500 lines
32 KiB
HTML
500 lines
32 KiB
HTML
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<!DOCTYPE html>
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<title>compute rdf command — LAMMPS documentation</title>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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<p class="caption"><span class="caption-text">Index</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
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<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Computes</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_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_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_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_cluster_atom.html">compute cluster/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_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_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_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_chunk.html">compute dipole/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_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_fep.html">compute fep 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_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_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_meso_e_atom.html">compute meso/e/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_rho_atom.html">compute meso/rho/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_t_atom.html">compute meso/t/atom 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_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_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_pressure.html">compute pressure 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_local.html">compute property/local command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">compute rdf 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="#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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</ul>
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</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_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_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_mesh_vertices.html">compute smd/triangle/mesh/vertices</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>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_stress.html">compute smd/ulsph/stress command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snav-atom-command">compute snav/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp.html#compute-temp-kk-command">compute temp/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd command</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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</ul>
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<div class="section" id="compute-rdf-command">
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<span id="index-0"></span><h1>compute rdf command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">rdf</span> <span class="n">Nbin</span> <span class="n">itype1</span> <span class="n">jtype1</span> <span class="n">itype2</span> <span class="n">jtype2</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
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<li>rdf = style name of this compute command</li>
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<li>Nbin = number of RDF bins</li>
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<li>itypeN = central atom type for Nth RDF histogram (see asterisk form below)</li>
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<li>jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<pre class="literal-block">
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compute 1 all rdf 100
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compute 1 all rdf 100 1 1
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compute 1 all rdf 100 * 3
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compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
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compute 1 fluid rdf 500 1*3 2 5 *10
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</pre>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Define a computation that calculates the radial distribution function
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(RDF), also called g(r), and the coordination number for a group of
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particles. Both are calculated in histogram form by binning pairwise
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distances into <em>Nbin</em> bins from 0.0 to the maximum force cutoff
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defined by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> command. The bins are of
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uniform size in radial distance. Thus a single bin encompasses a thin
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shell of distances in 3d and a thin ring of distances in 2d.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">If you have a bonded system, then the settings of
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<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included in the RDF. This does not apply when
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using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>, <em>coul/wolf</em> or
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similar. One way to get around this would be to set special_bond
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scaling factors to very tiny numbers that are not exactly zero
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(e.g. 1.0e-50). Another workaround is to write a dump file, and use
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the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to compute the RDF for snapshots in the
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dump file. The rerun script can use a
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<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command that includes all pairs in
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the neighbor list.</p>
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</div>
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<p>The <em>itypeN</em> and <em>jtypeN</em> arguments are optional. These arguments
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must come in pairs. If no pairs are listed, then a single histogram
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is computed for g(r) between all atom types. If one or more pairs are
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listed, then a separate histogram is generated for each
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<em>itype</em>,<em>jtype</em> pair.</p>
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<p>The <em>itypeN</em> and <em>jtypeN</em> settings can be specified in one of two
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ways. An explicit numeric value can be used, as in the 4th example
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above. Or a wild-card asterisk can be used to specify a range of atom
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types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
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number of atom types, then an asterisk with no numeric values means
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all types from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).</p>
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<p>If both <em>itypeN</em> and <em>jtypeN</em> are single values, as in the 4th example
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above, this means that a g(r) is computed where atoms of type <em>itypeN</em>
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are the central atom, and atoms of type <em>jtypeN</em> are the distribution
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atom. If either <em>itypeN</em> and <em>jtypeN</em> represent a range of values via
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the wild-card asterisk, as in the 5th example above, this means that a
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g(r) is computed where atoms of any of the range of types represented
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by <em>itypeN</em> are the central atom, and atoms of any of the range of
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types represented by <em>jtypeN</em> are the distribution atom.</p>
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<p>Pairwise distances are generated by looping over a pairwise neighbor
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list, just as they would be in a <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>
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computation. The distance between two atoms I and J is included in a
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specific histogram if the following criteria are met:</p>
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<ul class="simple">
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<li>atoms I,J are both in the specified compute group</li>
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<li>the distance between atoms I,J is less than the maximum force cutoff</li>
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<li>the type of the I atom matches itypeN (one or a range of types)</li>
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<li>the type of the J atom matches jtypeN (one or a range of types)</li>
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</ul>
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<p>It is OK if a particular pairwise distance is included in more than
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one individual histogram, due to the way the <em>itypeN</em> and <em>jtypeN</em>
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arguments are specified.</p>
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<p>The g(r) value for a bin is calculated from the histogram count by
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scaling it by the idealized number of how many counts there would be
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if atoms of type <em>jtypeN</em> were uniformly distributed. Thus it
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involves the count of <em>itypeN</em> atoms, the count of <em>jtypeN</em> atoms, the
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volume of the entire simulation box, and the volume of the bin’s thin
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shell in 3d (or the area of the bin’s thin ring in 2d).</p>
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<p>A coordination number coord(r) is also calculated, which is the number
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of atoms of type <em>jtypeN</em> within the current bin or closer, averaged
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over atoms of type <em>itypeN</em>. This is calculated as the area- or
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volume-weighted sum of g(r) values over all bins up to and including
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the current bin, multiplied by the global average volume density of
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atoms of type jtypeN.</p>
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<p>The simplest way to output the results of the compute rdf calculation
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to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command, for
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example:</p>
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<pre class="literal-block">
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compute myRDF all rdf 50
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fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp.rdf mode vector
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</pre>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global array with the number of rows =
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<em>Nbins</em>, and the number of columns = 1 + 2*Npairs, where Npairs is the
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number of I,J pairings specified. The first column has the bin
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coordinate (center of the bin), Each successive set of 2 columns has
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the g(r) and coord(r) values for a specific set of <em>itypeN</em> versus
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<em>jtypeN</em> interactions, as described above. These values can be used
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by any command that uses a global values from a compute as input. See
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<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section 6.15</span></a> for an overview of
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LAMMPS output options.</p>
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<p>The array values calculated by this compute are all “intensive”.</p>
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<p>The first column of array values will be in distance
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<a class="reference internal" href="units.html"><span class="doc">units</span></a>. The g(r) columns of array values are normalized
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numbers >= 0.0. The coordination number columns of array values are
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also numbers >= 0.0.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>The RDF is not computed for distances longer than the force cutoff,
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since processors (in parallel) don’t know about atom coordinates for
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atoms further away than that distance. If you want an RDF for larger
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distances, you can use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to post-process
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a dump file and set the cutoff for the potential to be longer in the
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rerun script. Note that in the rerun context, the force cutoff is
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arbitrary, since you aren’t running dynamics and thus are not changing
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your model. The definition of g(r) used by LAMMPS is only appropriate
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for characterizing atoms that are uniformly distributed throughout the
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simulation cell. In such cases, the coordination number is still
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correct and meaningful. As an example, if a large simulation cell
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contains only one atom of type <em>itypeN</em> and one of <em>jtypeN</em>, then g(r)
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will register an arbitrarily large spike at whatever distance they
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happen to be at, and zero everywhere else. Coord(r) will show a step
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change from zero to one at the location of the spike in g(r).</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a></p>
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<p><strong>Default:</strong> none</p>
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