smd/internal/energy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain.html">compute smd/plastic/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain_rate.html">compute smd/plastic/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_rho.html">compute smd/rho command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_defgrad.html">compute smd/tlsph/defgrad command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_dt.html">compute smd/tlsph/dt command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_num_neighs.html">compute smd/tlsph/num/neighs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_shape.html">compute smd/tlsph/shape command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain.html">compute smd/tlsph/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain_rate.html">compute smd/tlsph/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_stress.html">compute smd/tlsph/stress command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_triangle_vertices.html">compute smd/triangle/vertices command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_effm.html">compute smd/ulsph/effm command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_num_neighs.html">compute smd/ulsph/num/neighs command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain.html">compute smd/ulsph/strain command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain_rate.html">compute smd/ulsph/strain/rate command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_stress.html">compute smd/ulsph/stress command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snav-atom-command">compute snav/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snap-command">compute snap command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-sna-grid-command">compute sna/grid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-sna-grid-local-command">compute sna/grid/local command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sph_e_atom.html">compute sph/e/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sph_rho_atom.html">compute sph/rho/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sph_t_atom.html">compute sph/t/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_spin.html">compute spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html#compute-centroid-stress-atom-command">compute centroid/stress/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_cartesian.html">compute stress/cartesian command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html">compute stress/cylinder command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html#compute-stress-spherical-command">compute stress/spherical command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html">compute stress/mop command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html#compute-stress-mop-profile-command">compute stress/mop/profile command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-virial-tally-command">compute heat/flux/virial/tally command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_tdpd_cc_atom.html">compute tdpd/cc/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_temp_uef.html">compute temp/uef command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_viscosity_cos.html">compute viscosity/cos command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd command</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
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||
</ul>
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||
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||
</div>
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</div>
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<li class="breadcrumb-item active">compute pace command</li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="compute-pace-command">
|
||
<span id="index-0"></span><h1>compute pace command<a class="headerlink" href="#compute-pace-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">compute </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">pace</span><span class="w"> </span><span class="n">ace_potential_filename</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p></li>
|
||
<li><p>pace = style name of this compute command</p></li>
|
||
<li><p>ace_potential_filename = file name (in the .yace or .ace format from <a class="reference internal" href="pair_pace.html"><span class="doc">pace pair_style</span></a>) including ACE hyper-parameters, bonds, and generalized coupling coefficients</p></li>
|
||
<li><p>keyword = <em>bikflag</em> or <em>dgradflag</em></p>
|
||
<pre class="literal-block"><em>bikflag</em> value = <em>0</em> or <em>1</em>
|
||
<em>0</em> = descriptors are summed over atoms of each type
|
||
<em>1</em> = descriptors are listed separately for each atom
|
||
<em>dgradflag</em> value = <em>0</em> or <em>1</em>
|
||
<em>0</em> = descriptor gradients are summed over atoms of each type
|
||
<em>1</em> = descriptor gradients are listed separately for each atom pair</pre>
|
||
</li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">pace</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">pace</span><span class="w"> </span><span class="n">coupling_coefficients.yace</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">pace</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">pace</span><span class="w"> </span><span class="n">coupling_coefficients.yace</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">pace</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">pace</span><span class="w"> </span><span class="n">coupling_coefficients.yace</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</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 7Feb2024.</span></p>
|
||
</div>
|
||
<p>This compute calculates a set of quantities related to the atomic
|
||
cluster expansion (ACE) descriptors of the atoms in a group. ACE
|
||
