921 lines
76 KiB
HTML
921 lines
76 KiB
HTML
<!DOCTYPE html>
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<html class="writer-html5" lang="en" >
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<head>
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<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>compute chunk/atom command — LAMMPS documentation</title>
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<link rel="canonical" href="https://docs.lammps.org/compute_chunk_atom.html" />
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="next" title="compute chunk/spread/atom command" href="compute_chunk_spread_atom.html" />
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<link rel="prev" title="compute centro/atom command" href="compute_centro_atom.html" />
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<a href="Manual.html">
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<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
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</a>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<div class="lammps_release">git info: </div>
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</div>
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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 current"><a class="current reference internal" href="#">compute chunk/atom 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_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>
|
||
<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"><a class="reference internal" href="compute_saed.html">compute saed command</a></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>
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||
|
||
</div>
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</div>
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</nav>
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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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<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 chunk/atom command</li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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<a href="compute_centro_atom.html" class="btn btn-neutral float-left" title="compute centro/atom command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="compute_chunk_spread_atom.html" class="btn btn-neutral float-right" title="compute chunk/spread/atom command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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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-chunk-atom-command">
|
||
<span id="index-0"></span><h1>compute chunk/atom command<a class="headerlink" href="#compute-chunk-atom-command" title="Link to this heading"></a></h1>
|
||
<section id="syntax">
|
||
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">args</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</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>chunk/atom = style name of this compute command</p>
|
||
<pre class="literal-block">style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere</em> or <em>bin/cylinder</em> or <em>type</em> or <em>molecule</em> or c_ID, c_ID[I], f_ID, f_ID[I], v_name
|
||
<em>bin/1d</em> args = dim origin delta
|
||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||
delta = thickness of spatial bins in dim (distance units)
|
||
<em>bin/2d</em> args = dim origin delta dim origin delta
|
||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||
delta = thickness of spatial bins in dim (distance units)
|
||
<em>bin/3d</em> args = dim origin delta dim origin delta dim origin delta
|
||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||
delta = thickness of spatial bins in dim (distance units)
|
||
<em>bin/sphere</em> args = xorig yorig zorig rmin rmax nsbin
|
||
xorig,yorig,zorig = center point of sphere
|
||
srmin,srmax = bin from sphere radius rmin to rmax
|
||
nsbin = # of spherical shell bins between rmin and rmax
|
||
<em>bin/cylinder</em> args = dim origin delta c1 c2 rmin rmax ncbin
|
||
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder axis
|
||
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
|
||
delta = thickness of spatial bins in dim (distance units)
|
||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||
crmin,crmax = bin from cylinder radius rmin to rmax (distance units)
|
||
ncbin = # of concentric circle bins between rmin and rmax
|
||
<em>type</em> args = none
|
||
<em>molecule</em> args = none
|
||
c_ID, c_ID[I], f_ID, f_ID[I], v_name args = none
|
||
c_ID = per-atom vector calculated by a compute with ID
|
||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||
f_ID = per-atom vector calculated by a fix with ID
|
||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||
v_name = per-atom vector calculated by an atom-style variable with name</pre>
|
||
</li>
|
||
<li><p>zero or more keyword/values pairs may be appended</p></li>
|
||
<li><p>keyword = <em>region</em> or <em>nchunk</em> or <em>limit</em> or <em>ids</em> or <em>compress</em> or <em>discard</em> or <em>bound</em> or <em>pbc</em> or <em>units</em></p>
|
||
<pre class="literal-block"><em>region</em> value = region-ID
|
||
region-ID = ID of region atoms must be in to be part of a chunk
|
||
<em>nchunk</em> value = <em>once</em> or <em>every</em>
|
||
once = only compute the number of chunks once
|
||
every = re-compute the number of chunks whenever invoked
|
||
<em>limit</em> values = 0 or Nc max or Nc exact
|
||
0 = no limit on the number of chunks
|
||
Nc max = limit number of chunks to be <= Nc
|
||
Nc exact = set number of chunks to exactly Nc
|
||
<em>ids</em> value = <em>once</em> or <em>nfreq</em> or <em>every</em>
|
||
once = assign chunk IDs to atoms only once, they persist thereafter
|
||
nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> which sets Nfreq)
|
||
every = assign chunk IDs to atoms whenever invoked
|
||
<em>compress</em> value = <em>yes</em> or <em>no</em>
|
||
yes = compress chunk IDs to eliminate IDs with no atoms
|
||
no = do not compress chunk IDs even if some IDs have no atoms
|
||
<em>discard</em> value = <em>yes</em> or <em>no</em> or <em>mixed</em>
|
||
yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
|
||
no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
|
||
mixed = keep or discard such atoms according to spatial binning rule
|
||
<em>bound</em> values = x/y/z lo hi
|
||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound spatial bins in this dimension
|
||
lo = <em>lower</em> or coordinate value (distance units)
|
||
hi = <em>upper</em> or coordinate value (distance units)
|
||
<em>pbc</em> value = <em>no</em> or <em>yes</em>
|
||
yes = use periodic distance for bin/sphere and bin/cylinder styles
|
