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fix spring/chunk command
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fix adapt command
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fix adapt/fep command
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fix addforce command
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fix addtorque command
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fix append/atoms command
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<li
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"fix_atc.html"
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fix atc command
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><a
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"fix_atom_swap.html"
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fix atom/swap command
</a></li>
<li
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fix ave/atom command
</a></li>
<li
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fix ave/chunk command
</a></li>
<li
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class=
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fix ave/correlate command
</a></li>
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fix ave/correlate/long command
</a></li>
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fix ave/histo command
</a></li>
<li
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fix ave/histo/weight command
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fix ave/time command
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fix aveforce command
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fix balance command
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<li
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fix bond/break command
</a></li>
<li
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fix bond/create command
</a></li>
<li
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fix bond/swap command
</a></li>
<li
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class=
"reference internal"
href=
"fix_box_relax.html"
>
fix box/relax command
</a></li>
<li
class=
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"fix_colvars.html"
>
fix colvars command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
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"fix_controller.html"
>
fix controller command
</a></li>
<li
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"toctree-l2"
><a
class=
"reference internal"
href=
"fix_deform.html"
>
fix deform command
</a></li>
<li
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"toctree-l2"
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"reference internal"
href=
"fix_deform.html#fix-deform-kk-command"
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fix deform/kk command
</a></li>
<li
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"fix_deposit.html"
>
fix deposit command
</a></li>
<li
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><a
class=
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href=
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fix drag command
</a></li>
<li
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class=
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"fix_drude.html"
>
fix drude command
</a></li>
<li
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"reference internal"
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"fix_drude_transform.html"
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fix drude/transform/direct command
</a></li>
<li
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"toctree-l2"
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fix drude/transform/inverse command
</a></li>
<li
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"toctree-l2"
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fix dt/reset command
</a></li>
<li
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fix efield command
</a></li>
<li
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>
fix ehex command
</a></li>
<li
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fix enforce2d command
</a></li>
<li
class=
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fix eos/cv command
</a></li>
<li
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fix eos/table command
</a></li>
<li
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href=
"fix_eos_table_rx.html"
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fix eos/table/rx command
</a></li>
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fix evaporate command
</a></li>
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fix external command
</a></li>
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fix flow/gauss command
</a></li>
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>
fix freeze command
</a></li>
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fix gcmc command
</a></li>
<li
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fix gld command
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fix gle command
</a></li>
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>
fix gravity command
</a></li>
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href=
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>
fix gravity/omp command
</a></li>
<li
class=
"toctree-l2"
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class=
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href=
"fix_heat.html"
>
fix heat command
</a></li>
<li
class=
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><a
class=
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href=
"fix_imd.html"
>
fix imd command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_indent.html"
>
fix indent command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_ipi.html"
>
fix ipi command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_langevin.html"
>
fix langevin command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_langevin.html#fix-langevin-kk-command"
>
fix langevin/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
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href=
"fix_langevin_drude.html"
>
fix langevin/drude command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_langevin_eff.html"
>
fix langevin/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_lb_fluid.html"
>
fix lb/fluid command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_lb_momentum.html"
>
fix lb/momentum command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_lb_pc.html"
>
fix lb/pc command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_lb_rigid_pc_sphere.html"
>
fix lb/rigid/pc/sphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_lb_viscous.html"
>
fix lb/viscous command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_lineforce.html"
>
fix lineforce command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_manifoldforce.html"
>
fix manifoldforce command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_meso.html"
>
fix meso command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_meso_stationary.html"
>
fix meso/stationary command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_momentum.html"