descriptors are highly general atomic descriptors, encoding the radial
|
||
and angular distribution of neighbor atoms, up to arbitrary bond order
|
||
(rank). The detailed mathematical definition is given in the paper by
|
||
<a class="reference internal" href="#drautz19"><span class="std std-ref">(Drautz)</span></a>. These descriptors are used in the
|
||
<a class="reference internal" href="pair_pace.html"><span class="doc">pace pair_style</span></a>. Quantities obtained from <cite>compute
|
||
pace</cite> are related to those used in <a class="reference internal" href="pair_pace.html"><span class="doc">pace pair_style</span></a> to
|
||
evaluate atomic energies, forces, and stresses for linear ACE models.</p>
|
||
<p>For example, the energy for a linear ACE model is calculated as:
|
||
<span class="math notranslate nohighlight">\(E=\sum_i^{N\_atoms} \sum_{\boldsymbol{\nu}} c_{\boldsymbol{\nu}}
|
||
B_{i,\boldsymbol{\boldsymbol{\nu}}}\)</span>. The ACE descriptors for atom <cite>i</cite>
|
||
<span class="math notranslate nohighlight">\(B_{i,\boldsymbol{\nu}}\)</span>, and <span class="math notranslate nohighlight">\(c_{\nu}\)</span> are linear model
|
||
parameters. The detailed definition and indexing convention for ACE
|
||
descriptors is given in <a class="reference internal" href="#drautz19"><span class="std std-ref">(Drautz)</span></a>. In short, body
|
||
order <span class="math notranslate nohighlight">\(N\)</span>, angular character, radial character, and chemical
|
||
elements in the <em>N-body</em> descriptor are encoded by <span class="math notranslate nohighlight">\(\nu\)</span>. In the
|
||
<a class="reference internal" href="pair_pace.html"><span class="doc">pace pair_style</span></a>, the linear model parameters and the
|
||
ACE descriptors are combined for efficient evaluation of energies and
|
||
forces. The details and benefits of this efficient implementation are
|
||
given in <a class="reference internal" href="#lysogorskiy21"><span class="std std-ref">(Lysogorskiy)</span></a>, but the combined
|
||
descriptors and linear model parameters for the purposes of <cite>compute
|
||
pace</cite> may be expressed in terms of the ACE descriptors mentioned above.</p>
|
||
<p><span class="math notranslate nohighlight">\(c_{\boldsymbol{\nu}} B_{i,\boldsymbol{\nu}}= \sum_{\boldsymbol{\nu}' \in \boldsymbol{\nu} } \big[ c_{\boldsymbol{\nu}} C(\boldsymbol{\nu}') \big] A_{i,\boldsymbol{\nu}'}\)</span></p>
|
||
<p>where the bracketed terms on the right-hand side are the combined functions
|
||
with linear model parameters typically provided in the <cite><name>.yace</cite> potential
|
||
file for <cite>pace pair_style</cite>. When these bracketed terms are multiplied by the
|
||
products of the atomic base from <a class="reference internal" href="#drautz19"><span class="std std-ref">(Drautz)</span></a>,
|
||
<span class="math notranslate nohighlight">\(A_{i,\boldsymbol{\nu'}}\)</span>, the ACE descriptors are recovered but they
|
||
are also scaled by linear model parameters. The generalized coupling coefficients,
|
||
written in short-hand here as <span class="math notranslate nohighlight">\(C(\boldsymbol{\nu}')\)</span>, are the generalized
|
||
Clebsch-Gordan or generalized Wigner symbols. It may be desirable to reverse the
|
||
combination of these descriptors and the linear model parameters so that the
|
||
ACE descriptors themselves may be used. The ACE descriptors and their gradients
|
||
are often used when training ACE models, performing custom data analysis,
|
||
generalizing ACE model forms, and other tasks that involve direct computation of
|
||
descriptors. The key utility of <cite>compute pace</cite> is that it can compute the ACE
|
||
descriptors and gradients so that these tasks can be performed during a LAMMPS
|
||
simulation or so that LAMMPS can be used as a driver for tasks like ACE model
|
||
parameterization. To see how this command can be used within a Python workflow
|
||
to train ACE potentials, see the examples in
|
||
<a class="reference external" href="https://github.com/FitSNAP/FitSNAP">FitSNAP</a>. Examples on using outputs from
|
||
this compute to construct general ACE potential forms are demonstrated in
|
||
<a class="reference internal" href="#goff23"><span class="std std-ref">(Goff)</span></a>. The various keywords and inputs to <cite>compute pace</cite>
|
||
determine what ACE descriptors and related quantities are returned in a compute
|
||
array.</p>
|
||
<p>The coefficient file, <cite><name>.yace</cite>, ultimately defines the number of ACE
|
||
descriptors to be computed, their maximum body-order, the degree of angular
|
||
character they have, the degree of radial character they have, the chemical
|
||
character (which element-element interactions are encoded by descriptors),
|
||
and other hyper-parameters defined in <a class="reference internal" href="#drautz19"><span class="std std-ref">(Drautz)</span></a>. These may
|
||
be modeled after the potential files in <a class="reference internal" href="pair_pace.html"><span class="doc">pace pair_style</span></a>,
|
||
and have the same format. Details on how to generate the coefficient files
|
||
to train ACE models may be found in <a class="reference external" href="https://github.com/FitSNAP/FitSNAP">FitSNAP</a>.</p>
|
||
<p>The keyword <em>bikflag</em> determines whether or not to list the descriptors of
|
||
each atom separately, or sum them together and list in a single row. If
|
||
<em>bikflag</em> is set to <em>0</em> then a single descriptor row is used, which contains
|
||
the per-atom ACE descriptors <span class="math notranslate nohighlight">\(B_{i,\boldsymbol{\nu}}\)</span> summed over all
|
||
atoms <em>i</em> to produce <span class="math notranslate nohighlight">\(B_{\boldsymbol{\nu}}\)</span>. If <em>bikflag</em> is set to
|
||
<em>1</em> this is replaced by a separate per-atom ACE descriptor row for each atom.
