467 lines
42 KiB
HTML
467 lines
42 KiB
HTML
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<title>compute slcsa/atom command — LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<div class="lammps_release">git info: </div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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</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"><a class="reference internal" href="compute_pace.html">compute pace command</a></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 current"><a class="current reference internal" href="#">compute slcsa/atom 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_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>
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_sph_t_atom.html">compute sph/t/atom command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_spin.html">compute spin command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
|
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<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>
|
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<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>
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<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html#compute-stress-spherical-command">compute stress/spherical command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html">compute stress/mop command</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="compute_tdpd_cc_atom.html">compute tdpd/cc/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_uef.html">compute temp/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_viscosity_cos.html">compute viscosity/cos command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd 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="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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<li class="breadcrumb-item active">compute slcsa/atom 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>
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<section id="compute-slcsa-atom-command">
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<span id="index-0"></span><h1>compute slcsa/atom command<a class="headerlink" href="#compute-slcsa-atom-command" title="Link to this heading"></a></h1>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">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">slcsa</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">twojmax</span><span class="w"> </span><span class="n">nclasses</span><span class="w"> </span><span class="n">db_mean_descriptor_file</span><span class="w"> </span><span class="n">lda_file</span><span class="w"> </span><span class="n">lr_decision_file</span><span class="w"> </span><span class="n">lr_bias_file</span><span class="w"> </span><span class="n">maha_file</span><span class="w"> </span><span class="n">value</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li><p>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p></li>
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<li><p>slcsa/atom = style name of this compute command</p></li>
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<li><p>twojmax = band limit for bispectrum components (non-negative integer)</p></li>
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<li><p>nclasses = number of crystal structures used in the database for the classifier SL-CSA</p></li>
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<li><p>db_mean_descriptor_file = file name of file containing the database mean descriptor</p></li>
|
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<li><p>lda_file = file name of file containing the linear discriminant analysis matrix for dimension reduction</p></li>
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<li><p>lr_decision_file = file name of file containing the scaling matrix for logistic regression classification</p></li>
|
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<li><p>lr_bias_file = file name of file containing the bias vector for logistic regression classification</p></li>
|
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<li><p>maha_file = file name of file containing for each crystal structure: the Mahalanobis distance threshold for sanity check purposes, the average reduced descriptor and the inverse of the corresponding covariance matrix</p></li>
|
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<li><p>c_ID[*] = compute ID of previously required <em>compute sna/atom</em> command</p></li>
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</ul>
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</section>
