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<title>compute saed command &mdash; LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
<div class="lammps_release">git info: </div>
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Compute Styles</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_adf.html">compute adf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ave_sphere_atom.html">compute ave/sphere/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_chunk_spread_atom.html">compute chunk/spread/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-fragment-atom-command">compute fragment/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-aggregate-atom-command">compute aggregate/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cnp_atom.html">compute cnp/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_composition_atom.html">compute composition/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_count_type.html">compute count/type command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html">compute dipole command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html#compute-dipole-tip4p-command">compute dipole/tip4p command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_edpd_temp_atom.html">compute edpd/temp/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_efield_atom.html">compute efield/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_efield_wolf_atom.html">compute efield/wolf/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_entropy_atom.html">compute entropy/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fabric.html">compute fabric command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fep_ta.html">compute fep/ta command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_global_atom.html">compute global/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape.html">compute gyration/shape command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape_chunk.html">compute gyration/shape/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_hma.html">compute hma command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_mliap.html">compute mliap command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_momentum.html">compute momentum command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd.html">compute msd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_nbond_atom.html">compute nbond/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pace.html">compute pace command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pair.html">compute pair command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html">compute pod/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-podd-atom-command">compute podd/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-local-command">compute pod/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-global-command">compute pod/global command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure_alchemy.html">compute pressure/alchemy command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure_uef.html">compute pressure/uef command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_grid.html">compute property/grid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ptm_atom.html">compute ptm/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rattlers_atom.html">compute rattlers/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reaxff_atom.html">compute reaxff/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce_chunk.html">compute reduce/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rheo_property_atom.html">compute rheo/property/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">compute saed 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_slcsa_atom.html">compute slcsa/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_slice.html">compute slice command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_contact_radius.html">compute smd/contact/radius command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_damage.html">compute smd/damage command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_hourglass_error.html">compute smd/hourglass/error command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_internal_energy.html">compute smd/internal/energy command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain.html">compute smd/plastic/strain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain_rate.html">compute smd/plastic/strain/rate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_rho.html">compute smd/rho command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_defgrad.html">compute smd/tlsph/defgrad command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_dt.html">compute smd/tlsph/dt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_num_neighs.html">compute smd/tlsph/num/neighs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_shape.html">compute smd/tlsph/shape command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain.html">compute smd/tlsph/strain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain_rate.html">compute smd/tlsph/strain/rate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_stress.html">compute smd/tlsph/stress command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_triangle_vertices.html">compute smd/triangle/vertices command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_effm.html">compute smd/ulsph/effm command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_num_neighs.html">compute smd/ulsph/num/neighs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain.html">compute smd/ulsph/strain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain_rate.html">compute smd/ulsph/strain/rate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_stress.html">compute smd/ulsph/stress command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snav-atom-command">compute snav/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snap-command">compute snap command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-sna-grid-command">compute sna/grid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-sna-grid-local-command">compute sna/grid/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sph_e_atom.html">compute sph/e/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sph_rho_atom.html">compute sph/rho/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sph_t_atom.html">compute sph/t/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_spin.html">compute spin command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html#compute-centroid-stress-atom-command">compute centroid/stress/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_cartesian.html">compute stress/cartesian command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html">compute stress/cylinder command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html#compute-stress-spherical-command">compute stress/spherical command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html">compute stress/mop command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html#compute-stress-mop-profile-command">compute stress/mop/profile command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-virial-tally-command">compute heat/flux/virial/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tdpd_cc_atom.html">compute tdpd/cc/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_uef.html">compute temp/uef command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_viscosity_cos.html">compute viscosity/cos command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd command</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="compute-saed-command">