||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em></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">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">type</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">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">bin</span><span class="o">/</span><span class="m">1</span><span class="n">d</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">lower</span><span class="w"> </span><span class="m">0.02</span><span class="w"> </span><span class="n">units</span><span class="w"> </span><span class="n">reduced</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">bin</span><span class="o">/</span><span class="m">2</span><span class="n">d</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">lower</span><span class="w"> </span><span class="m">1.0</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">2.5</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">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">molecule</span><span class="w"> </span><span class="k">region </span><span class="nv nv-Identifier">sphere</span><span class="w"> </span><span class="n">nchunk</span><span class="w"> </span><span class="n">once</span><span class="w"> </span><span class="n">ids</span><span class="w"> </span><span class="n">once</span><span class="w"> </span><span class="n">compress</span><span class="w"> </span><span class="n">yes</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">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">bin</span><span class="o">/</span><span class="n">sphere</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="m">5.0</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="n">discard</span><span class="w"> </span><span class="n">yes</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">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">bin</span><span class="o">/</span><span class="n">cylinder</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">lower</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="m">5.0</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="n">discard</span><span class="w"> </span><span class="n">yes</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">chunk</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">c_cluster</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 an integer chunk ID from 1 to
|
||
Nchunk for each atom in the group. Values of chunk IDs are determined
|
||
by the <em>style</em> of chunk, which can be based on atom type or molecule
|
||
ID or spatial binning or a per-atom property or value calculated by
|
||
another <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>. Per-atom chunk IDs can be used by other
|
||
computes with “chunk” in their style name, such as <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> or <a class="reference internal" href="compute_msd_chunk.html"><span class="doc">compute msd/chunk</span></a>. Or they can be used by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command to sum and time average a
|
||
variety of per-atom properties over the atoms in each chunk. Or they
|
||
can simply be accessed by any command that uses per-atom values from a
|
||
compute as input, as discussed on the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a>
|
||
doc page.</p>
|
||
<p>See the <a class="reference internal" href="Howto_chunk.html"><span class="doc">Howto chunk</span></a> page for an overview of how
|
||
this compute can be used with a variety of other commands to tabulate
|
||
properties of a simulation. The page gives several examples of input
|
||
script commands that can be used to calculate interesting properties.</p>
|
||
<p>Conceptually it is important to realize that this compute does two
|
||
simple things. First, it sets the value of <em>Nchunk</em> = the number of
|
||
chunks, which can be a constant value or change over time. Second, it
|
||
assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1
|
||
to <em>Nchunk</em> inclusive; some chunks may have no atoms assigned to them.
|
||
Atoms that do not belong to any chunk are assigned a value of 0. Note
|
||
that the two operations are not always performed together. For
|
||
example, spatial bins can be setup once (which sets <em>Nchunk</em>), and
|
||
atoms assigned to those bins many times thereafter (setting their
|
||
chunk IDs).</p>
|
||
<p>All other commands in LAMMPS that use chunk IDs assume there are
|
||
<em>Nchunk</em> number of chunks, and that every atom is assigned to one of
|
||
those chunks, or not assigned to any chunk.</p>
|
||
<p>There are many options for specifying for how and when <em>Nchunk</em> is
|
||
calculated, and how and when chunk IDs are assigned to atoms. The
|
||
details depend on the chunk <em>style</em> and its <em>args</em>, as well as
|
||
optional keyword settings. They can also depend on whether a <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command is using this compute, since
|
||
that command requires <em>Nchunk</em> to remain static across windows of
|
||
timesteps it specifies, while it accumulates per-chunk averages.</p>
|
||
<p>The details are described below.</p>
|
||
<hr class="docutils" />
|
||
<p>The different chunk styles operate as follows. For each style, how it
|
||
calculates <em>Nchunk</em> and assigns chunk IDs to atoms is explained. Note
|
||
that using the optional keywords can change both of those actions, as
|
||
described further below where the keywords are discussed.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>binning</em> styles perform a spatial binning of atoms, and assign an
|
||
atom the chunk ID corresponding to the bin number it is in. <em>Nchunk</em>
|
||
is set to the number of bins, which can change if the simulation box
|
||
size changes. This also depends on the setting of the <em>units</em>
|
||
keyword (e.g., for <em>reduced</em> units the number of chunks may not change
|
||
even if the box size does).</p>
|
||
<p>The <em>bin/1d</em>, <em>bin/2d</em>, and <em>bin/3d</em> styles define bins as 1d layers
|
||
(slabs), 2d pencils, or 3d boxes. The <em>dim</em>, <em>origin</em>, and <em>delta</em>
|
||
settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is
|
||
no restriction on specifying dim = <em>x</em> before dim = <em>y</em> or <em>z</em>, or dim = <em>y</em>
|
||
before dim = <em>z</em>. Bins in a particular <em>dim</em> have a bin size in that
|
||
dimension given by <em>delta</em>. In each dimension, bins are defined
|
||
relative to a specified <em>origin</em>, which may be the lower/upper edge of
|
||
the simulation box (in that dimension), or its center point, or a
|
||
specified coordinate value. Starting at the origin, sufficient bins
|
||
are created in both directions to completely span the simulation box
|
||
or the bounds specified by the optional <em>bounds</em> keyword.</p>
|
||
<p>For orthogonal simulation boxes, the bins are layers, pencils, or
|
||
boxes aligned with the xyz coordinate axes. For triclinic
|
||
(non-orthogonal) simulation boxes, the bin faces are parallel to the
|
||
tilted faces of the simulation box. See the <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto triclinic</span></a> page for a discussion of the
|
||
geometry of triclinic boxes in LAMMPS. As described there, a tilted
|
||
simulation box has edge vectors <span class="math notranslate nohighlight">\(\vec a\)</span>, <span class="math notranslate nohighlight">\(\vec b\)</span>, and
|
||
<span class="math notranslate nohighlight">\(\vec c\)</span>. In that nomenclature, bins in
|
||
the <em>x</em> dimension have faces with normals in the <span class="math notranslate nohighlight">\(\vec b \times \vec c\)</span>
|
||
direction, bins in <em>y</em> have faces normal to the <span class="math notranslate nohighlight">\(\vec a \times \vec c\)</span>
|
||
direction, and bins in <em>z</em> have faces normal to the <span class="math notranslate nohighlight">\(\vec a \times \vec b\)</span>
|
||
direction. Note that in order to define the size and position of
|
||
these bins in an unambiguous fashion, the <em>units</em> option must be set
|
||
to <em>reduced</em> when using a triclinic simulation box, as noted below.</p>
|
||
<p>The meaning of <em>origin</em> and <em>delta</em> for triclinic boxes is as follows.
