480 lines
42 KiB
HTML
480 lines
42 KiB
HTML
<!DOCTYPE html>
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<title>compute coord/atom command — LAMMPS documentation</title>
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<link rel="canonical" href="https://docs.lammps.org/compute_coord_atom.html" />
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="next" title="compute count/type command" href="compute_count_type.html" />
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<link rel="prev" title="compute contact/atom command" href="compute_contact_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><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Compute Styles</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_adf.html">compute adf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ave_sphere_atom.html">compute ave/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_spread_atom.html">compute chunk/spread/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-fragment-atom-command">compute fragment/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-aggregate-atom-command">compute aggregate/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cnp_atom.html">compute cnp/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_composition_atom.html">compute composition/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">compute coord/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_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>
|
||
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
</div>
|
||
</nav>
|
||
|
||
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
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<a href="Manual.html">LAMMPS</a>
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</nav>
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<div class="wy-nav-content">
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<div class="rst-content style-external-links">
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<div role="navigation" aria-label="Page navigation">
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
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<li class="breadcrumb-item"><a href="computes.html">Compute Styles</a></li>
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<li class="breadcrumb-item active">compute coord/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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</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
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<a href="compute_contact_atom.html" class="btn btn-neutral float-left" title="compute contact/atom command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="compute_count_type.html" class="btn btn-neutral float-right" title="compute count/type command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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<hr/>
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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|
||
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="compute-coord-atom-command">
|
||
<span id="index-1"></span><span id="index-0"></span><h1>compute coord/atom command<a class="headerlink" href="#compute-coord-atom-command" title="Link to this heading"></a></h1>
|
||
<p>Accelerator Variants: <em>coord/atom/kk</em></p>
|
||
<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">coord</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">...</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>coord/atom = style name of this compute command</p></li>
|
||
<li><p>style = <em>cutoff</em> or <em>orientorder</em></p>
|
||
<pre class="literal-block"><em>cutoff</em> args = cutoff [<em>group</em> group2-ID] typeN
|
||
cutoff = distance within which to count coordination neighbors (distance units)
|
||
<em>group</em> group2-ID = select group-ID to restrict which atoms to consider for coordination number (optional)
|
||
typeN = atom type for Nth coordination count (see asterisk form below)
|
||
<em>orientorder</em> args = orientorderID threshold
|
||
orientorderID = ID of an orientorder/atom compute
|
||
threshold = minimum value of the product of two "connected" atoms</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">coord</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">cutoff</span><span class="w"> </span><span class="m">2.0</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">coord</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">cutoff</span><span class="w"> </span><span class="m">6.0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</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">coord</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">cutoff</span><span class="w"> </span><span class="m">6.0</span><span class="w"> </span><span class="m">2</span><span class="o">*</span><span class="m">4</span><span class="w"> </span><span class="m">5</span><span class="o">*</span><span class="m">8</span><span class="w"> </span><span class="o">*</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">solute</span><span class="w"> </span><span class="n">coord</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">cutoff</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="k">group </span><span class="nv nv-Identifier">solvent</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">coord</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">orientorder</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.5</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>This compute performs calculations between neighboring atoms to
|
||
determine a coordination value. The specific calculation and the
|
||
meaning of the resulting value depend on the <em>cstyle</em> keyword used.</p>
|
||
<p>The <em>cutoff</em> cstyle calculates one or more traditional coordination
|
||
numbers for each atom. A coordination number is defined as the number
|
||
of neighbor atoms with specified atom type(s), and optionally within
|
||
the specified group, that are within the specified cutoff distance from
|
||
the central atom. The compute group selects only the central atoms; all
|
||
neighboring atoms, unless selected by type, type range, or group option,
|
||
are included in the coordination number tally.</p>
|
||
<p>The optional <em>group</em> keyword allows to specify from which group atoms
|
||
contribute to the coordination number. Default setting is group ‘all.’</p>
|
||
<p>The <em>typeN</em> keywords allow specification of which atom types
|
||
contribute to each coordination number. One coordination number is
|
||
computed for each of the <em>typeN</em> keywords listed. If no <em>typeN</em>
|
||
keywords are listed, a single coordination number is calculated, which
|
||
includes atoms of all types (same as the “*” format, see below).</p>
|
||
<p>The <em>typeN</em> keywords can be specified in one of two ways. An explicit
|
||
numeric value can be used, as in the second example above. Or a
|
||
wild-card asterisk can be used to specify a range of atom types. This
|
||
takes the form “*” or “*n” or “m*” or “m*n”. If <span class="math notranslate nohighlight">\(N\)</span> is the number of
|
||
atom types, then an asterisk with no numeric values means all types
|
||
from 1 to <span class="math notranslate nohighlight">\(N\)</span>. A leading asterisk means all types from 1 to n
|
||
(inclusive). A trailing asterisk means all types from m to <span class="math notranslate nohighlight">\(N\)</span>
|
||
(inclusive). A middle asterisk means all types from m to n
|
||
(inclusive).</p>
|
||
<p>The <em>orientorder</em> cstyle calculates the number of “connected” neighbor
|
||
atoms <em>j</em> around each central atom <em>i</em>. For this <em>cstyle</em>, connected is
|
||
defined by the orientational order parameter calculated by the
|
||
<a class="reference internal" href="compute_orientorder_atom.html"><span class="doc">compute orientorder/atom</span></a> command.
