593 lines
56 KiB
HTML
593 lines
56 KiB
HTML
<!DOCTYPE html>
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<head>
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<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>compute stress/atom command — LAMMPS documentation</title>
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<link rel="canonical" href="https://docs.lammps.org/compute_stress_atom.html" />
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="next" title="compute stress/cartesian command" href="compute_stress_cartesian.html" />
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<a href="Manual.html">
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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</a>
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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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<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"><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"><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>
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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>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
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<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 current"><a class="current reference internal" href="#">compute stress/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="#compute-centroid-stress-atom-command">compute centroid/stress/atom command</a><ul>
|
||
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#output-info">Output info</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
|
||
</ul>
|
||
</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>
|
||
</ul>
|
||
|
||
</div>
|
||
</div>
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||
</nav>
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||
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<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
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<a href="Manual.html">LAMMPS</a>
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</nav>
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<div class="wy-nav-content">
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<div class="rst-content style-external-links">
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<div role="navigation" aria-label="Page navigation">
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
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<li class="breadcrumb-item"><a href="computes.html">Compute Styles</a></li>
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<li class="breadcrumb-item active">compute stress/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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</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
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<a href="compute_spin.html" class="btn btn-neutral float-left" title="compute spin command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<hr/>
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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-stress-atom-command">
|
||
<span id="index-1"></span><span id="index-0"></span><h1>compute stress/atom command<a class="headerlink" href="#compute-stress-atom-command" title="Link to this heading"></a></h1>
|
||
</section>
|
||
<section id="compute-centroid-stress-atom-command">
|
||
<h1>compute centroid/stress/atom command<a class="headerlink" href="#compute-centroid-stress-atom-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">style</span><span class="w"> </span><span class="n">temp</span><span class="o">-</span><span class="n">ID</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul class="simple">
|
||
<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>style = <em>stress/atom</em> or <em>centroid/stress/atom</em></p></li>
|
||
<li><p>temp-ID = ID of compute that calculates temperature, can be NULL if not needed</p></li>
|
||
<li><p>zero or more keywords may be appended</p></li>
|
||
<li><p>keyword = <em>ke</em> or <em>pair</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>kspace</em> or <em>fix</em> or <em>virial</em></p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">mobile</span><span class="w"> </span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">NULL</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">mobile</span><span class="w"> </span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">myRamp</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">NULL</span><span class="w"> </span><span class="n">pair</span><span class="w"> </span><span class="n">bond</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">centroid</span><span class="o">/</span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">NULL</span><span class="w"> </span><span class="n">bond</span><span class="w"> </span><span class="n">dihedral</span><span class="w"> </span><span class="n">improper</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Define a computation that computes per-atom stress tensor for each
|
||
atom in a group. In case of compute <em>stress/atom</em>, the tensor for
|
||
each atom is symmetric with 6 components and is stored as a 6-element
|
||
vector in the following order: <span class="math notranslate nohighlight">\(xx\)</span>, <span class="math notranslate nohighlight">\(yy\)</span>, <span class="math notranslate nohighlight">\(zz\)</span>,
|
||
<span class="math notranslate nohighlight">\(xy\)</span>, <span class="math notranslate nohighlight">\(xz\)</span>, <span class="math notranslate nohighlight">\(yz\)</span>. In case of compute
|
||
<em>centroid/stress/atom</em>, the tensor for each atom is asymmetric with 9
|
||
components and is stored as a 9-element vector in the following order:
|
||
<span class="math notranslate nohighlight">\(xx\)</span>, <span class="math notranslate nohighlight">\(yy\)</span>, <span class="math notranslate nohighlight">\(zz\)</span>, <span class="math notranslate nohighlight">\(xy\)</span>, <span class="math notranslate nohighlight">\(xz\)</span>,
|
||
<span class="math notranslate nohighlight">\(yz\)</span>, <span class="math notranslate nohighlight">\(yx\)</span>, <span class="math notranslate nohighlight">\(zx\)</span>, <span class="math notranslate nohighlight">\(zy\)</span>. See the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute
|
||
pressure</span></a> command if you want the stress tensor
|
||
(pressure) of the entire system.</p>
|
||
<p>The stress tensor for atom <span class="math notranslate nohighlight">\(I\)</span> is given by the following
|
||
formula, where <span class="math notranslate nohighlight">\(a\)</span> and <span class="math notranslate nohighlight">\(b\)</span> take on values <span class="math notranslate nohighlight">\(x\)</span>,
|
||
<span class="math notranslate nohighlight">\(y\)</span>, <span class="math notranslate nohighlight">\(z\)</span> to generate the components of the tensor:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[S_{ab} = - m v_a v_b - W_{ab}\]</div>
|
||
<p>The first term is a kinetic energy contribution for atom <span class="math notranslate nohighlight">\(I\)</span>.