|
||
Consider a triclinic box with bins that are 1d layers or slabs in the
|
||
x dimension. No matter how the box is tilted, an <em>origin</em> of 0.0
|
||
means start layers at the lower <span class="math notranslate nohighlight">\(\vec b \times \vec c\)</span> plane of the
|
||
simulation box and an <em>origin</em> of 1.0 means to start layers at the upper
|
||
<span class="math notranslate nohighlight">\(\vec b \times \vec c\)</span> face of the box. A <em>delta</em> value of 0.1 in
|
||
<em>reduced</em> units means there will be 10 layers from 0.0 to 1.0, regardless of
|
||
the current size or shape of the simulation box.</p>
|
||
<p>The <em>bin/sphere</em> style defines a set of spherical shell bins around
|
||
the origin (<em>xorig</em>,<em>yorig</em>,<em>zorig</em>), using <em>nsbin</em> bins with radii
|
||
equally spaced between <em>srmin</em> and <em>srmax</em>. This is effectively a 1d
|
||
vector of bins. For example, if <em>srmin</em> = 1.0 and <em>srmax</em> = 10.0 and
|
||
<em>nsbin</em> = 9, then the first bin spans <span class="math notranslate nohighlight">\(1.0 < r < 2.0\)</span>, and the last bin
|
||
spans <span class="math notranslate nohighlight">\(9.0 < r < 10.0\)</span>. The geometry of the bins is the same whether the
|
||
simulation box is orthogonal or triclinic (i.e., the spherical shells
|
||
are not tilted or scaled differently in different dimensions to
|
||
transform them into ellipsoidal shells).</p>
|
||
<p>The <em>bin/cylinder</em> style defines bins for a cylinder oriented along
|
||
the axis <em>dim</em> with the axis coordinates in the other two radial
|
||
dimensions at (<em>c1</em>,<em>c2</em>). For dim = <em>x</em>, <span class="math notranslate nohighlight">\(c_1/c_2 = y/z\)</span>;
|
||
for dim = <em>y</em>, <span class="math notranslate nohighlight">\(c_1/c_2 = x/z\)</span>; for dim = <em>z</em>,
|
||
<span class="math notranslate nohighlight">\(c_1/c_2 = x/y\)</span>. This is effectively a 2d array of bins. The first
|
||
dimension is along the cylinder axis, the second dimension is radially outward
|
||
from the cylinder axis. The bin size and positions along the cylinder axis are
|
||
specified by the <em>origin</em> and <em>delta</em> values, the same as for the <em>bin/1d</em>,
|
||
<em>bin/2d</em>, and <em>bin/3d</em> styles. There are <em>ncbin</em> concentric circle bins in the
|
||
radial direction from the cylinder axis with radii equally spaced
|
||
between <em>crmin</em> and <em>crmax</em>. For example, if <em>crmin</em> = 1.0 and
|
||
<em>crmax</em> = 10.0 and <em>ncbin</em> = 9, then the first bin spans <span class="math notranslate nohighlight">\(1.0 < r < 2.0\)</span>
|
||
and the last bin spans <span class="math notranslate nohighlight">\(9.0 < r < 10.0\)</span>. The geometry of the bins in
|
||
the radial dimensions is the same whether the simulation box is
|
||
orthogonal or triclinic (i.e., the concentric circles are not tilted or
|
||
scaled differently in the two different dimensions to transform them
|
||
into ellipses).</p>
|
||
<p>The created bins (and hence the chunk IDs) are numbered consecutively
|
||
from 1 to the number of bins = <em>Nchunk</em>. For <em>bin2d</em> and <em>bin3d</em>, the
|
||
numbering varies most rapidly in the first dimension (which could be
|
||
<em>x</em>, <em>y</em>, or <em>z</em>), next rapidly in the second dimension, and most slowly in the
|
||
third dimension. For <em>bin/sphere</em>, the bin with smallest radii is chunk
|
||
1 and the bin with largest radii is chunk Nchunk = <em>ncbin</em>. For
|
||
<em>bin/cylinder</em>, the numbering varies most rapidly in the dimension
|
||
along the cylinder axis and most slowly in the radial direction.</p>
|
||
<p>Each time this compute is invoked, each atom is mapped to a bin based
|
||
on its current position. Note that between reneighboring timesteps,
|
||
atoms can move outside the current simulation box. If the box is
|
||
periodic (in that dimension) the atom is remapping into the periodic
|
||
box for purposes of binning. If the box in not periodic, the atom may
|
||
have moved outside the bounds of all bins. If an atom is not inside
|
||
any bin, the <em>discard</em> keyword is used to determine how a chunk ID is
|
||
assigned to the atom.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>type</em> style uses the atom type as the chunk ID. <em>Nchunk</em> is set
|
||
to the number of atom types defined for the simulation (e.g., via the
|
||
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> commands).</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>molecule</em> style uses the molecule ID of each atom as its chunk
|
||
ID. <em>Nchunk</em> is set to the largest chunk ID. Note that this excludes
|
||
molecule IDs for atoms which are not in the specified group or
|
||
optional region.</p>
|
||
<p>There is no requirement that all atoms in a particular molecule are
|
||
assigned the same chunk ID (zero or non-zero), though you probably
|
||
want that to be the case, if you wish to compute a per-molecule
|
||
property. LAMMPS will issue a warning if that is not the case, but
|
||
only the first time that <em>Nchunk</em> is calculated.</p>
|
||
<p>Note that atoms with a molecule ID = 0, which may be non-molecular
|
||
solvent atoms, have an out-of-range chunk ID. These atoms are
|
||
discarded (not assigned to any chunk) or assigned to <em>Nchunk</em>,
|
||
depending on the value of the <em>discard</em> keyword.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>compute/fix/variable</em> styles set the chunk ID of each atom based
|
||
on a quantity calculated and stored by a compute, fix, or variable.
