552 lines
49 KiB
HTML
552 lines
49 KiB
HTML
<!DOCTYPE html>
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<html class="writer-html5" lang="en" >
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<head>
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<title>compute adf command — LAMMPS documentation</title>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="next" title="compute angle command" href="compute_angle.html" />
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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</a>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<div class="lammps_release">git info: </div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Compute Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">compute adf command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#output-info">Output info</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ave_sphere_atom.html">compute ave/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_spread_atom.html">compute chunk/spread/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-fragment-atom-command">compute fragment/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-aggregate-atom-command">compute aggregate/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cnp_atom.html">compute cnp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_composition_atom.html">compute composition/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_count_type.html">compute count/type command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html">compute dipole command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html#compute-dipole-tip4p-command">compute dipole/tip4p command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html#compute-dipole-tip4p-chunk-command">compute dipole/tip4p/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_edpd_temp_atom.html">compute edpd/temp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_efield_atom.html">compute efield/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_efield_wolf_atom.html">compute efield/wolf/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_entropy_atom.html">compute entropy/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_fabric.html">compute fabric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_fep_ta.html">compute fep/ta command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_global_atom.html">compute global/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape.html">compute gyration/shape command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape_chunk.html">compute gyration/shape/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_hma.html">compute hma command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_mliap.html">compute mliap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_momentum.html">compute momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd.html">compute msd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_nbond_atom.html">compute nbond/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pace.html">compute pace command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pair.html">compute pair command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html">compute pod/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-podd-atom-command">compute podd/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-local-command">compute pod/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-global-command">compute pod/global command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure_alchemy.html">compute pressure/alchemy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure_uef.html">compute pressure/uef command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_grid.html">compute property/grid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ptm_atom.html">compute ptm/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rattlers_atom.html">compute rattlers/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reaxff_atom.html">compute reaxff/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce_chunk.html">compute reduce/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rheo_property_atom.html">compute rheo/property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_saed.html">compute saed command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_slcsa_atom.html">compute slcsa/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_slice.html">compute slice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_contact_radius.html">compute smd/contact/radius command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_damage.html">compute smd/damage command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_hourglass_error.html">compute smd/hourglass/error command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_internal_energy.html">compute smd/internal/energy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain.html">compute smd/plastic/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain_rate.html">compute smd/plastic/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_rho.html">compute smd/rho command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_defgrad.html">compute smd/tlsph/defgrad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_dt.html">compute smd/tlsph/dt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_num_neighs.html">compute smd/tlsph/num/neighs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_shape.html">compute smd/tlsph/shape command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain.html">compute smd/tlsph/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain_rate.html">compute smd/tlsph/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_stress.html">compute smd/tlsph/stress command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_triangle_vertices.html">compute smd/triangle/vertices command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_effm.html">compute smd/ulsph/effm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_num_neighs.html">compute smd/ulsph/num/neighs command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain.html">compute smd/ulsph/strain command</a></li>
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||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain_rate.html">compute smd/ulsph/strain/rate command</a></li>
|
||
<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>
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||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
