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edca6eb4dbf98a7d8853bf04cbce2331bf25d7c2
lammps/doc/html/compute_cluster_atom.html
Barak Hirshberg edca6eb4db this is a lost cause
2025-01-13 14:55:48 +00:00

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<title>compute cluster/atom command &mdash; LAMMPS documentation</title>
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
<div class="lammps_release">git info: </div>
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<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Compute Styles</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_adf.html">compute adf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ave_sphere_atom.html">compute ave/sphere/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_chunk_spread_atom.html">compute chunk/spread/atom command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">compute cluster/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-fragment-atom-command">compute fragment/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-aggregate-atom-command">compute aggregate/atom command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#output-info">Output info</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cnp_atom.html">compute cnp/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_composition_atom.html">compute composition/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_count_type.html">compute count/type command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html">compute dipole command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html#compute-dipole-tip4p-command">compute dipole/tip4p command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html#compute-dipole-tip4p-chunk-command">compute dipole/tip4p/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_edpd_temp_atom.html">compute edpd/temp/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_efield_atom.html">compute efield/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_efield_wolf_atom.html">compute efield/wolf/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_entropy_atom.html">compute entropy/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fabric.html">compute fabric command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fep_ta.html">compute fep/ta command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_global_atom.html">compute global/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape.html">compute gyration/shape command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape_chunk.html">compute gyration/shape/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_hma.html">compute hma command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_mliap.html">compute mliap command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_momentum.html">compute momentum command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd.html">compute msd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_nbond_atom.html">compute nbond/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pace.html">compute pace command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pair.html">compute pair command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html">compute pod/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-podd-atom-command">compute podd/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-local-command">compute pod/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-global-command">compute pod/global command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure_alchemy.html">compute pressure/alchemy command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure_uef.html">compute pressure/uef command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_grid.html">compute property/grid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ptm_atom.html">compute ptm/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rattlers_atom.html">compute rattlers/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reaxff_atom.html">compute reaxff/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce_chunk.html">compute reduce/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rheo_property_atom.html">compute rheo/property/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
<li class="toctree-l2"><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>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="compute-cluster-atom-command">
<span id="index-2"></span><span id="index-1"></span><span id="index-0"></span><h1>compute cluster/atom command<a class="headerlink" href="#compute-cluster-atom-command" title="Link to this heading"></a></h1>
</section>
<section id="compute-fragment-atom-command">
<h1>compute fragment/atom command<a class="headerlink" href="#compute-fragment-atom-command" title="Link to this heading"></a></h1>
</section>
<section id="compute-aggregate-atom-command">
<h1>compute aggregate/atom command<a class="headerlink" href="#compute-aggregate-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">cluster</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">cutoff</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">fragment</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
<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">aggregate</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">cutoff</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><em>cluster/atom</em> or <em>fragment/atom</em> or <em>aggregate/atom</em> = style name of this compute command</p></li>
<li><p>cutoff = distance within which to label atoms as part of same cluster (distance units)</p></li>
<li><p>zero or more keyword/value pairs may be appended to <em>fragment/atom</em></p></li>
<li><p>keyword = <em>single</em></p>
<blockquote>
<div><pre class="literal-block"><em>single</em> value = <em>yes</em> or <em>no</em> to treat single atoms (no bonds) as fragments</pre>
</div></blockquote>
</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">cluster</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">3.5</span>
<span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">fragment</span><span class="o">/</span><span class="n">atom</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">fragment</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">single</span><span class="w"> </span><span class="n">no</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">aggregate</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">3.5</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 assigns each atom a cluster, fragment, or
aggregate ID. Only atoms in the compute group are clustered and
assigned cluster IDs. Atoms not in the compute group are assigned an
ID = 0.</p>
<p>A cluster is defined as a set of atoms, each of which is within the
cutoff distance from one or more other atoms in the cluster. If an
atom has no neighbors within the cutoff distance, then it is a 1-atom
cluster.</p>
<p>A fragment is similarly defined as a set of atoms, each of which has a
bond to another atom in the fragment. Bonds can be defined initially
via the <a class="reference internal" href="read_data.html"><span class="doc">data file</span></a> or <a class="reference internal" href="create_bonds.html"><span class="doc">create_bonds</span></a> commands, or dynamically by fixes which create or
break bonds like <a class="reference internal" href="fix_bond_react.html"><span class="doc">fix bond/react</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix
bond/create</span></a>, <a class="reference internal" href="fix_bond_swap.html"><span class="doc">fix bond/swap</span></a>,
or <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>. The cluster ID or fragment
ID of every atom in the cluster will be set to the smallest atom ID of
any atom in the cluster or fragment, respectively.</p>
<p>For the <em>fragment/atom</em> style, the <em>single</em> keyword determines whether
single atoms (not bonded to another atom) are treated as one-atom
fragments or not, based on the <em>yes</em> or <em>no</em> setting. If the setting
is <em>no</em> (the default), their fragment IDs are set to 0.</p>
<p>An aggregate is defined by combining the rules for clusters and
fragments (i.e., a set of atoms, where each of them is within the cutoff
distance from one or more atoms within a fragment that is part of
the same cluster). This measure can be used to track molecular assemblies
like micelles.</p>
<p>For computes <em>cluster/atom</em> and <em>aggregate/atom</em> a neighbor list
needed to compute cluster IDs is constructed each time the compute is
invoked. Thus it can be inefficient to compute/dump this quantity too
frequently or to have multiple <em>cluster/atom</em> or <em>aggregate/atom</em>
style computes.</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 when computing the clusters. This
does not apply when using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>,
<em>coul/wolf</em> or similar. One way to get around this would be to set
special_bond scaling factors to very tiny numbers that are not exactly
zero (e.g., <span class="math notranslate nohighlight">\(1.0 \times 10^{-50}\)</span>). Another workaround is to write a
dump file and use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to compute the clusters
for snapshots in the dump file. The rerun script can use a
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command that includes all pairs in
the neighbor list.</p>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>For the compute fragment/atom style, each fragment is identified
using the current bond topology. This will not account for bonds
broken by the <a class="reference internal" href="bond_quartic.html"><span class="doc">bond_style quartic</span></a> command
because it does not perform a full update of the bond topology data
structures within LAMMPS.</p>
</div>
</section>
<section id="output-info">
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
<p>This compute calculates a per-atom vector, which 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> page for an overview of
LAMMPS output options.</p>
<p>The per-atom vector values will be an ID <span class="math notranslate nohighlight">\(&gt; 0\)</span>, as explained above.</p>
</section>
<section id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
<p>none</p>
</section>
<section id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
<p><a class="reference internal" href="compute_coord_atom.html"><span class="doc">compute coord/atom</span></a></p>
</section>
<section id="default">
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
<p>The default for fragment/atom is single=no.</p>
</section>
</section>
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