|
||
In each case, it must be a per-atom quantity. In each case the
|
||
referenced floating point values are converted to an integer chunk ID
|
||
as follows. The floating point value is truncated (rounded down) to
|
||
an integer value. If the integer value is <span class="math notranslate nohighlight">\(\le 0\)</span>, then a chunk ID of 0
|
||
is assigned to the atom. If the integer value is <span class="math notranslate nohighlight">\(> 0\)</span>, it becomes the
|
||
chunk ID to the atom. <em>Nchunk</em> is set to the largest chunk ID. Note
|
||
that this excludes atoms which are not in the specified group or
|
||
optional region.</p>
|
||
<p>If the style begins with “c_”, a compute ID must follow which has been
|
||
previously defined in the input script. If no bracketed integer is
|
||
appended, the per-atom vector calculated by the compute is used. If a
|
||
bracketed integer is appended, the Ith column of the per-atom array
|
||
calculated by the compute is used. Users can also write code for
|
||
their own compute styles and <a class="reference internal" href="Modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||
<p>If the style begins with “f_”, a fix ID must follow which has been
|
||
previously defined in the input script. If no bracketed integer is
|
||
appended, the per-atom vector calculated by the fix is used. If a
|
||
bracketed integer is appended, the Ith column of the per-atom array
|
||
calculated by the fix is used. Note that some fixes only produce
|
||
their values on certain timesteps, which must be compatible with the
|
||
timestep on which this compute accesses the fix, else an error
|
||
results. Users can also write code for their own fix styles and <a class="reference internal" href="Modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||
<p>If a value begins with “v_”, a variable name for an <em>atom</em> or
|
||
<em>atomfile</em> style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> must follow which has been
|
||
previously defined in the input script. Variables of style <em>atom</em> can
|
||
reference thermodynamic keywords and various per-atom attributes, or
|
||
invoke other computes, fixes, or variables when they are evaluated, so
|
||
this is a very general means of generating per-atom quantities to
|
||
treat as a chunk ID.</p>
|
||
<hr class="docutils" />
|
||
<p>Normally, <em>Nchunk</em> = the number of chunks, is re-calculated every time
|
||
this fix is invoked, though the value may or may not change. As
|
||
explained below, the <em>nchunk</em> keyword can be set to <em>once</em> which means
|
||
<em>Nchunk</em> will never change.</p>
|
||
<p>If a <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command uses this compute, it
|
||
can also turn off the re-calculation of <em>Nchunk</em> for one or more
|
||
windows of timesteps. The extent of the windows, during which Nchunk
|
||
is held constant, are determined by the <em>Nevery</em>, <em>Nrepeat</em>, <em>Nfreq</em>
|
||
values and the <em>ave</em> keyword setting that are used by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command.</p>
|
||
<p>Specifically, if <em>ave</em> = <em>one</em>, then for each span of <em>Nfreq</em>
|
||
timesteps, <em>Nchunk</em> is held constant between the first timestep when
|
||
averaging is done (within the Nfreq-length window), and the last
|
||
timestep when averaging is done (multiple of Nfreq). If <em>ave</em> =
|
||
<em>running</em> or <em>window</em>, then <em>Nchunk</em> is held constant forever,
|
||
starting on the first timestep when the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command invokes this compute.</p>
|
||
<p>Note that multiple <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> commands can use
|
||
the same compute chunk/atom compute. However, the time windows they
|
||
induce for holding <em>Nchunk</em> constant must be identical, else an error
|
||
will be generated.</p>
|
||
<hr class="docutils" />
|
||
<p>The various optional keywords operate as follows. Note that some of
|
||
them function differently or are ignored by different chunk styles.