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</ul>
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<li class="breadcrumb-item active">compute adf command</li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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<div itemprop="articleBody">
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="compute-adf-command">
|
||
<span id="index-0"></span><h1>compute adf command<a class="headerlink" href="#compute-adf-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">adf</span><span class="w"> </span><span class="n">Nbin</span><span class="w"> </span><span class="n">itype1</span><span class="w"> </span><span class="n">jtype1</span><span class="w"> </span><span class="n">ktype1</span><span class="w"> </span><span class="n">Rjinner1</span><span class="w"> </span><span class="n">Rjouter1</span><span class="w"> </span><span class="n">Rkinner1</span><span class="w"> </span><span class="n">Rkouter1</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>adf = style name of this compute command</p></li>
|
||
<li><p>Nbin = number of ADF bins</p></li>
|
||
<li><p>itypeN = central atom type for Nth ADF histogram (see asterisk form below)</p></li>
|
||
<li><p>jtypeN = J atom type for Nth ADF histogram (see asterisk form below)</p></li>
|
||
<li><p>ktypeN = K atom type for Nth ADF histogram (see asterisk form below)</p></li>
|
||
<li><p>RjinnerN = inner radius of J atom shell for Nth ADF histogram (distance units)</p></li>
|
||
<li><p>RjouterN = outer radius of J atom shell for Nth ADF histogram (distance units)</p></li>
|
||
<li><p>RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units)</p></li>
|
||
<li><p>RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units)</p></li>
|
||
<li><p>zero or one keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>ordinate</em></p>
|
||
<pre class="literal-block"><em>ordinate</em> value = <em>degree</em> or <em>radian</em> or <em>cosine</em>
|
||
Choose the ordinate parameter for the histogram</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">fluid</span><span class="w"> </span><span class="n">adf</span><span class="w"> </span><span class="m">32</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="m">0.0</span><span class="w"> </span><span class="m">1.2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.2</span><span class="w"> </span><span class="o">&</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">2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.5</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.5</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.5</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="m">2</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">0.0</span><span class="w"> </span><span class="m">1.2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.2</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.5</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="m">3.5</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="m">3.5</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="m">3.5</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">fluid</span><span class="w"> </span><span class="n">adf</span><span class="w"> </span><span class="m">32</span><span class="w"> </span><span class="m">1</span><span class="o">*</span><span class="m">2</span><span class="w"> </span><span class="m">1</span><span class="o">*</span><span class="m">2</span><span class="w"> </span><span class="m">1</span><span class="o">*</span><span class="m">2</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">3.5</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">fluid</span><span class="w"> </span><span class="n">adf</span><span class="w"> </span><span class="m">32</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 one or more angular distribution functions
|
||
(ADF) for a group of particles. Each ADF is calculated in histogram form
|
||
by measuring the angle formed by a central atom and two neighbor atoms and
|
||
binning these angles into <em>Nbin</em> bins.
|
||
Only neighbors for which <em>Rinner</em> < <em>R</em> < <em>Router</em> are counted, where
|
||
<em>Rinner</em> and <em>Router</em> are specified separately for the first and second
|
||
neighbor atom in each requested ADF.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you have a bonded system, then the settings of
|
||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command can remove pairwise
|
||
interactions between atoms in the same bond, angle, or dihedral. This
|
||
is the default setting for the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
|
||
command, and means those pairwise interactions do not appear in the
|
||
neighbor list. Because this fix uses a neighbor list, it also means
|
||
those pairs will not be included in the ADF. This does not apply when
|
||
using long-range coulomb interactions (<em>coul/long</em>, <em>coul/msm</em>,
|
||
<em>coul/wolf</em> or similar. One way to get around this would be to set
|
||
special_bond scaling factors to very tiny numbers that are not exactly
|
||
zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
|
||
use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to compute the ADF for snapshots in
|
||
the dump file. The rerun script can use a
|
||
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command that includes all pairs in
|
||
the neighbor list.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you request any outer cutoff <em>Router</em> > force cutoff, or if no
|
||
pair style is defined, e.g. the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command is being used to
|
||
post-process a dump file of snapshots you must ensure ghost atom information
|
||
out to the largest value of <em>Router</em> + <em>skin</em> is communicated, via the
|
||
<a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify cutoff</span></a> command, else the ADF computation
|
||
cannot be performed, and LAMMPS will give an error message. The <em>skin</em> value
|
||
is what is specified with the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a> command.</p>
|
||
</div>
|
||
<p>The <em>itypeN</em>,<em>jtypeN</em>,<em>ktypeN</em> settings can be specified in one of two
|
||
ways. An explicit numeric value can be used, as in the first example
|
||
above. Or a wild-card asterisk can be used to specify a range of atom
|
||
types as in the second example above.