|
||
In this case, the entries in the final column for these rows are set to zero.</p>
|
||
<p>The keyword <em>dgradflag</em> determines whether to sum atom gradients or list
|
||
them separately. If <em>dgradflag</em> is set to 0, the ACE
|
||
descriptor gradients w.r.t. atom <em>j</em> are summed over all atoms <em>i’</em>
|
||
of, which may be useful when training linear ACE models on atomic forces.
|
||
If <em>dgradflag</em> is set to 1, gradients are listed separately for each pair of atoms.
|
||
Each row corresponds
|
||
to a single term <span class="math notranslate nohighlight">\(\frac{\partial {B_{i,\boldsymbol{\nu}}}}{\partial {r}^a_j}\)</span>
|
||
where <span class="math notranslate nohighlight">\({r}^a_j\)</span> is the <em>a-th</em> position coordinate of the atom with global
|
||
index <em>j</em>. This also changes the number of columns to be equal to the number of
|
||
ACE descriptors, with 3 additional columns representing the indices <span class="math notranslate nohighlight">\(i\)</span>,
|
||
<span class="math notranslate nohighlight">\(j\)</span>, and <span class="math notranslate nohighlight">\(a\)</span>, as explained more in the Output info section below.
|
||
The option <em>dgradflag=1</em> requires that <em>bikflag=1</em>.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>It is noted here that in contrast to <a class="reference internal" href="pair_pace.html"><span class="doc">pace pair_style</span></a>,
|
||
the <em>.yace</em> file for <cite>compute pace</cite> typically should not contain linear
|
||
parameters for an ACE potential. If <span class="math notranslate nohighlight">\(c_{\nu}\)</span> are included,
|
||
the value of the descriptor will not be returned in the <cite>compute</cite> array,
|
||
but instead, the energy contribution from that descriptor will be returned.
|
||
Do not do this unless it is the desired behavior.
|
||
<em>In short, you should not plug in a ‘.yace’ for a pace potential into this
|
||
compute to evaluate descriptors.</em></p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p><em>Generalized Clebsch-Gordan or Generalized Wigner symbols (with appropriate
|
||
factors) must be used to evaluate ACE descriptors with this compute.</em> There
|
||
are multiple ways to define the generalized coupling coefficients. Because
|
||
of this, this compute will not revert your potential file to a coupling
|
||
coefficient file. Instead this compute allows the user to supply coupling
|
||
coefficients that follow any convention.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Using <em>dgradflag</em> = 1 produces a global array with <span class="math notranslate nohighlight">\(N + 3N^2 + 1\)</span> rows
|
||
which becomes expensive for systems with more than 1000 atoms.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you have a bonded system, then the settings of <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command can remove pairwise interactions between
|
||
atoms in the same bond, angle, or dihedral. This is the default
|
||
setting for the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command, and
|
||
means those pairwise interactions do not appear in the neighbor list.
|
||
Because this fix uses the neighbor list, it also means those pairs
|
||
will not be included in the calculation. One way to get around this,
|
||
is to write a dump file, and use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to
|
||
compute the ACE descriptors for snapshots in the dump file.
|
||
The rerun script can use a <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
|
||
command that includes all pairs in the neighbor list.</p>
|
||
</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="output-info">
|
||
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
|
||
<p>Compute <em>pace</em> evaluates a global array. The columns are arranged into
|
||
<em>ntypes</em> blocks, listed in order of atom type <em>I</em>. Each block contains
|
||
one column for each ACE descriptor, the same as for compute
|
||
<em>sna/atom</em>in <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snap</span></a>. A final column contains the corresponding energy, force
|
||
component on an atom, or virial stress component. The rows of the array
|
||
appear in the following order:</p>
|
||
<ul class="simple">
|
||
<li><p>1 row: <em>pace</em> average descriptor values for all atoms of type <em>I</em></p></li>
|
||
<li><p>3*<em>n</em> force rows: quantities, with derivatives w.r.t. x, y, and z coordinate of atom <em>i</em> appearing in consecutive rows. The atoms are sorted based on atom ID and run up to the total number of atoms, <em>n</em>.</p></li>
|
||
<li><p>6 rows: <em>virial</em> quantities summed for all atoms of type <em>I</em></p></li>
|
||
</ul>
|
||
<p>For example, if <span class="math notranslate nohighlight">\(\# \; B_{i, \boldsymbol{\nu}}\)</span> =30 and ntypes=1, the number of columns in the
|
||
The number of columns in the global array generated by <em>pace</em> are 31, and
|
||
931, respectively, while the number of rows is 1+3*<em>n</em>+6, where <em>n</em>
|
||
is the total number of atoms.</p>
|
||
<p>If the <em>bik</em> keyword is set to 1, the structure of the pace array is expanded.