|
||
Some of them also have different default values, depending on
|
||
the chunk style, as listed below.</p>
|
||
<p>The <em>region</em> keyword applies to all chunk styles. If used, an atom
|
||
must be in both the specified group and the specified geometric
|
||
<a class="reference internal" href="region.html"><span class="doc">region</span></a> to be assigned to a chunk.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>nchunk</em> keyword applies to all chunk styles. It specifies how
|
||
often <em>Nchunk</em> is recalculated, which in turn can affect the chunk IDs
|
||
assigned to individual atoms.</p>
|
||
<p>If <em>nchunk</em> is set to <em>once</em>, then <em>Nchunk</em> is only calculated once,
|
||
the first time this compute is invoked. If <em>nchunk</em> is set to
|
||
<em>every</em>, then <em>Nchunk</em> is re-calculated every time the compute is
|
||
invoked. Note that, as described above, the use of this compute
|
||
by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command can override
|
||
the <em>every</em> setting.</p>
|
||
<p>The default values for <em>nchunk</em> are listed below and depend on the
|
||
chunk style and other system and keyword settings. They attempt to
|
||
represent typical use cases for the various chunk styles. The
|
||
<em>nchunk</em> value can always be set explicitly if desired.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>limit</em> keyword can be used to limit the calculated value of
|
||
<em>Nchunk</em> = the number of chunks. The limit is applied each time
|
||
<em>Nchunk</em> is calculated, which also limits the chunk IDs assigned to
|
||
any atom. The <em>limit</em> keyword is used by all chunk styles except the
|
||
<em>binning</em> styles, which ignore it. This is because the number of bins
|
||
can be tailored using the <em>bound</em> keyword (described below) which
|
||
effectively limits the size of <em>Nchunk</em>.</p>
|
||
<p>If <em>limit</em> is set to <em>Nc</em> = 0, then no limit is imposed on <em>Nchunk</em>,
|
||
though the <em>compress</em> keyword can still be used to reduce <em>Nchunk</em>, as
|
||
described below.</p>
|
||
<p>If <em>Nc</em> <span class="math notranslate nohighlight">\(>\)</span> 0, then the effect of the <em>limit</em> keyword depends on whether
|
||
the <em>compress</em> keyword is also used with a setting of <em>yes</em>, and
|
||
whether the <em>compress</em> keyword is specified before the <em>limit</em> keyword
|
||
or after.</p>
|
||
<p>In all cases, <em>Nchunk</em> is first calculated in the usual way for each
|
||
chunk style, as described above.</p>
|
||
<p>First, here is what occurs if <em>compress yes</em> is not set. If <em>limit</em>
|
||
is set to <em>Nc max</em>, then <em>Nchunk</em> is reset to the smaller of <em>Nchunk</em>
|
||
and <em>Nc</em>. If <em>limit</em> is set to <em>Nc exact</em>, then <em>Nchunk</em> is reset to
|
||
<em>Nc</em>, whether the original <em>Nchunk</em> was larger or smaller than <em>Nc</em>.
|
||
If <em>Nchunk</em> shrank due to the <em>limit</em> setting, then atom chunk IDs <span class="math notranslate nohighlight">\(>\)</span>
|
||
<em>Nchunk</em> will be reset to 0 or <em>Nchunk</em>, depending on the setting of
|
||
the <em>discard</em> keyword. If <em>Nchunk</em> grew, there will simply be some
|
||
chunks with no atoms assigned to them.</p>
|
||
<p>If <em>compress yes</em> is set, and the <em>compress</em> keyword comes before the
|
||
<em>limit</em> keyword, the compression operation is performed first, as
|
||
described below, which resets <em>Nchunk</em>. The <em>limit</em> keyword is then
|
||
applied to the new <em>Nchunk</em> value, exactly as described in the
|
||
preceding paragraph. Note that in this case, all atoms will end up
|
||
with chunk IDs <span class="math notranslate nohighlight">\(\le\)</span> <em>Nc</em>, but their original values (e.g., molecule ID
|
||
or compute/fix/variable) may have been <span class="math notranslate nohighlight">\(>\)</span> <em>Nc</em>, because of the
|
||
compression operation.</p>
|
||
<p>If <em>compress yes</em> is set, and the <em>compress</em> keyword comes after the
|
||
<em>limit</em> keyword, then the <em>limit</em> value of <em>Nc</em> is applied first to
|
||
the uncompressed value of <em>Nchunk</em>, but only if <em>Nc</em> <span class="math notranslate nohighlight">\(<\)</span> <em>Nchunk</em>
|
||
(whether <em>Nc max</em> or <em>Nc exact</em> is used). This effectively means all
|
||
atoms with chunk IDs <span class="math notranslate nohighlight">\(>\)</span> <em>Nc</em> have their chunk IDs reset to 0 or <em>Nc</em>,
|
||
depending on the setting of the <em>discard</em> keyword. The compression
|
||
operation is then performed, which may shrink <em>Nchunk</em> further. If
|
||
the new <em>Nchunk</em> <span class="math notranslate nohighlight">\(<\)</span> <em>Nc</em> and <em>limit</em> = <em>Nc exact</em> is specified, then
|
||
<em>Nchunk</em> is reset to <em>Nc</em>, which results in extra chunks with no atoms
|
||
assigned to them. Note that in this case, all atoms will end up with
|
||
chunk IDs <span class="math notranslate nohighlight">\(\le\)</span> <em>Nc</em>, and their original values (e.g., molecule ID or
|
||
compute/fix/variable value) will also have been <span class="math notranslate nohighlight">\(\le\)</span> <em>Nc</em>.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>ids</em> keyword applies to all chunk styles. If the setting is
|
||
<em>once</em> then the chunk IDs assigned to atoms the first time this
|
||
compute is invoked will be permanent, and never be re-computed.</p>