<span id="index-0"></span><h1>compute saed command<a class="headerlink" href="#compute-saed-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">saed</span><span class="w"> </span><span class="n">lambda</span><span class="w"> </span><span class="n">type1</span><span class="w"> </span><span class="n">type2</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">typeN</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
</pre></div>
</div>
<ul>
<li><p>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p></li>
<li><p>saed = style name of this compute command</p></li>
<li><p>lambda = wavelength of incident radiation (length units)</p></li>
<li><p>type1 type2 … typeN = chemical symbol of each atom type (see valid options below)</p></li>
<li><p>zero or more keyword/value pairs may be appended</p></li>
<li><p>keyword = <em>Kmax</em> or <em>Zone</em> or <em>dR_Ewald</em> or <em>c</em> or <em>manual</em> or <em>echo</em></p>
<pre class="literal-block"><em>Kmax</em> value = Maximum distance explored from reciprocal space origin
(inverse length units)
<em>Zone</em> values = z1 z2 z3
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
reciprocal space will be meshed up to <em>Kmax</em>
<em>dR_Ewald</em> value = Thickness of Ewald sphere slice intercepting
reciprocal space (inverse length units)
<em>c</em> values = c1 c2 c3
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
lattice nodes in the h, k, and l directions respectively
<em>manual</em> = flag to use manual spacing of reciprocal lattice points
based on the values of the <em>c</em> parameters
<em>echo</em> = flag to provide extra output for debugging purposes</pre>
</li>
</ul>
</section>
<section id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">saed</span><span class="w"> </span><span class="m">0.0251</span><span class="w"> </span><span class="n">Al</span><span class="w"> </span><span class="n">O</span><span class="w"> </span><span class="n">Kmax</span><span class="w"> </span><span class="m">1.70</span><span class="w"> </span><span class="n">Zone</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">dR_Ewald</span><span class="w"> </span><span class="m">0.01</span><span class="w"> </span><span class="n">c</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">0.5</span>
<span class="k">compute </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">saed</span><span class="w"> </span><span class="m">0.0251</span><span class="w"> </span><span class="n">Ni</span><span class="w"> </span><span class="n">Kmax</span><span class="w"> </span><span class="m">1.70</span><span class="w"> </span><span class="n">Zone</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="n">c</span><span class="w"> </span><span class="m">0.05</span><span class="w"> </span><span class="m">0.05</span><span class="w"> </span><span class="m">0.05</span><span class="w"> </span><span class="n">manual</span><span class="w"> </span><span class="n">echo</span>
<span class="k">fix </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">saed</span><span class="o">/</span><span class="n">vtk</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">c_1</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">Al2O3_001.saed</span>
<span class="k">fix </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">saed</span><span class="o">/</span><span class="n">vtk</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">c_2</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">Ni_000.saed</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 calculates electron diffraction intensity as
described in <a class="reference internal" href="#saed-coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes
defined by the entire simulation domain (or manually) using simulated
radiation of wavelength lambda.</p>
<p>The electron diffraction intensity I at each reciprocal lattice point
is computed from the structure factor F using the equations:</p>
<div class="math notranslate nohighlight">
\[\begin{split}I = &amp; \frac{F^{*}F}{N} \\
F(\mathbf{k}) = &amp; \sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k} \cdot \mathbf{r}_j)\end{split}\]</div>
<p>Here, K is the location of the reciprocal lattice node, <span class="math notranslate nohighlight">\(r_j\)</span> is the
position of each atom, <span class="math notranslate nohighlight">\(f_j\)</span> are atomic scattering factors.</p>
<p>Diffraction intensities are calculated on a three-dimensional mesh of
reciprocal lattice nodes. The mesh spacing is defined either (a) by
the entire simulation domain or (b) manually using selected values as
shown in the 2D diagram below.</p>
<a class="reference internal image-reference" href="_images/saed_mesh.png"><img alt="_images/saed_mesh.png" class="align-center" src="_images/saed_mesh.png" style="width: 384.0px; height: 337.5px;" />
</a>
<p>For a mesh defined by the simulation domain, a rectilinear grid is
constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
axis. Where A are the vectors corresponding to the edges of the
simulation cell. If one or two directions has non-periodic boundary
conditions, then the spacing in these directions is defined from the
average of the (inversed) box lengths with periodic boundary conditions.
Meshes defined by the simulation domain must contain at least one periodic
boundary.</p>
<p>If the <em>manual</em> flag is included, the mesh of reciprocal lattice nodes
will defined using the <em>c</em> values for the spacing along each reciprocal
lattice axis. Note that manual mapping of the reciprocal space mesh is
good for comparing diffraction results from multiple simulations; however
it can reduce the likelihood that Bragg reflections will be satisfied
unless small spacing parameters (<span class="math notranslate nohighlight">\(&lt;0.05~\AA^-1\)</span>)
are implemented. Meshes with manual spacing do not require a periodic
boundary.</p>
<p>The limits of the reciprocal lattice mesh are determined by the use of
the <em>Kmax</em>, <em>Zone</em>, and <em>dR_Ewald</em> parameters. The rectilinear mesh
created about the origin of reciprocal space is terminated at the
boundary of a sphere of radius <em>Kmax</em> centered at the origin. If
<em>Zone</em> parameters <em>z1</em> = <em>z2</em> = <em>z3</em> = 0 are used, diffraction intensities are
computed throughout the entire spherical volume - note this can
greatly increase the cost of computation. Otherwise, <em>Zone</em>
parameters will denote the <span class="math notranslate nohighlight">\(z1=h\)</span>, <span class="math notranslate nohighlight">\(z2=k\)</span>, and <span class="math notranslate nohighlight">\(z3=\ell\)</span>
(in a global sense) zone axis of an intersecting Ewald sphere. Diffraction
intensities will only be computed at the intersection of the reciprocal lattice
mesh and a <em>dR_Ewald</em> thick surface of the Ewald sphere. See the
example 3D intensity data and the intersection of a [010] zone axis
in the below image.</p>
<a class="reference internal image-reference" href="_images/saed_ewald_intersect.jpg"><img alt="_images/saed_ewald_intersect.jpg" class="align-center" src="_images/saed_ewald_intersect.jpg" style="width: 384.0px; height: 384.0px;" />
</a>
<p>The atomic scattering factors, fj, accounts for the reduction in
diffraction intensity due to Compton scattering. Compute saed uses
analytical approximations of the atomic scattering factors that vary
for each atom type (type1 type2 … typeN) and angle of diffraction.