|
||
This <em>cstyle</em> thus allows one to apply the ten Wolde’s criterion to
|
||
identify crystal-like atoms in a system, as discussed in <a class="reference internal" href="#tenwolde1"><span class="std std-ref">ten Wolde</span></a>.</p>
|
||
<p>The ID of the previously specified <a class="reference internal" href="compute_orientorder_atom.html"><span class="doc">compute orientorder/atom</span></a> command is specified as
|
||
<em>orientorderID</em>. The compute must invoke its <em>components</em> option to
|
||
calculate components of the <em>Ybar_lm</em> vector for each atoms, as
|
||
described in its documentation. Note that orientorder/atom compute
|
||
defines its own criteria for identifying neighboring atoms. If the
|
||
scalar product (<em>Ybar_lm(i)</em>, <em>Ybar_lm(j)</em>), calculated by the
|
||
orientorder/atom compute is larger than the specified <em>threshold</em>,
|
||
then <em>i</em> and <em>j</em> are connected, and the coordination value of <em>i</em> is
|
||
incremented by one.</p>
|
||
<p>For all <em>cstyle</em> settings, all coordination values will be 0.0 for
|
||
atoms not in the specified compute group.</p>
|
||
<p>The neighbor list needed to compute this quantity is constructed each
|
||
time the calculation is performed (i.e., each time a snapshot of atoms
|
||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||
too frequently.</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 the neighbor list, it also means
|
||
those pairs will not be included in the coordination count. One way
|
||
to get around this, 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 coordination 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>
|
||
<hr class="docutils" />
|
||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||
functionally the same as the corresponding style without the suffix.
|
||
They have been optimized to run faster, depending on your available
|
||
hardware, as discussed on the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a>
|
||
page. The accelerated styles take the same arguments and should
|
||
produce the same results, except for round-off and precision issues.</p>
|
||
<p>These accelerated styles are part of the GPU, INTEL, KOKKOS,
|
||
OPENMP, and OPT packages, respectively. They are only enabled if
|
||
LAMMPS was built with those packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
<p>You can specify the accelerated styles explicitly in your input script
|
||
by including their suffix, or you can use the <a class="reference internal" href="Run_options.html"><span class="doc">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can use the
|
||
<a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||
<p>See the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a> page for more
|
||
instructions on how to use the accelerated styles effectively.</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>For <em>cstyle</em> cutoff, this compute can calculate a per-atom vector or
|
||
array. If single <em>type1</em> keyword is specified (or if none are
|
||
specified), this compute calculates a per-atom vector. If multiple
|
||
<em>typeN</em> keywords are specified, this compute calculates a per-atom
|
||
array, with <span class="math notranslate nohighlight">\(N\)</span> columns.</p>
|
||
<p>For <em>cstyle</em> orientorder, this compute calculates a per-atom vector.</p>
|
||
<p>These values can be accessed by any command that uses per-atom values
|
||
from a compute as input. See the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> doc
|
||
page for an overview of LAMMPS output options.</p>
|
||
<p>The per-atom vector or array values will be a number <span class="math notranslate nohighlight">\(\ge 0.0\)</span>, as
|
||
explained above.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<blockquote>
|
||
<div><p>none</p>
|
||
</div></blockquote>
|
||
</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_cluster_atom.html"><span class="doc">compute cluster/atom</span></a>
|
||
<a class="reference internal" href="compute_orientorder_atom.html"><span class="doc">compute orientorder/atom</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>group = all</p>
|
||
<hr class="docutils" />
|
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<p id="tenwolde1"><strong>(tenWolde)</strong> P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
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J. Chem. Phys. 104, 9932 (1996).</p>
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