|
||
<p>If the setting is <em>nfreq</em> and if a <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>
|
||
command is using this compute, then in each of the <em>Nchunk</em> = constant
|
||
time windows (discussed above), the chunk ID’s assigned to atoms on
|
||
the first step of the time window will persist until the end of the
|
||
time window.</p>
|
||
<p>If the setting is <em>every</em>, which is the default, then chunk IDs are
|
||
re-calculated on any timestep this compute is invoked.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you want the persistent chunk-IDs calculated by this compute
|
||
to be continuous when running from a <a class="reference internal" href="read_restart.html"><span class="doc">restart file</span></a>,
|
||
then you should use the same ID for this compute, as in the original
|
||
run. This is so that the fix this compute creates to store per-atom
|
||
quantities will also have the same ID, and thus be initialized
|
||
correctly with chunk IDs from the restart file.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>compress</em> keyword applies to all chunk styles and affects how
|
||
<em>Nchunk</em> is calculated, which in turn affects the chunk IDs assigned
|
||
to each atom. It is useful for converting a “sparse” set of chunk IDs
|
||
(with many IDs that have no atoms assigned to them), into a “dense”
|
||
set of IDs, where every chunk has one or more atoms assigned to it.</p>
|
||
<p>Two possible use cases are as follows. If a large simulation box is
|
||
mostly empty space, then the <em>binning</em> style may produce many bins
|
||
with no atoms. If <em>compress</em> is set to <em>yes</em>, only bins with atoms
|
||
will be contribute to <em>Nchunk</em>. Likewise, the <em>molecule</em> or
|
||
<em>compute/fix/variable</em> styles may produce large <em>Nchunk</em> values. For
|
||
example, the <a class="reference internal" href="compute_cluster_atom.html"><span class="doc">compute cluster/atom</span></a> command
|
||
assigns every atom an atom ID for one of the atoms it is clustered
|
||
with. For a million-atom system with 5 clusters, there would only be
|
||
5 unique chunk IDs, but the largest chunk ID might be 1 million,
|
||
resulting in <em>Nchunk</em> = 1 million. If <em>compress</em> is set to <em>yes</em>,
|
||
<em>Nchunk</em> will be reset to 5.</p>
|
||
<p>If <em>compress</em> is set to <em>no</em>, which is the default, no compression is
|
||
done. If it is set to <em>yes</em>, all chunk IDs with no atoms are removed
|
||
from the list of chunk IDs, and the list is sorted. The remaining
|
||
chunk IDs are renumbered from 1 to <em>Nchunk</em> where <em>Nchunk</em> is the new
|
||
length of the list. The chunk IDs assigned to each atom reflect
|
||
the new renumbering from 1 to <em>Nchunk</em>.</p>
|
||
<p>The original chunk IDs (before renumbering) can be accessed by the
|
||
<a class="reference internal" href="compute_property_chunk.html"><span class="doc">compute property/chunk</span></a> command and its
|
||
<em>id</em> keyword, or by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command
|
||
which outputs the original IDs as one of the columns in its global
|
||
output array. For example, using the “compute cluster/atom” command
|
||
discussed above, the original 5 unique chunk IDs might be atom IDs
|
||
(27,4982,58374,857838,1000000). After compression, these will be
|
||
renumbered to (1,2,3,4,5). The original values (27,…,1000000) can
|
||
be output to a file by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command,
|
||
or by using the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command in
|
||
conjunction with the <a class="reference internal" href="compute_property_chunk.html"><span class="doc">compute property/chunk</span></a> command.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>The compression operation requires global communication across
|
||
all processors to share their chunk ID values. It can require large
|
||
memory on every processor to store them, even after they are
|
||
compressed, if there are a large number of unique chunk IDs with
|
||
atoms assigned to them. It uses a STL map to find unique chunk IDs
|
||
and store them in sorted order. Each time an atom is assigned a
|
||
compressed chunk ID, it must access the STL map. All of this means
|
||
that compression can be expensive, both in memory and CPU time. The
|
||
use of the <em>limit</em> keyword in conjunction with the <em>compress</em> keyword
|
||
can affect these costs, depending on which keyword is used first. So
|
||
use this option with care.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>discard</em> keyword applies to all chunk styles. It affects what
|
||
chunk IDs are assigned to atoms that do not match one of the valid
|
||
chunk IDs from 1 to <em>Nchunk</em>. Note that it does not apply to atoms
|
||
that are not in the specified group or optionally specified region.
|
||
Those atoms are always assigned a chunk ID = 0.</p>
|
||
<p>If the calculated chunk ID for an atom is not within the range 1 to
|
||
<em>Nchunk</em> then it is a “discard” atom. Note that <em>Nchunk</em> may have
|
||
been shrunk by the <em>limit</em> keyword. Or the <em>compress</em> keyword may
|
||
have eliminated chunk IDs that were valid before the compression took
|
||
place, and are now not in the compressed list. Also note that for the
|
||
<em>molecule</em> chunk style, if new molecules are added to the system,
|
||
their chunk IDs may exceed a previously calculated <em>Nchunk</em>.