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<section id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">b1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">sna</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">9.0</span><span class="w"> </span><span class="m">0.99363</span><span class="w"> </span><span class="m">8</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">rmin0</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="n">nnn</span><span class="w"> </span><span class="m">24</span><span class="w"> </span><span class="n">wmode</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">delta</span><span class="w"> </span><span class="m">0.3</span>
|
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<span class="k">compute </span><span class="nv nv-Identifier">b2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">slcsa</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">8</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="n">mean_descriptors.dat</span><span class="w"> </span><span class="n">lda_scalings.dat</span><span class="w"> </span><span class="n">lr_decision.dat</span><span class="w"> </span><span class="n">lr_bias.dat</span><span class="w"> </span><span class="n">maha_thresholds.dat</span><span class="w"> </span><span class="n">c_b1[</span><span class="o">*</span><span class="n">]</span>
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</pre></div>
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</div>
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</section>
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<section id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
|
<div class="versionadded">
|
|
<p><span class="versionmodified added">Added in version 7Feb2024.</span></p>
|
|
</div>
|
|
<p>Define a computation that performs the Supervised Learning Crystal
|
|
Structure Analysis (SL-CSA) from <a class="reference internal" href="#lafourcade2023-1"><span class="std std-ref">(Lafourcade)</span></a>
|
|
for each atom in the group. The SL-CSA tool takes as an input a per-atom
|
|
descriptor (bispectrum) that is computed through the <em>compute sna/atom</em>
|
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command and then proceeds to a dimension reduction step followed by a
|
|
logistic regression in order to assign a probable crystal structure to
|
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each atom in the group. The SL-CSA tool is pre-trained on a database
|
|
containing <span class="math notranslate nohighlight">\(C\)</span> distinct crystal structures from which a crystal
|
|
structure classifier is derived and a tutorial to build such a tool is
|
|
available at <a class="reference external" href="https://github.com/lafourcadep/SL-CSA">SL-CSA</a>.</p>
|
|
<p>The first step of the SL-CSA tool consists in performing a dimension
|
|
reduction of the per-atom descriptor <span class="math notranslate nohighlight">\(\mathbf{B}^i \in
|
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\mathbb{R}^{D}\)</span> through the Linear Discriminant Analysis (LDA) method,
|
|
leading to a new projected descriptor
|
|
<span class="math notranslate nohighlight">\(\mathbf{x}^i=\mathrm{P}_\mathrm{LDA}(\mathbf{B}^i):\mathbb{R}^D
|
|
\rightarrow \mathbb{R}^{d=C-1}\)</span>:</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[\mathbf{x}^i = \mathbf{C}^T_\mathrm{LDA} \cdot (\mathbf{B}^i - \mu^\mathbf{B}_\mathrm{db})\]</div>
|
|
<p>where <span class="math notranslate nohighlight">\(\mathbf{C}^T_\mathrm{LDA} \in \mathbb{R}^{D \times d}\)</span> is
|
|
the reduction coefficients matrix of the LDA model read in file
|
|
<em>lda_file</em>, <span class="math notranslate nohighlight">\(\mathbf{B}^i \in \mathbb{R}^{D}\)</span> is the bispectrum of
|
|
atom <span class="math notranslate nohighlight">\(i\)</span> and <span class="math notranslate nohighlight">\(\mu^\mathbf{B}_\mathrm{db} \in \mathbb{R}^{D}\)</span>
|
|
is the average descriptor of the entire database. The latter is computed
|
|
from the average descriptors of each crystal structure read from the
|
|
file <em>mean_descriptors_file</em>.</p>
|
|
<p>The new projected descriptor with dimension <span class="math notranslate nohighlight">\(d=C-1\)</span> allows for a
|
|
good separation of different crystal structures fingerprints in the
|
|
latent space.</p>
|
|
<p>Once the dimension reduction step is performed by means of LDA, the new
|
|
descriptor <span class="math notranslate nohighlight">\(\mathbf{x}^i \in \mathbb{R}^{d=C-1}\)</span> is taken as an
|
|
input for performing a multinomial logistic regression (LR) which
|
|
provides a score vector
|
|
<span class="math notranslate nohighlight">\(\mathbf{s}^i=\mathrm{P}_\mathrm{LR}(\mathbf{x}^i):\mathbb{R}^d