The analytic approximation is computed using the formula
<a class="reference internal" href="#brown"><span class="std std-ref">(Brown)</span></a>:</p>
<div class="math notranslate nohighlight">
\[f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )\]</div>
<p>Coefficients parameterized by <a class="reference internal" href="#fox"><span class="std std-ref">(Fox)</span></a> are assigned for each
atom type designating the chemical symbol and charge of each atom
type. Valid chemical symbols for compute saed are:</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>H</p></td>
<td><p>He</p></td>
<td><p>Li</p></td>
<td><p>Be</p></td>
<td><p>B</p></td>
<td><p>C</p></td>
<td><p>N</p></td>
<td><p>O</p></td>
<td><p>F</p></td>
<td><p>Ne</p></td>
<td><p>Na</p></td>
<td><p>Mg</p></td>
<td><p>Al</p></td>
<td><p>Si</p></td>
<td><p>P</p></td>
<td><p>S</p></td>
<td><p>Cl</p></td>
<td><p>Ar</p></td>
<td><p>K</p></td>
<td><p>Ca</p></td>
</tr>
<tr class="row-even"><td><p>Sc</p></td>
<td><p>Ti</p></td>
<td><p>V</p></td>
<td><p>Cr</p></td>
<td><p>Mn</p></td>
<td><p>Fe</p></td>
<td><p>Co</p></td>
<td><p>Ni</p></td>
<td><p>Cu</p></td>
<td><p>Zn</p></td>
<td><p>Ga</p></td>
<td><p>Ge</p></td>
<td><p>As</p></td>
<td><p>Se</p></td>
<td><p>Br</p></td>
<td><p>Kr</p></td>
<td><p>Rb</p></td>
<td><p>Sr</p></td>
<td><p>Y</p></td>
<td><p>Zr</p></td>
</tr>
<tr class="row-odd"><td><p>Nb</p></td>
<td><p>Mo</p></td>
<td><p>Tc</p></td>
<td><p>Ru</p></td>
<td><p>Rh</p></td>
<td><p>Pd</p></td>
<td><p>Ag</p></td>
<td><p>Cd</p></td>
<td><p>In</p></td>
<td><p>Sn</p></td>
<td><p>Sb</p></td>
<td><p>Te</p></td>
<td><p>I</p></td>
<td><p>Xe</p></td>
<td><p>Cs</p></td>
<td><p>Ba</p></td>
<td><p>La</p></td>
<td><p>Ce</p></td>
<td><p>Pr</p></td>
<td><p>Nd</p></td>
</tr>
<tr class="row-even"><td><p>Pm</p></td>
<td><p>Sm</p></td>
<td><p>Eu</p></td>
<td><p>Gd</p></td>
<td><p>Tb</p></td>
<td><p>Dy</p></td>
<td><p>Ho</p></td>
<td><p>Er</p></td>
<td><p>Tm</p></td>
<td><p>Yb</p></td>
<td><p>Lu</p></td>
<td><p>Hf</p></td>
<td><p>Ta</p></td>
<td><p>W</p></td>
<td><p>Re</p></td>
<td><p>Os</p></td>
<td><p>Ir</p></td>
<td><p>Pt</p></td>
<td><p>Au</p></td>
<td><p>Hg</p></td>
</tr>
<tr class="row-odd"><td><p>Tl</p></td>
<td><p>Pb</p></td>
<td><p>Bi</p></td>
<td><p>Po</p></td>
<td><p>At</p></td>
<td><p>Rn</p></td>
<td><p>Fr</p></td>
<td><p>Ra</p></td>
<td><p>Ac</p></td>
<td><p>Th</p></td>
<td><p>Pa</p></td>
<td><p>U</p></td>
<td><p>Np</p></td>
<td><p>Pu</p></td>
<td><p>Am</p></td>
<td><p>Cm</p></td>
<td><p>Bk</p></td>
<td><p>Cf</p></td>
<td></td>
<td></td>
</tr>
</tbody>
</table>
<p>If the <em>echo</em> keyword is specified, compute saed will provide extra
reporting information to the screen.</p>
</section>
<section id="output-info">
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
<p>This compute calculates a global vector. The length of the vector is
the number of reciprocal lattice nodes that are explored by the mesh.
The entries of the global vector are the computed diffraction
intensities as described above.</p>
<p>The vector can be accessed by any command that uses global values from
a compute as input. See the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> doc page
for an overview of LAMMPS output options.</p>
<p>All array values calculated by this compute are “intensive”.</p>
</section>
<section id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
<p>This compute is part of the DIFFRACTION package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
<p>The compute_saed command does not work for triclinic cells.</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="fix_saed_vtk.html"><span class="doc">fix saed_vtk</span></a>, <a class="reference internal" href="compute_xrd.html"><span class="doc">compute xrd</span></a></p>
</section>
<section id="default">
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
<p>The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
0.01.</p>
<hr class="docutils" />
<p id="saed-coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
(2013).</p>
<p id="brown"><strong>(Brown)</strong> Brown et al. International Tables for Crystallography
Volume C: Mathematical and Chemical Tables, 554-95 (2004).</p>
<p id="fox"><strong>(Fox)</strong> Fox, OKeefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
(1989).</p>
</section>
</section>
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