|
||
See details below on how the specified <em>temp-ID</em> can affect the
|
||
velocities used in this calculation. The second term is the virial
|
||
contribution due to intra and intermolecular interactions, where the
|
||
exact computation details are determined by the compute style.</p>
|
||
<p>In case of compute <em>stress/atom</em>, the virial contribution is:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\begin{split} W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) \\
|
||
& + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
|
||
& + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}\end{split}\]</div>
|
||
<p>The first term is a pairwise energy contribution where <span class="math notranslate nohighlight">\(n\)</span> loops
|
||
over the <span class="math notranslate nohighlight">\(N_p\)</span> neighbors of atom <span class="math notranslate nohighlight">\(I\)</span>, <span class="math notranslate nohighlight">\(\mathbf{r}_1\)</span>
|
||
and <span class="math notranslate nohighlight">\(\mathbf{r}_2\)</span> are the positions of the two atoms in the
|
||
pairwise interaction, and <span class="math notranslate nohighlight">\(\mathbf{F}_1\)</span> and
|
||
<span class="math notranslate nohighlight">\(\mathbf{F}_2\)</span> are the forces on the two atoms resulting from the
|
||
pairwise interaction. The second term is a bond contribution of
|
||
similar form for the <span class="math notranslate nohighlight">\(N_b\)</span> bonds which atom <span class="math notranslate nohighlight">\(I\)</span> is part
|
||
of. There are similar terms for the <span class="math notranslate nohighlight">\(N_a\)</span> angle, <span class="math notranslate nohighlight">\(N_d\)</span>
|
||
dihedral, and <span class="math notranslate nohighlight">\(N_i\)</span> improper interactions atom <span class="math notranslate nohighlight">\(I\)</span> is part
|
||
of. There is also a term for the KSpace contribution from long-range
|
||
Coulombic interactions, if defined. Finally, there is a term for the
|
||
<span class="math notranslate nohighlight">\(N_f\)</span> <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> that apply internal constraint forces
|
||
to atom <span class="math notranslate nohighlight">\(I\)</span>. Currently, only the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>
|
||
and <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> commands contribute to this term. As
|
||
the coefficients in the formula imply, a virial contribution produced
|
||
by a small set of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a
|
||
Tersoff 3-body interaction) is assigned in equal portions to each atom
|
||
in the set. E.g. 1/4 of the dihedral virial to each of the 4 atoms,
|
||
or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
|
||
a water molecule via the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command.
|
||
As an exception, the virial contribution from
|
||
constraint forces in <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> on each atom
|
||
is computed from the constraint force acting on the corresponding atom
|
||
and its position, i.e. the total virial is not equally distributed.</p>
|
||
<p>In case of compute <em>centroid/stress/atom</em>, the virial contribution is:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\begin{split} W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
|
||
& + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}\end{split}\]</div>
|
||
<p>As with compute <em>stress/atom</em>, the first, second, third, fourth and
|
||
fifth terms are pairwise, bond, angle, dihedral and improper
|
||
contributions, but instead of assigning the virial contribution
|
||
equally to each atom, only the force <span class="math notranslate nohighlight">\(\mathbf{F}_I\)</span> acting on
|
||
atom <span class="math notranslate nohighlight">\(I\)</span> due to the interaction and the relative position
|
||
<span class="math notranslate nohighlight">\(\mathbf{r}_{I0}\)</span> of the atom <span class="math notranslate nohighlight">\(I\)</span> to the geometric center
|
||
of the interacting atoms, i.e. centroid, is used. As the geometric
|
||
center is different for each interaction, the <span class="math notranslate nohighlight">\(\mathbf{r}_{I0}\)</span>
|
||
also differs. The sixth term, Kspace contribution,
|
||
is computed identically to compute <em>stress/atom</em>.
