567 lines
38 KiB
HTML
567 lines
38 KiB
HTML
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<title>compute temp/chunk 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"><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_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 current"><a class="current reference internal" href="#">compute temp/chunk 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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<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_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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<li>compute temp/chunk command</li>
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<div class="section" id="compute-temp-chunk-command">
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<span id="index-0"></span><h1>compute temp/chunk 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">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">chunkID</span> <span class="n">value1</span> <span class="n">value2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p>
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</li>
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<li><p class="first">temp/chunk = style name of this compute command</p>
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</li>
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<li><p class="first">chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</p>
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</li>
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<li><p class="first">zero or more values can be listed as value1,value2,etc</p>
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</li>
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<li><p class="first">value = <em>temp</em> or <em>kecom</em> or <em>internal</em></p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">temp</span> <span class="o">=</span> <span class="n">temperature</span> <span class="n">of</span> <span class="n">each</span> <span class="n">chunk</span>
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<span class="n">kecom</span> <span class="o">=</span> <span class="n">kinetic</span> <span class="n">energy</span> <span class="n">of</span> <span class="n">each</span> <span class="n">chunk</span> <span class="n">based</span> <span class="n">on</span> <span class="n">velocity</span> <span class="n">of</span> <span class="n">center</span> <span class="n">of</span> <span class="n">mass</span>
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<span class="n">internal</span> <span class="o">=</span> <span class="n">internal</span> <span class="n">kinetic</span> <span class="n">energy</span> <span class="n">of</span> <span class="n">each</span> <span class="n">chunk</span>
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</pre></div>
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</div>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>com</em> or <em>bias</em> or <em>adof</em> or <em>cdof</em></p>
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<pre class="literal-block">
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<em>com</em> value = <em>yes</em> or <em>no</em>
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yes = subtract center-of-mass velocity from each chunk before calculating temperature
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no = do not subtract center-of-mass velocity
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<em>bias</em> value = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias
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<em>adof</em> value = dof_per_atom
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dof_per_atom = define this many degrees-of-freedom per atom
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<em>cdof</em> value = dof_per_chunk
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dof_per_chunk = define this many degrees-of-freedom per chunk
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</pre>
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</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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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span>
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<span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span> <span class="n">temp</span> <span class="n">internal</span>
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<span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span> <span class="n">bias</span> <span class="n">tpartial</span> <span class="n">adof</span> <span class="mf">2.0</span>
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</pre></div>
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</div>
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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 temperature of a group of
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atoms that are also in chunks, after optionally subtracting out the
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center-of-mass velocity of each chunk. By specifying optional values,
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it can also calulate the per-chunk temperature or energies of the
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multiple chunks of atoms.</p>
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<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> doc page and <a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section 6.23</span></a> for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.</p>
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<p>The temperature is calculated by the formula KE = DOF/2 k T, where KE =
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total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
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v^2), DOF = the total number of degrees of freedom for those atoms, k
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= Boltzmann constant, and T = temperature.</p>
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<p>The DOF is calculated as N*adof + Nchunk*cdof, where N = number of
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atoms contributing to the KE, adof = degrees of freedom per atom, and
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cdof = degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a>
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command, and cdof = 0.0. This gives the usual formula for
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temperature.</p>
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<p>A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.</p>
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<p>Note that the number of atoms contributing to the temperature is
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calculated each time the temperature is evaluated since it is assumed
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the atoms may be dynamically assigned to chunks. Thus there is no
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need to use the <em>dynamic</em> option of the
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<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command for this compute style.</p>
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<p>If any optional values are specified, then per-chunk quantities are
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also calculated and stored in a global array, as described below.</p>
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<p>The <em>temp</em> value calculates the temperature for each chunk by the
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formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk
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of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of
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freedom for all atoms in the chunk, k = Boltzmann constant, and T =
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temperature.</p>
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<p>The DOF in this case is calculated as N*adof + cdof, where N = number
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of atoms in the chunk, adof = degrees of freedom per atom, and cdof =
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degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a>
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command, and cdof = 0.0. This gives the usual formula for
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temperature.</p>
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<p>The <em>kecom</em> value calculates the kinetic energy of each chunk as if
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all its atoms were moving with the velocity of the center-of-mass of
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the chunk.</p>
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<p>The <em>internal</em> value calculates the internal kinetic energy of each
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chunk. The interal KE is summed over the atoms in the chunk using an
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internal “thermal” velocity for each atom, which is its velocity minus
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the center-of-mass velocity of the chunk.</p>
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<hr class="docutils" />
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<p>Note that currently the global and per-chunk temperatures calculated
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by this compute only include translational degrees of freedom for each
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atom. No rotational degrees of freedom are included for finite-size
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particles. Also no degrees of freedom are subtracted for any velocity
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bias or constraints that are applied, such as <a class="reference internal" href="compute_temp_partial.html"><span class="doc">compute temp/partial</span></a>, or <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>
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or <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>. This is because those degrees of
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freedom (e.g. a constrained bond) could apply to sets of atoms that
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are both included and excluded from a specific chunk, and hence the
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concept is somewhat ill-defined. In some cases, you can use the
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<em>adof</em> and <em>cdof</em> keywords to adjust the calculated degress of freedom
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appropriately, as explained below.</p>
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<p>Note that the per-chunk temperature calulated by this compute and the
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<a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk temp</span></a> command can be different.
