582 lines
44 KiB
HTML
582 lines
44 KiB
HTML
<!DOCTYPE html>
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<title>compute saed command — LAMMPS documentation</title>
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<link rel="next" title="compute slcsa/atom command" href="compute_slcsa_atom.html" />
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Compute Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_adf.html">compute adf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ave_sphere_atom.html">compute ave/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_spread_atom.html">compute chunk/spread/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-fragment-atom-command">compute fragment/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-aggregate-atom-command">compute aggregate/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cnp_atom.html">compute cnp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_composition_atom.html">compute composition/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_count_type.html">compute count/type command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html">compute dipole command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html#compute-dipole-tip4p-command">compute dipole/tip4p command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html#compute-dipole-tip4p-chunk-command">compute dipole/tip4p/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_edpd_temp_atom.html">compute edpd/temp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_efield_atom.html">compute efield/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_efield_wolf_atom.html">compute efield/wolf/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_entropy_atom.html">compute entropy/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_fabric.html">compute fabric command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_fep_ta.html">compute fep/ta command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_global_atom.html">compute global/atom command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
|
||
<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>
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||
<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>
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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>
|
||
<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>
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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>
|
||
<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>
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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>
|
||
<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>
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||
<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>
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||
<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>
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<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>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
</div>
|
||
</nav>
|
||
|
||
<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 saed 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_rigid_local.html" class="btn btn-neutral float-left" title="compute rigid/local command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="compute_slcsa_atom.html" class="btn btn-neutral float-right" title="compute slcsa/atom command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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<hr/>
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</div>
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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-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">
|
||
\[\begin{split}I = & \frac{F^{*}F}{N} \\
|
||
F(\mathbf{k}) = & \sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k} \cdot \mathbf{r}_j)\end{split}\]</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">\(<0.05~\AA^-1\)</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, O’Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
|
||
(1989).</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
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