|
||
The seventh term is handed differently depending on
|
||
if the constraint forces are due to <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>
|
||
or <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>.
|
||
In case of SHAKE constraints, each distance constraint is
|
||
handed as a pairwise interaction.
|
||
E.g. in case of a water molecule, two OH and one HH distance
|
||
constraints are treated as three pairwise interactions.
|
||
In case of <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>,
|
||
all constraint forces in the molecule are treated
|
||
as a single many-body interaction with a single centroid position.
|
||
In case of water molecule, the formula expression would become
|
||
identical to that of the three-body angle interaction.
|
||
Although the total system virial is the same as
|
||
compute <em>stress/atom</em>, compute <em>centroid/stress/atom</em> is know to
|
||
result in more consistent heat flux values for angle, dihedrals,
|
||
improper and constraint force contributions
|
||
when computed via <a class="reference internal" href="compute_heat_flux.html"><span class="doc">compute heat/flux</span></a>.</p>
|
||
<p>If no extra keywords are listed, the kinetic contribution <em>and</em> all
|
||
of the virial contribution terms are included in the per-atom stress
|
||
tensor. If any extra keywords are listed, only those terms are
|
||
summed to compute the tensor. The <em>virial</em> keyword means include all
|
||
terms except the kinetic energy <em>ke</em>.</p>
|
||
<p>Note that the stress for each atom is due to its interaction with all
|
||
other atoms in the simulation, not just with other atoms in the group.</p>
|
||
<p>Details of how compute <em>stress/atom</em> obtains the virial for individual
|
||
atoms for either pairwise or many-body potentials, and including the
|
||
effects of periodic boundary conditions is discussed in
|
||
<a class="reference internal" href="#thompson2"><span class="std std-ref">(Thompson)</span></a>. The basic idea for many-body
|
||
potentials is to treat each component of the force computation between
|
||
a small cluster of atoms in the same manner as in the formula above
|
||
for bond, angle, dihedral, etc interactions. Namely the quantity
|
||
<span class="math notranslate nohighlight">\(\mathbf{r} \cdot \mathbf{F}\)</span> is summed over the atoms in the
|
||
interaction, with the <span class="math notranslate nohighlight">\(r\)</span> vectors unwrapped by periodic
|
||
boundaries so that the cluster of atoms is close together. The total
|
||
contribution for the cluster interaction is divided evenly among those
|
||
atoms.</p>
|
||
<p>Details of how compute <em>centroid/stress/atom</em> obtains the virial for
|
||
individual atoms are given in <a class="reference internal" href="#surblys1"><span class="std std-ref">(Surblys2019)</span></a> and
|
||
<a class="reference internal" href="#surblys2"><span class="std std-ref">(Surblys2021)</span></a>, where the
|
||
idea is that the virial of the atom <span class="math notranslate nohighlight">\(I\)</span> is the result of only
|
||
the force <span class="math notranslate nohighlight">\(\mathbf{F}_I\)</span> on the atom due to the interaction and
|
||
its positional vector <span class="math notranslate nohighlight">\(\mathbf{r}_{I0}\)</span>, relative to the
|
||
geometric center of the interacting atoms, regardless of the number of
|
||
participating atoms. The periodic boundary treatment is identical to
|
||
that of compute <em>stress/atom</em>, and both of them reduce to identical
|
||
expressions for two-body interactions, i.e. computed values for
|
||
contributions from bonds and two-body pair styles, such as
|
||
<a class="reference internal" href="pair_lj.html"><span class="doc">Lennard-Jones</span></a>, will be the same, while contributions
|
||
from angles, dihedrals and impropers will be different.</p>
|
||
<p>The <a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style charmm</span></a> style calculates
|
||
pairwise interactions between 1-4 atoms. The virial contribution of
|
||
these terms is included in the pair virial, not the dihedral virial.</p>
|
||
<p>The KSpace contribution is calculated using the method in
|
||
<a class="reference internal" href="#heyes2"><span class="std std-ref">(Heyes)</span></a> for the Ewald method and by the methodology
|
||
described in <a class="reference internal" href="#sirk1"><span class="std std-ref">(Sirk)</span></a> for PPPM. The choice of KSpace
|
||
solver is specified by the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm</span></a>
|
||
command. Note that for PPPM, the calculation requires 6 extra FFTs
|
||
each timestep that per-atom stress is calculated. Thus it can
|
||