|
|
\rightarrow \mathbb{R}^C\)</span> defined as:</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[\mathbf{s}^i = \mathbf{b}_\mathrm{LR} + \mathbf{D}_\mathrm{LR} \cdot {\mathbf{x}^i}^T\]</div>
|
|
<p>with <span class="math notranslate nohighlight">\(\mathbf{b}_\mathrm{LR} \in \mathbb{R}^C\)</span> and
|
|
<span class="math notranslate nohighlight">\(\mathbf{D}_\mathrm{LR} \in \mathbb{R}^{C \times d}\)</span> the bias
|
|
vector and decision matrix of the LR model after training both read in
|
|
files <em>lr_fil1</em> and <em>lr_file2</em> respectively.</p>
|
|
<p>Finally, a probability vector
|
|
<span class="math notranslate nohighlight">\(\mathbf{p}^i=\mathrm{P}_\mathrm{LR}(\mathbf{x}^i):\mathbb{R}^d
|
|
\rightarrow \mathbb{R}^C\)</span> is defined as:</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[\mathbf{p}^i = \frac{\mathrm{exp}(\mathbf{s}^i)}{\sum\limits_{j} \mathrm{exp}(s^i_j) }\]</div>
|
|
<p>from which the crystal structure assigned to each atom with descriptor
|
|
<span class="math notranslate nohighlight">\(\mathbf{B}^i\)</span> and projected descriptor <span class="math notranslate nohighlight">\(\mathbf{x}^i\)</span> is
|
|
computed as the <em>argmax</em> of the probability vector
|
|
<span class="math notranslate nohighlight">\(\mathbf{p}^i\)</span>. Since the logistic regression step systematically
|
|
attributes a crystal structure to each atom, a sanity check is needed to
|
|
avoid misclassification. To this end, a per-atom Mahalanobis distance to
|
|
each crystal structure <em>CS</em> present in the database is computed:</p>
|
|
<div class="math notranslate nohighlight">
|
|
\[d_\mathrm{Mahalanobis}^{i \rightarrow \mathrm{CS}} = \sqrt{(\mathbf{x}^i - \mathbf{\mu}^\mathbf{x}_\mathrm{CS})^\mathrm{T} \cdot \mathbf{\Sigma}^{-1}_\mathrm{CS} \cdot (\mathbf{x}^i - \mathbf{\mu}^\mathbf{x}_\mathrm{CS}) }\]</div>
|
|
<p>where <span class="math notranslate nohighlight">\(\mathbf{\mu}^\mathbf{x}_\mathrm{CS} \in \mathbb{R}^{d}\)</span> is
|
|
the average projected descriptor of crystal structure <em>CS</em> in the
|
|
database and where <span class="math notranslate nohighlight">\(\mathbf{\Sigma}_\mathrm{CS} \in \mathbb{R}^{d
|
|
\times d}\)</span> is the corresponding covariance matrix. Finally, if the
|
|
Mahalanobis distance to crystal structure <em>CS</em> for atom <em>i</em> is greater
|
|
than the pre-determined threshold, no crystal structure is assigned to
|
|
atom <em>i</em>. The Mahalanobis distance thresholds are read in file
|
|
<em>maha_file</em> while the covariance matrices are read in file
|
|
<em>covmat_file</em>.</p>
|
|
<p>The <a class="reference external" href="https://github.com/lafourcadep/SL-CSA">SL-CSA</a> framework provides
|
|
an automatic computation of the different matrices and thresholds
|
|
required for a proper classification and writes down all the required
|
|
files for calling the <em>compute slcsa/atom</em> command.</p>
|
|
<p>The <em>compute slcsa/atom</em> command requires that the <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute
|
|
sna/atom</span></a> command is called before as it takes the
|
|
resulting per-atom bispectrum as an input. In addition, it is crucial
|
|
that the value <em>twojmax</em> is set to the same value of the value <em>twojmax</em>
|
|
used in the <em>compute sna/atom</em> command, as well as that the value
|
|
<em>nclasses</em> is set to the number of crystal structures used in the
|
|
database to train the SL-CSA tool.</p>
|
|
</section>
|
|
<section id="output-info">
|
|
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
|
|
<p>By default, this compute computes the Mahalanobis distances to the
|
|
different crystal structures present in the database in addition to
|
|
assigning a crystal structure for each atom as a per-atom vector, which
|
|
can be accessed by any command that uses per-atom values from a compute
|
|
as input. See the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> 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>This compute is part of the EXTRA-COMPUTE 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="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a></p>
|
|
</section>
|
|
<section id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
|
<p>none</p>
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<p id="lafourcade2023-1"><strong>(Lafourcade)</strong> Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica,
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<a class="reference external" href="https://doi.org/10.1016/j.commatsci.2023.112534">Comp. Mat. Science, 230, 112534 (2023)</a></p>
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