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This compute calculates the temperature for each chunk for a single
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snapshot. Fix ave/chunk can do that but can also time average those
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values over many snapshots, or it can compute a temperature as if the
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atoms in the chunk on different timesteps were collected together as
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one set of atoms to calculate their temperature. This compute allows
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the center-of-mass velocity of each chunk to be subtracted before
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calculating the temperature; fix ave/chunk does not.</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">Only atoms in the specified group contribute to the calculations
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performed by this compute. The <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command defines its own group;
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atoms will have a chunk ID = 0 if they are not in that group,
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signifying they are not assigned to a chunk, and will thus also not
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contribute to this calculation. You can specify the “all” group for
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this command if you simply want to include atoms with non-zero chunk
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IDs.</p>
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</div>
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<p>The simplest way to output the per-chunk results of the compute
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temp/chunk calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command, for example:</p>
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<pre class="literal-block">
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|
compute cc1 all chunk/atom molecule
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compute myChunk all temp/chunk cc1 temp
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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</pre>
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<hr class="docutils" />
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<p>The keyword/value option pairs are used in the following ways.</p>
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<p>The <em>com</em> keyword can be used with a value of <em>yes</em> to subtract the
|
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velocity of the center-of-mass for each chunk from the velocity of the
|
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atoms in that chunk, before calculating either the global or per-chunk
|
|
temperature. This can be useful if the atoms are streaming or
|
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otherwise moving collectively, and you wish to calculate only the
|
|
thermal temperature.</p>
|
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<p>For the <em>bias</em> keyword, <em>bias-ID</em> refers to the ID of a temperature
|
|
compute that removes a “bias” velocity from each atom. This also
|
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allows calculation of the global or per-chunk temperature using only
|
|
the thermal temperature of atoms in each chunk after the translational
|
|
kinetic energy components have been altered in a prescribed way,
|
|
e.g. to remove a velocity profile. It also applies to the calculation
|
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of the other per-chunk values, such as <em>kecom</em> or <em>internal</em>, which
|
|
involve the center-of-mass velocity of each chunk, which is calculated
|
|
after the velocity bias is removed from each atom. Note that the
|
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temperature compute will apply its bias globally to the entire system,
|
|
not on a per-chunk basis.</p>
|
|
<p>The <em>adof</em> and <em>cdof</em> keywords define the values used in the degree of
|
|
freedom (DOF) formulas used for the global or per-chunk temperature,
|
|
as described above. They can be used to calculate a more appropriate
|
|
temperature for some kinds of chunks. Here are 3 examples:</p>
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|
<p>If spatially binned chunks contain some number of water molecules and
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<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> is used to make each molecule rigid, then
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|
you could calculate a temperature with 6 degrees of freedom (DOF) (3
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translational, 3 rotational) per molecule by setting <em>adof</em> to 2.0.</p>
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<p>If <a class="reference internal" href="compute_temp_partial.html"><span class="doc">compute temp/partial</span></a> is used with the
|
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<em>bias</em> keyword to only allow the x component of velocity to contribute
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to the temperature, then <em>adof</em> = 1.0 would be appropriate.</p>
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<p>If each chunk consists of a large molecule, with some number of its
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bonds constrained by <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or the entire molecule
|
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by <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a>, <em>adof</em> = 0.0 and <em>cdof</em> could be
|
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set to the remaining degrees of freedom for the entire molecule
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(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
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molecule.</p>
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<hr class="docutils" />
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
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options.</p>
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<p>This compute also optionally calculates a global array, if one or more
|
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of the optional values are specified. The number of rows in the array
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= the number of chunks <em>Nchunk</em> as calculated by the specified
|
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<a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of
|
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columns is the number of specifed values (1 or more). These values
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can be accessed by any command that uses global array values from a
|
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compute as input. Again, see <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section 6.15</span></a> for an overview of LAMMPS output
|
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options.</p>
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<p>The scalar value calculated by this compute is “intensive”. The
|
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vector values are “extensive”. The array values are “intensive”.</p>
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<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The
|
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vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The array values
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will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a> for the <em>temp</em> value, and in
|
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energy <a class="reference internal" href="units.html"><span class="doc">units</span></a> for the <em>kecom</em> and <em>internal</em> values.</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 <em>com</em> and <em>bias</em> keywords cannot be used together.</p>
|
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</div>
|
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<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk temp</span></a></p>
|
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</div>
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<div class="section" id="default">
|
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<h2>Default</h2>
|
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<p>The option defaults are com no, no bias, adof = dimensionality of the
|
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system (2 or 3), and cdof = 0.0.</p>
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