|
||
This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
|
||
number of atom types, then an asterisk with no numeric values means
|
||
all types from 1 to N. A leading asterisk means all types from 1 to n
|
||
(inclusive). A trailing asterisk means all types from n to N
|
||
(inclusive). A middle asterisk means all types from m to n
|
||
(inclusive).</p>
|
||
<p>If <em>itypeN</em>, <em>jtypeN</em>, and <em>ktypeN</em> are single values, as in the first example
|
||
above, this means that the ADF is computed where atoms of type <em>itypeN</em>
|
||
are the central atom, and neighbor atoms of type <em>jtypeN</em> and <em>ktypeN</em>
|
||
are forming the angle. If any of <em>itypeN</em>, <em>jtypeN</em>, or <em>ktypeN</em>
|
||
represent a range of values via
|
||
the wild-card asterisk, as in the second example above, this means that the
|
||
ADF is computed where atoms of any of the range of types represented
|
||
by <em>itypeN</em> are the central atom, and the angle is formed by two neighbors,
|
||
one neighbor in the range of types represented by <em>jtypeN</em> and another neighbor
|
||
in the range of types represented by <em>ktypeN</em>.</p>
|
||
<p>If no <em>itypeN</em>, <em>jtypeN</em>, <em>ktypeN</em> settings are specified, then
|
||
LAMMPS will generate a single ADF for all atoms in the group.
|
||
The inner cutoff is set to zero and the outer cutoff is set
|
||
to the force cutoff. If no pair_style is specified, there is no
|
||
force cutoff and LAMMPS will give an error message. Note that
|
||
in most cases, generating an ADF for all atoms is not a good thing.
|
||
Such an ADF is both uninformative and
|
||
extremely expensive to compute. For example, with liquid water
|
||
with a 10 A force cutoff, there are 80,000 angles per atom.
|
||
In addition, most of the interesting angular structure occurs for
|
||
neighbors that are the closest to the central atom, involving
|
||
just a few dozen angles.</p>
|
||
<p>Angles for each ADF are generated by double-looping over the list of
|
||
neighbors of each central atom I,
|
||
just as they would be in the force calculation for
|
||
a three-body potential such as <a class="reference internal" href="pair_sw.html"><span class="doc">Stillinger-Weber</span></a>.
|
||
The angle formed by central atom I and neighbor atoms J and K is included in an
|
||
ADF if the following criteria are met:</p>
|
||
<ul class="simple">
|
||
<li><p>atoms I,J,K are all in the specified compute group</p></li>
|
||
<li><p>the distance between atoms I,J is between Rjinner and Rjouter</p></li>
|
||
<li><p>the distance between atoms I,K is between Rkinner and Rkouter</p></li>
|
||
<li><p>the type of the I atom matches itypeN (one or a range of types)</p></li>
|
||
<li><p>atoms I,J,K are distinct</p></li>
|
||
<li><p>the type of the J atom matches jtypeN (one or a range of types)</p></li>
|
||
<li><p>the type of the K atom matches ktypeN (one or a range of types)</p></li>
|
||
</ul>
|
||
<p>Each unique angle satisfying the above criteria is counted only once, regardless
|
||
of whether either or both of the neighbor atoms making up the
|
||
angle appear in both the J and K lists.
|
||
It is OK if a particular angle is included in more than
|
||
one individual histogram, due to the way the <em>itypeN</em>, <em>jtypeN</em>, <em>ktypeN</em>
|
||
arguments are specified.</p>
|
||
<p>The first ADF value for a bin is calculated from the histogram count by
|
||
dividing by the total number of triples satisfying the criteria,
|
||
so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF
|
||
is a probability density function.</p>
|
||
<p>The second ADF value is reported as a cumulative sum of
|
||
all bins up to the current bins, averaged
|
||
over atoms of type <em>itypeN</em>. It represents the
|
||
number of angles per central atom with angle less
|
||
than or equal to the angle of the current bin,
|
||
analogous to the coordination
|
||
number radial distribution function.</p>
|
||
<p>The <em>ordinate</em> optional keyword determines
|
||
whether the bins are of uniform angular size from zero
|
||
to 180 (<em>degree</em>), zero to Pi (<em>radian</em>), or the
|
||
cosine of the angle uniform in the range [-1,1] (<em>cosine</em>).