|
||
The first <span class="math notranslate nohighlight">\(N\)</span> rows of the pace array
|
||
correspond to <span class="math notranslate nohighlight">\(\# \; B_{i,\boldsymbol{\nu}}\)</span> instead of a single row summed over atoms <span class="math notranslate nohighlight">\(i\)</span>.
|
||
In this case, the entries in the final column for these rows
|
||
are set to zero. Also, each row contains only non-zero entries for the
|
||
columns corresponding to the type of that atom. This is not true in the case
|
||
of <em>dgradflag</em> keyword = 1 (see below).</p>
|
||
<p>If the <em>dgradflag</em> keyword is set to 1, this changes the structure of the
|
||
global array completely.
|
||
Here the per-atom quantities are replaced with rows corresponding to
|
||
descriptor gradient components on single atoms:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\frac{\partial {B_{i,\boldsymbol{\nu}} }}{\partial {r}^a_j}\]</div>
|
||
<p>where <span class="math notranslate nohighlight">\({r}^a_j\)</span> is the <em>a-th</em> position coordinate of the atom with global
|
||
index <em>j</em>. The rows are
|
||
organized in chunks, where each chunk corresponds to an atom with global index
|
||
<span class="math notranslate nohighlight">\(j\)</span>. The rows in an atom <span class="math notranslate nohighlight">\(j\)</span> chunk correspond to
|
||
atoms with global index <span class="math notranslate nohighlight">\(i\)</span>. The total number of rows for
|
||
these descriptor gradients is therefore <span class="math notranslate nohighlight">\(3N^2\)</span>.
|
||
The number of columns is equal to the number of ACE descriptors,
|
||
plus 3 additional left-most columns representing the global atom indices
|
||
<span class="math notranslate nohighlight">\(i\)</span>, <span class="math notranslate nohighlight">\(j\)</span>,
|
||
and Cartesian direction <span class="math notranslate nohighlight">\(a\)</span> (0, 1, 2, for x, y, z).
|
||
The first 3 columns of the first <span class="math notranslate nohighlight">\(N\)</span> rows belong to the reference
|
||
potential force components. The remaining K columns contain the
|
||
<span class="math notranslate nohighlight">\(B_{i,\boldsymbol{\nu}}\)</span> per-atom descriptors corresponding to the non-zero entries
|
||
obtained when <em>bikflag</em> = 1.
|
||
The first column of the last row, after the first
|
||
<span class="math notranslate nohighlight">\(N + 3N^2\)</span> rows, contains the reference potential
|
||
energy. The virial components are not used with this option. The total number of
|
||
rows is therefore <span class="math notranslate nohighlight">\(N + 3N^2 + 1\)</span> and the number of columns is <span class="math notranslate nohighlight">\(K + 3\)</span>.</p>
|
||
<p>These values can be accessed by any command that uses global values
|
||
from a compute as input. See the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> doc
|
||
page for an overview of LAMMPS output options.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>These computes are part of the ML-PACE package. They are 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_pace.html"><span class="doc">pair_style pace</span></a>
|
||
<a class="reference internal" href="pair_snap.html"><span class="doc">pair_style snap</span></a>
|
||
<a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snap</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The optional keyword defaults are <em>bikflag</em> = 0,
|
||
<em>dgradflag</em> = 0</p>
|
||
<hr class="docutils" />
|
||
<p id="drautz19"><strong>(Drautz)</strong> Drautz, Phys Rev B, 99, 014104 (2019).</p>
|
||
<p id="lysogorskiy21"><strong>(Lysogorskiy)</strong> Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).</p>
|
||
<p id="goff23"><strong>(Goff)</strong> Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).</p>
|
||
</section>
|
||
</section>
|
||
|
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