significantly increase the cost of the PPPM calculation if it is
|
||
needed on a large fraction of the simulation timesteps.</p>
|
||
<p>The <em>temp-ID</em> argument can be used to affect the per-atom velocities
|
||
used in the kinetic energy contribution to the total stress. If the
|
||
kinetic energy is not included in the stress, than the temperature
|
||
compute is not used and can be specified as NULL. If the kinetic
|
||
energy is included and you wish to use atom velocities as-is, then
|
||
<em>temp-ID</em> can also be specified as NULL. If desired, the specified
|
||
temperature compute can be one that subtracts off a bias to leave each
|
||
atom with only a thermal velocity to use in the formula above, e.g. by
|
||
subtracting a background streaming velocity. See the doc pages for
|
||
individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones
|
||
include a bias.</p>
|
||
<hr class="docutils" />
|
||
<p>Note that as defined in the formula, per-atom stress is the negative
|
||
of the per-atom pressure tensor. It is also really a stress*volume
|
||
formulation, meaning the computed quantity is in units of
|
||
pressure*volume. It would need to be divided by a per-atom volume to
|
||
have units of stress (pressure), but an individual atom’s volume is
|
||
not well defined or easy to compute in a deformed solid or a liquid.
|
||
See the <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a> command for
|
||
one possible way to estimate a per-atom volume.</p>
|
||
<p>Thus, if the diagonal components of the per-atom stress tensor are
|
||
summed for all atoms in the system and the sum is divided by
|
||
<span class="math notranslate nohighlight">\(dV\)</span>, where <span class="math notranslate nohighlight">\(d\)</span> = dimension and <span class="math notranslate nohighlight">\(V\)</span> is the volume of
|
||
the system, the result should be <span class="math notranslate nohighlight">\(-P\)</span>, where <span class="math notranslate nohighlight">\(P\)</span> is the
|
||
total pressure of the system.</p>
|
||
<p>These lines in an input script for a 3d system should yield that
|
||
result. I.e. the last 2 columns of thermo output will be the same:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">peratom</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">NULL</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">p</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">reduce</span><span class="w"> </span><span class="n">sum</span><span class="w"> </span><span class="n">c_peratom[1]</span><span class="w"> </span><span class="n">c_peratom[2]</span><span class="w"> </span><span class="n">c_peratom[3]</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">press</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="o">-</span><span class="nv">(c_p[1]+c_p[2]+c_p[3])</span><span class="o">/</span><span class="nv">(3*vol)</span>
|
||
<span class="k">thermo_style</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="n">step</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="n">etotal</span><span class="w"> </span><span class="n">press</span><span class="w"> </span><span class="n">v_press</span>
|
||
</pre></div>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>The per-atom stress does not include any Lennard-Jones tail
|
||
corrections to the pressure added by the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify tail yes</span></a> command, since those are contributions to the global
|
||
system pressure.</p>
|
||
</div>
|
||
<p>The compute stress/atom can be used in a number of ways. Here is an
|
||
example to compute a 1-d pressure profile in x-direction across the
|
||
complete simulation box. You will need to adjust the number of bins and the
|
||
selections for time averaging to your specific simulation. This assumes
|
||
that the dimensions of the simulation cell does not change.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="c"># set number of bins</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">nbins</span><span class="w"> </span><span class="n">index</span><span class="w"> </span><span class="m">20</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">fraction</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">1.0</span><span class="o">/</span><span class="n">v_nbins</span>
|
||
<span class="c"># define bins as chunks</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">cchunk</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">bin</span><span class="o">/</span><span class="m">1</span><span class="n">d</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="n">lower</span><span class="w"> </span><span class="nv">${fraction}</span><span class="w"> </span><span class="n">units</span><span class="w"> </span><span class="n">reduced</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">stress</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">NULL</span>