>
fix momentum command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_move.html"
>
fix move command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_msst.html"
>
fix msst command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_neb.html"
>
fix neb command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html"
>
fix nvt command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-nvt-intel-command"
>
fix nvt/intel command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-nvt-kk-command"
>
fix nvt/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-nvt-omp-command"
>
fix nvt/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-npt-command"
>
fix npt command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-npt-intel-command"
>
fix npt/intel command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-npt-kk-command"
>
fix npt/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-npt-omp-command"
>
fix npt/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-nph-command"
>
fix nph command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-nph-kk-command"
>
fix nph/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh.html#fix-nph-omp-command"
>
fix nph/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh_eff.html"
>
fix nvt/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh_eff.html#fix-npt-eff-command"
>
fix npt/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nh_eff.html#fix-nph-eff-command"
>
fix nph/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nph_asphere.html"
>
fix nph/asphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nph_asphere.html#fix-nph-asphere-omp-command"
>
fix nph/asphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nph_body.html"
>
fix nph/body command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nph_sphere.html"
>
fix nph/sphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nph_sphere.html#fix-nph-sphere-omp-command"
>
fix nph/sphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nphug.html"
>
fix nphug command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nphug.html#fix-nphug-omp-command"
>
fix nphug/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_npt_asphere.html"
>
fix npt/asphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_npt_asphere.html#fix-npt-asphere-omp-command"
>
fix npt/asphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_npt_body.html"
>
fix npt/body command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_npt_sphere.html"
>
fix npt/sphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_npt_sphere.html#fix-npt-sphere-omp-command"
>
fix npt/sphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve.html"
>
fix nve command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve.html#fix-nve-intel-command"
>
fix nve/intel command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve.html#fix-nve-kk-command"
>
fix nve/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve.html#fix-nve-omp-command"
>
fix nve/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_asphere.html"
>
fix nve/asphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_asphere.html#fix-nve-asphere-intel-command"
>
fix nve/asphere/intel command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_asphere_noforce.html"
>
fix nve/asphere/noforce command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_body.html"
>
fix nve/body command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_eff.html"
>
fix nve/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_limit.html"
>
fix nve/limit command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_line.html"
>
fix nve/line command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_manifold_rattle.html"
>
fix nve/manifold/rattle command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_noforce.html"
>
fix nve/noforce command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_sphere.html"
>
fix nve/sphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_sphere.html#fix-nve-sphere-omp-command"
>
fix nve/sphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nve_tri.html"
>
fix nve/tri command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_asphere.html"
>
fix nvt/asphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_asphere.html#fix-nvt-asphere-omp-command"
>
fix nvt/asphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_body.html"
>
fix nvt/body command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_manifold_rattle.html"
>
fix nvt/manifold/rattle command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_sllod.html"
>
fix nvt/sllod command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_sllod.html#fix-nvt-sllod-intel-command"
>
fix nvt/sllod/intel command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_sllod.html#fix-nvt-sllod-omp-command"
>
fix nvt/sllod/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_sllod_eff.html"
>
fix nvt/sllod/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_sphere.html"
>
fix nvt/sphere command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_nvt_sphere.html#fix-nvt-sphere-omp-command"
>
fix nvt/sphere/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_oneway.html"
>
fix oneway command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_orient.html"
>
fix orient/fcc command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_orient.html#fix-orient-bcc-command"
>
fix orient/bcc command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_phonon.html"
>
fix phonon command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_pimd.html"
>
fix pimd command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_planeforce.html"
>
fix planeforce command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_poems.html"
>
fix poems
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_pour.html"
>
fix pour command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_press_berendsen.html"
>
fix press/berendsen command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_print.html"
>
fix print command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_property_atom.html"
>
fix property/atom command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qbmsst.html"
>
fix qbmsst command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq.html"
>
fix qeq/point command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq.html#fix-qeq-shielded-command"
>
fix qeq/shielded command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq.html#fix-qeq-slater-command"
>
fix qeq/slater command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq.html#fix-qeq-dynamic-command"
>
fix qeq/dynamic command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq.html#fix-qeq-fire-command"
>
fix qeq/fire command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq_comb.html"
>
fix qeq/comb command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq_comb.html#fix-qeq-comb-omp-command"
>
fix qeq/comb/omp command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq_reax.html"
>
fix qeq/reax command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qeq_reax.html#fix-qeq-reax-kk-command"
>
fix qeq/reax/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qmmm.html"
