forked from lijiext/lammps
466 lines
29 KiB
HTML
466 lines
29 KiB
HTML
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<title>compute msd command — LAMMPS documentation</title>
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<link rel="next" title="compute msd/chunk command" href="compute_msd_chunk.html"/>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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<p class="caption"><span class="caption-text">Index</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
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<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Computes</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_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_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_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_cluster_atom.html">compute cluster/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_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_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_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_chunk.html">compute dipole/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_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_fep.html">compute fep 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_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_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_meso_e_atom.html">compute meso/e/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_rho_atom.html">compute meso/rho/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_t_atom.html">compute meso/t/atom command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">compute msd command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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</li>
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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_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_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_pressure.html">compute pressure 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_local.html">compute property/local 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_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_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_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_mesh_vertices.html">compute smd/triangle/mesh/vertices</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>
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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_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-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_temp.html">compute temp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp.html#compute-temp-kk-command">compute temp/kk 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_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_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">Bonds</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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</ul>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="compute-msd-command">
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<span id="index-0"></span><h1>compute msd command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">msd</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p>
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</li>
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<li><p class="first">msd = style name of this compute command</p>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>com</em> or <em>average</em></p>
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<pre class="literal-block">
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<em>com</em> value = <em>yes</em> or <em>no</em>
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<em>average</em> value = <em>yes</em> or <em>no</em>
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</pre>
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</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">msd</span>
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<span class="n">compute</span> <span class="mi">1</span> <span class="n">upper</span> <span class="n">msd</span> <span class="n">com</span> <span class="n">yes</span> <span class="n">average</span> <span class="n">yes</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Define a computation that calculates the mean-squared displacement
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(MSD) of the group of atoms, including all effects due to atoms
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passing thru periodic boundaries. For computation of the non-Gaussian
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parameter of mean-squared displacement, see the <a class="reference internal" href="compute_msd_nongauss.html"><span class="doc">compute msd/nongauss</span></a> command.</p>
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<p>A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are the squared dx,dy,dz displacements, summed
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and averaged over atoms in the group. The 4th element is the total
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squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
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averaged over atoms in the group.</p>
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<p>The slope of the mean-squared displacement (MSD) versus time is
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proportional to the diffusion coefficient of the diffusing atoms.</p>
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<p>The displacement of an atom is from its reference position. This is
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normally the original position at the time
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the compute command was issued, unless the <em>average</em> keyword is set to <em>yes</em>.
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The value of the displacement will be
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0.0 for atoms not in the specified compute group.</p>
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<p>If the <em>com</em> option is set to <em>yes</em> then the effect of any drift in
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the center-of-mass of the group of atoms is subtracted out before the
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displacment of each atom is calculated.</p>
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<p>If the <em>average</em> option is set to <em>yes</em> then the reference position of
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an atom is based on the average position of that atom, corrected for
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center-of-mass motion if requested. The average position is a running
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average over all previous calls to the compute, including the current
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call. So on the first call it is current position, on the second call
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it is the arithmetic average of the current position and the position
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on the first call, and so on. Note that when using this option, the
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precise value of the mean square displacement will depend on the
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number of times the compute is called. So, for example, changing the
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frequency of thermo output may change the computed displacement. Also,
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the precise values will be changed if a single simulation is broken up
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into two parts, using either multiple run commands or a restart
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file. It only makes sense to use this option if the atoms are not
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diffusing, so that their average positions relative to the center of
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mass of the system are stationary. The most common case is crystalline
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solids undergoing thermal motion.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Initial coordinates are stored in “unwrapped” form, by using the
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image flags associated with each atom. See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command for a discussion of “unwrapped” coordinates.
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See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for a
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discussion of image flags and how they are set for each atom. You can
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reset the image flags (e.g. to 0) before invoking this compute by
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using the <a class="reference internal" href="set.html"><span class="doc">set image</span></a> command.</p>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">If you want the quantities calculated by this compute to be
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continuous when running from a <a class="reference internal" href="read_restart.html"><span class="doc">restart file</span></a>, then
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you should use the same ID for this compute, as in the original run.
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This is so that the fix this compute creates to store per-atom
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quantities will also have the same ID, and thus be initialized
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correctly with atom reference positions from the restart file. When
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<em>average</em> is set to yes, then the atom reference positions are
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restored correctly, but not the number of samples used obtain them. As
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a result, the reference positions from the restart file are combined
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with subsequent positions as if they were from a single sample,
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instead of many, which will change the values of msd somewhat.</p>
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</div>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global vector of length 4, which can be
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accessed by indices 1-4 by any command that uses global vector values
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from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
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options.</p>
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<p>The vector values are “intensive”. The vector values will be in
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distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="compute_msd_nongauss.html"><span class="doc">compute msd/nongauss</span></a>, <a class="reference internal" href="compute_displace_atom.html"><span class="doc">compute displace_atom</span></a>, <a class="reference internal" href="fix_store_state.html"><span class="doc">fix store/state</span></a>, <a class="reference internal" href="compute_msd_chunk.html"><span class="doc">compute msd/chunk</span></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default</h2>
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<p>The option default are com = no, average = no.</p>
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