|
||
Likewise, evaluation of a compute/fix/variable on a later timestep may
|
||
return chunk IDs that are invalid for the previously calculated
|
||
<em>Nchunk</em>.</p>
|
||
<p>All the chunk styles except the <em>binning</em> styles, must use <em>discard</em>
|
||
set to either <em>yes</em> or <em>no</em>. If <em>discard</em> is set to <em>yes</em>, which is
|
||
the default, then every “discard” atom has its chunk ID set to 0. If
|
||
<em>discard</em> is set to <em>no</em>, every “discard” atom has its chunk ID set to
|
||
<em>Nchunk</em>. I.e. it becomes part of the last chunk.</p>
|
||
<p>The <em>binning</em> styles use the <em>discard</em> keyword to decide whether to
|
||
discard atoms outside the spatial domain covered by bins, or to assign
|
||
them to the bin they are nearest to.</p>
|
||
<p>For the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em> styles the details are as
|
||
follows. If <em>discard</em> is set to <em>yes</em>, an out-of-domain atom will
|
||
have its chunk ID set to 0. If <em>discard</em> is set to <em>no</em>, the atom
|
||
will have its chunk ID set to the first or last bin in that dimension.
|
||
If <em>discard</em> is set to <em>mixed</em>, which is the default, it will only
|
||
have its chunk ID set to the first or last bin if bins extend to the
|
||
simulation box boundary in that dimension. This is the case if the
|
||
<em>bound</em> keyword settings are <em>lower</em> and <em>upper</em>, which is the
|
||
default. If the <em>bound</em> keyword settings are numeric values, then the
|
||
atom will have its chunk ID set to 0 if it is outside the bounds of
|
||
any bin. Note that in this case, it is possible that the first or
|
||
last bin extends beyond the numeric <em>bounds</em> settings, depending on
|
||
the specified <em>origin</em>. If this is the case, the chunk ID of the atom
|
||
is only set to 0 if it is outside the first or last bin, not if it is
|
||
simply outside the numeric <em>bounds</em> setting.</p>
|
||
<p>For the <em>bin/sphere</em> style the details are as follows. If <em>discard</em>
|
||
is set to <em>yes</em>, an out-of-domain atom will have its chunk ID set to
|
||
0. If <em>discard</em> is set to <em>no</em> or <em>mixed</em>, the atom will have its
|
||
chunk ID set to the first or last bin, i.e. the innermost or outermost
|
||
spherical shell. If the distance of the atom from the origin is less
|
||
than <em>rmin</em>, it will be assigned to the first bin. If the distance of
|
||
the atom from the origin is greater than <em>rmax</em>, it will be assigned
|
||
to the last bin.</p>
|
||
<p>For the <em>bin/cylinder</em> style the details are as follows. If <em>discard</em>
|
||
is set to <em>yes</em>, an out-of-domain atom will have its chunk ID set to
|
||
0. If <em>discard</em> is set to <em>no</em>, the atom will have its chunk ID set
|
||
to the first or last bin in both the radial and axis dimensions. If
|
||
<em>discard</em> is set to <em>mixed</em>, which is the default, the radial
|
||
dimension is treated the same as for <em>discard</em> = no. But for the axis
|
||
dimension, it will only have its chunk ID set to the first or last
|
||
bin if bins extend to the simulation box boundary in the axis
|
||
dimension. This is the case if the <em>bound</em> keyword settings are
|
||
<em>lower</em> and <em>upper</em>, which is the default. If the <em>bound</em> keyword
|
||
settings are numeric values, then the atom will have its chunk ID set
|
||
to 0 if it is outside the bounds of any bin. Note that in this case,
|
||
it is possible that the first or last bin extends beyond the numeric
|
||
<em>bounds</em> settings, depending on the specified <em>origin</em>. If this is
|
||
the case, the chunk ID of the atom is only set to 0 if it is outside
|
||
the first or last bin, not if it is simply outside the numeric
|
||
<em>bounds</em> setting.</p>
|
||
<p>If <em>discard</em> is set to <em>no</em> or <em>mixed</em>, the atom will have its
|
||
chunk ID set to the first or last bin, i.e. the innermost or outermost
|
||
spherical shell. If the distance of the atom from the origin is less
|
||
than <em>rmin</em>, it will be assigned to the first bin. If the distance of
|
||
the atom from the origin is greater than <em>rmax</em>, it will be assigned
|
||
to the last bin.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>bound</em> keyword only applies to the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em>
|
||
styles and to the axis dimension of the <em>bin/cylinder</em> style;
|
||
otherwise it is ignored. It can be used one or more times to limit
|
||
the extent of bin coverage in a specified dimension, i.e. to only bin
|
||
a portion of the box. If the <em>lo</em> setting is <em>lower</em> or the <em>hi</em>
|
||
setting is <em>upper</em>, the bin extent in that direction extends to the
|
||
box boundary. If a numeric value is used for <em>lo</em> and/or <em>hi</em>, then
|
||
the bin extent in the <em>lo</em> or <em>hi</em> direction extends only to that
|
||
value, which is assumed to be inside (or at least near) the simulation
|
||
box boundaries, though LAMMPS does not check for this. Note that
|
||
using the <em>bound</em> keyword typically reduces the total number of bins
|
||
and thus the number of chunks <em>Nchunk</em>.</p>
|
||
<p>The <em>pbc</em> keyword only applies to the <em>bin/sphere</em> and <em>bin/cylinder</em>
|
||
styles. If set to <em>yes</em>, the distance an atom is from the sphere
|
||
origin or cylinder axis is calculated in a minimum image sense with
|
||
respect to periodic dimensions, when determining which bin the atom is
|
||
in. I.e. if x is a periodic dimension and the distance between the