|
||
<span class="c"># apply conversion to pressure early since we have no variable style for processing chunks</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">press</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="o">-</span><span class="nv">(c_stress[1]+c_stress[2]+c_stress[3])</span><span class="o">/</span><span class="nv">(3.0*vol*${fraction})</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">binpress</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">reduce</span><span class="o">/</span><span class="n">chunk</span><span class="w"> </span><span class="n">cchunk</span><span class="w"> </span><span class="n">sum</span><span class="w"> </span><span class="n">v_press</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">avg</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">ave</span><span class="o">/</span><span class="n">time</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">40</span><span class="w"> </span><span class="m">400</span><span class="w"> </span><span class="n">c_binpress</span><span class="w"> </span><span class="n">mode</span><span class="w"> </span><span class="n">vector</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">ave_stress.txt</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="output-info">
|
||
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
|
||
<p>Compute <em>stress/atom</em> calculates a per-atom array with 6 columns,
|
||
which can be accessed by indices 1-6 by any command that uses per-atom
|
||
values from a compute as input. Compute <em>centroid/stress/atom</em>
|
||
produces a per-atom array with 9 columns, but otherwise can be used in
|
||
an identical manner to compute <em>stress/atom</em>. 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>
|
||
<p>The ordering of the 6 columns for <em>stress/atom</em> is as follows: xx, yy,
|
||
zz, xy, xz, yz. The ordering of the 9 columns for
|
||
<em>centroid/stress/atom</em> is as follows: xx, yy, zz, xy, xz, yz, yx, zx,
|
||
zy.</p>
|
||
<p>The per-atom array values will be in pressure*volume <a class="reference internal" href="units.html"><span class="doc">units</span></a> as discussed above.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>Currently, compute <em>centroid/stress/atom</em> does not support pair styles
|
||
with many-body interactions (<a class="reference internal" href="pair_eam.html"><span class="doc">EAM</span></a> is an exception,
|
||
since its computations are performed pairwise), nor granular pair
|
||
styles with pairwise forces which are not aligned with the vector
|
||
between the pair of particles. All bond styles are supported. All
|
||
angle, dihedral, improper styles are supported with the exception of
|
||
INTEL and KOKKOS variants of specific styles. It also does not
|
||
support models with long-range Coulombic or dispersion forces,
|
||
i.e. the kspace_style command in LAMMPS. It also does not implement the
|
||
following fixes which add rigid-body constraints:
|
||
<a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a> and the OpenMP accelerated version of <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a>,
|
||
while all other <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*/small</span></a> are implemented.</p>
|
||
<p>LAMMPS will generate an error if one of these options is included in
|
||
your model. Extension of centroid stress calculations to these force
|
||
and fix styles is planned for the future.</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_pe.html"><span class="doc">compute pe</span></a>, <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>By default the compute includes contributions from the keywords:
|
||
<code class="docutils literal notranslate"><span class="pre">ke</span> <span class="pre">pair</span> <span class="pre">bond</span> <span class="pre">angle</span> <span class="pre">dihedral</span> <span class="pre">improper</span> <span class="pre">kspace</span> <span class="pre">fix</span></code></p>
|
||
<hr class="docutils" />
|
||
<p id="heyes2"><strong>(Heyes)</strong> Heyes, Phys Rev B, 49, 755 (1994).</p>
|
||
<p id="sirk1"><strong>(Sirk)</strong> Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).</p>
|
||
<p id="thompson2"><strong>(Thompson)</strong> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).</p>
|
||
<p id="surblys1"><strong>(Surblys2019)</strong> Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).</p>
|
||
<p id="surblys2"><strong>(Surblys2021)</strong> Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
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