|
||
<em>cosine</em> has the advantage of eliminating the <em>acos()</em> function
|
||
call, which speeds up the compute by 2-3x, and it is also preferred
|
||
on physical grounds, because the for uniformly distributed particles
|
||
in 3D, the angular probability density w.r.t dtheta is
|
||
sin(theta)/2, while for d(cos(theta)), it is 1/2,
|
||
Regardless of which ordinate is chosen, the first column of ADF
|
||
values is normalized w.r.t. the range of that ordinate, so that
|
||
the integral is 1.</p>
|
||
<p>The simplest way to output the results of the compute adf calculation
|
||
to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command, for
|
||
example:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">myADF</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">adf</span><span class="w"> </span><span class="m">32</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">3.5</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">3.5</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">ave</span><span class="o">/</span><span class="n">time</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">c_myADF[</span><span class="o">*</span><span class="n">]</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">tmp.adf</span><span class="w"> </span><span class="n">mode</span><span class="w"> </span><span class="n">vector</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="output-info">
|
||
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
|
||
<p>This compute calculates a global array with the number of rows =
|
||
<em>Nbins</em> and the number of columns = <span class="math notranslate nohighlight">\(1 + 2 \times\)</span> <em>Ntriples</em>, where <em>Ntriples</em>
|
||
is the number of I,J,K triples specified. The first column has the bin
|
||
coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
|
||
the two ADF values for a specific set of (<em>itypeN</em>,<em>jtypeN</em>,<em>ktypeN</em>)
|
||
interactions, as described above. These values can be used
|
||
by any command that uses a global values from a compute as input. See
|
||
the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> page for an overview of
|
||
LAMMPS output options.</p>
|
||
<p>The array values calculated by this compute are all “intensive”.</p>
|
||
<p>The first column of array values is the angle-related ordinate, either
|
||
the angle in degrees or radians, or the cosine of the angle. Each
|
||
subsequent pair of columns gives the first and second kinds of ADF
|
||
for a specific set of (<em>itypeN</em>,<em>jtypeN</em>,<em>ktypeN</em>). The values
|
||
in the first ADF column are normalized numbers <span class="math notranslate nohighlight">\(\ge 0.0\)</span>,
|
||
whose integral w.r.t. the ordinate is 1,
|
||
i.e. the first ADF is a normalized probability distribution.
|
||
The values in the second ADF column are also numbers <span class="math notranslate nohighlight">\(\ge 0.0\)</span>.
|
||
They are the cumulative density distribution of angles per atom.
|
||
By definition, this ADF is monotonically increasing from zero to
|
||
a maximum value equal to the average total number of
|
||
angles per atom satisfying the ADF criteria.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This compute is part of the EXTRA-COMPUTE package. It is only enabled
|
||
if LAMMPS was built with that package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
<p>By default, the ADF is not computed for distances longer than the
|
||
largest force cutoff, since the neighbor list creation will only contain
|
||
pairs up to that distance (plus neighbor list skin). If you use outer
|
||
cutoffs larger than that, you must use <a class="reference internal" href="neighbor.html"><span class="doc">neighbor style ‘bin’ or
|
||
‘nsq’</span></a>.</p>
|
||
<p>If you want an ADF for a larger outer cutoff, you can also use the
|
||
<a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to post-process a dump file, use <a class="reference internal" href="pair_zero.html"><span class="doc">pair
|
||
style zero</span></a> and set the force cutoff to be larger in the
|
||
rerun script. Note that in the rerun context, the force cutoff is
|
||
arbitrary and with pair style zero you are not computing any forces, and
|
||
since you are not running dynamics you are not changing the model that
|
||
generated the trajectory.</p>
|
||
<p>The ADF is not computed for neighbors outside the force cutoff,
|
||
since processors (in parallel) don’t know about atom coordinates for
|
||
atoms further away than that distance. If you want an ADF for larger
|
||
distances, you can use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to post-process
|
||
a dump file and set the cutoff for the potential to be longer in the
|
||
rerun script. Note that in the rerun context, the force cutoff is
|
||
arbitrary, since you are not running dynamics and thus are not changing
|
||
your model.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="compute_rdf.html"><span class="doc">compute rdf</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The keyword default is ordinate = degree.</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
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|
||
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