|
||
atom and the sphere center in the x dimension is greater than 0.5 *
|
||
simulation box length in x, then a box length is subtracted to give a
|
||
distance < 0.5 * simulation box length. This allosws the sphere or
|
||
cylinder center to be near a box edge, and atoms on the other side of
|
||
the periodic box will still be close to the center point/axis. Note
|
||
that with a setting of <em>yes</em>, the outer sphere or cylinder radius must
|
||
also be <= 0.5 * simulation box length in any periodic dimension
|
||
except for the cylinder axis dimension, or an error is generated.</p>
|
||
<p>The <em>units</em> keyword only applies to the <em>binning</em> styles; otherwise it
|
||
is ignored. For the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em> styles, it
|
||
determines the meaning of the distance units used for the bin sizes
|
||
<em>delta</em> and for <em>origin</em> and <em>bounds</em> values if they are coordinate
|
||
values. For the <em>bin/sphere</em> style it determines the meaning of the
|
||
distance units used for <em>xorig</em>,<em>yorig</em>,<em>zorig</em> and the radii <em>srmin</em>
|
||
and <em>srmax</em>. For the <em>bin/cylinder</em> style it determines the meaning
|
||
of the distance units used for <em>delta</em>,<em>c1</em>,<em>c2</em> and the radii <em>crmin</em>
|
||
and <em>crmax</em>.</p>
|
||
<p>For orthogonal simulation boxes, any of the 3 options may
|
||
be used. For non-orthogonal (triclinic) simulation boxes, only the
|
||
<em>reduced</em> option may be used.</p>
|
||
<p>A <em>box</em> value selects standard distance units as defined by the
|
||
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command (e.g., <span class="math notranslate nohighlight">\(\AA\)</span> for units = <em>real</em> or <em>metal</em>).
|
||
A <em>lattice</em> value means the distance units are in lattice spacings.
|
||
The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
|
||
define the lattice spacing. A <em>reduced</em> value means normalized
|
||
unitless values between 0 and 1, which represent the lower and upper
|
||
faces of the simulation box respectively. Thus an <em>origin</em> value of
|
||
0.5 means the center of the box in any dimension. A <em>delta</em> value of
|
||
0.1 means 10 bins span the box in that dimension.</p>
|
||
<p>Note that for the <em>bin/sphere</em> style, the radii <em>srmin</em> and <em>srmax</em> are
|
||
scaled by the lattice spacing or reduced value of the <em>x</em> dimension.</p>
|
||
<p>Note that for the <em>bin/cylinder</em> style, the radii <em>crmin</em> and <em>crmax</em>
|
||
are scaled by the lattice spacing or reduced value of the first
|
||
dimension perpendicular to the cylinder axis (e.g., <em>y</em> for an <em>x</em>-axis
|
||
cylinder, <em>x</em> for a <em>y</em>-axis cylinder, and <em>x</em> for a <em>z</em>-axis cylinder).</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<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 per-atom vector (the chunk ID), which can
|
||
be accessed by any command that uses per-atom values from a compute
|
||
as input. It also calculates a global scalar (the number of chunks),
|
||
which can be similarly accessed everywhere outside of a per-atom context.
|
||
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 per-atom vector values are unitless chunk IDs, ranging from 1 to
|
||
<em>Nchunk</em> (inclusive) for atoms assigned to chunks, and 0 for atoms not
|
||
belonging to a chunk. The scalar contains the value of <em>Nchunk</em>.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>Even if the <em>nchunk</em> keyword is set to <em>once</em>, the chunk IDs assigned
|
||
to each atom are not stored in a restart files. This means you cannot
|
||
expect those assignments to persist in a restarted simulation.
|
||
Instead you must re-specify this command and assign atoms to chunks when
|
||
the restarted simulation begins.</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_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>,
|
||
<a class="reference internal" href="compute_global_atom.html"><span class="doc">compute global/atom</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 as follows:</p>
|
||
<ul class="simple">
|
||
<li><p>region = none</p></li>
|
||
<li><p>nchunk = every, if compress is yes, overriding other defaults listed here</p></li>
|
||
<li><p>nchunk = once, for type style</p></li>
|
||
<li><p>nchunk = once, for mol style if region is none</p></li>
|
||
<li><p>nchunk = every, for mol style if region is set</p></li>
|
||
<li><p>nchunk = once, for binning style if the simulation box size is static or units = reduced</p></li>
|
||
<li><p>nchunk = every, for binning style if the simulation box size is dynamic and units is lattice or box</p></li>
|
||
<li><p>nchunk = every, for compute/fix/variable style</p></li>
|
||
<li><p>limit = 0</p></li>
|
||
<li><p>ids = every</p></li>
|
||
<li><p>compress = no</p></li>
|
||
<li><p>discard = yes, for all styles except binning</p></li>
|
||
<li><p>discard = mixed, for binning styles</p></li>
|
||
<li><p>bound = lower and upper in all dimensions</p></li>
|
||
<li><p>pbc = no</p></li>
|
||
<li><p>units = lattice</p></li>
|
||
</ul>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="compute_centro_atom.html" class="btn btn-neutral float-left" title="compute centro/atom command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="compute_chunk_spread_atom.html" class="btn btn-neutral float-right" title="compute chunk/spread/atom command" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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||
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