>
fix qmmm command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_qtb.html"
>
fix qtb command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_reax_bonds.html"
>
fix reax/bonds command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_reax_bonds.html#fix-reax-c-bonds-command"
>
fix reax/c/bonds command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_reaxc_species.html"
>
fix reax/c/species command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_recenter.html"
>
fix recenter command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_restrain.html"
>
fix restrain command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html"
>
fix rigid command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-nve-command"
>
fix rigid/nve command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-nvt-command"
>
fix rigid/nvt command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-npt-command"
>
fix rigid/npt command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-nph-command"
>
fix rigid/nph command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-small-command"
>
fix rigid/small command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-nve-small-command"
>
fix rigid/nve/small command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-nvt-small-command"
>
fix rigid/nvt/small command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-npt-small-command"
>
fix rigid/npt/small command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rigid.html#fix-rigid-nph-small-command"
>
fix rigid/nph/small command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_rx.html"
>
fix rx command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_saed_vtk.html"
>
fix saed/vtk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_setforce.html"
>
fix setforce command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_setforce.html#fix-setforce-kk-command"
>
fix setforce/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_shake.html"
>
fix shake command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_shake.html#fix-rattle-command"
>
fix rattle command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_shardlow.html"
>
fix shardlow command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd.html"
>
fix smd command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd_adjust_dt.html"
>
fix smd/adjust_dt command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd_integrate_tlsph.html"
>
fix smd/integrate_tlsph command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd_integrate_ulsph.html"
>
fix smd/integrate_ulsph command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd_move_triangulated_surface.html"
>
fix smd/move_tri_surf command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd_setvel.html"
>
fix smd/setvel command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_smd_wall_surface.html"
>
fix smd/wall_surface command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_spring.html"
>
fix spring command
</a></li>
<li
class=
"toctree-l2 current"
><a
class=
"current reference internal"
href=
"#"
>
fix spring/chunk command
</a><ul>
<li
class=
"toctree-l3"
><a
class=
"reference internal"
href=
"#syntax"
>
Syntax
</a></li>
<li
class=
"toctree-l3"
><a
class=
"reference internal"
href=
"#examples"
>
Examples
</a></li>
<li
class=
"toctree-l3"
><a
class=
"reference internal"
href=
"#description"
>
Description
</a></li>
<li
class=
"toctree-l3"
><a
class=
"reference internal"
href=
"#restrictions"
>
Restrictions
</a></li>
<li
class=
"toctree-l3"
><a
class=
"reference internal"
href=
"#related-commands"
>
Related commands
</a></li>
</ul>
</li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_spring_rg.html"
>
fix spring/rg command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_spring_self.html"
>
fix spring/self command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_srd.html"
>
fix srd command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_store_force.html"
>
fix store/force command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_store_state.html"
>
fix store/state command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_temp_berendsen.html"
>
fix temp/berendsen command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_temp_csvr.html"
>
fix temp/csvr command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_temp_csvr.html#fix-temp-csld-command"
>
fix temp/csld command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_temp_rescale.html"
>
fix temp/rescale command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_temp_rescale_eff.html"
>
fix temp/rescale/eff command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_tfmc.html"
>
fix tfmc command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_thermal_conductivity.html"
>
fix thermal/conductivity command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_ti_rs.html"
>
fix ti/rs command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_ti_spring.html"
>
fix ti/spring command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_tmd.html"
>
fix tmd command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_ttm.html"
>
fix ttm command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_ttm.html#fix-ttm-mod-command"
>
fix ttm/mod command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_tune_kspace.html"
>
fix tune/kspace command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_vector.html"
>
fix vector command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_viscosity.html"
>
fix viscosity command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_viscous.html"
>
fix viscous command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall.html"
>
fix wall/lj93 command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall.html#fix-wall-lj126-command"
>
fix wall/lj126 command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall.html#fix-wall-lj1043-command"
>
fix wall/lj1043 command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall.html#fix-wall-colloid-command"
>
fix wall/colloid command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall.html#fix-wall-harmonic-command"
>
fix wall/harmonic command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall_gran.html"
>
fix wall/gran command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall_piston.html"
>
fix wall/piston command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall_reflect.html"
>
fix wall/reflect command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall_reflect.html#fix-wall-reflect-kk-command"
>
fix wall/reflect/kk command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall_region.html"
>
fix wall/region command
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"fix_wall_srd.html"
>
fix wall/srd command
</a></li>
</ul>
</li>
<li
class=
"toctree-l1"
><a
class=
"reference internal"
href=
"computes.html"
>
Computes
</a></li>
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fix spring/chunk command
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<div
class=
"section"
id=
"fix-spring-chunk-command"
>
<span
id=
"index-0"
></span><h1>
fix spring/chunk command
</h1>
<div
class=
"section"
id=
"syntax"
>
<h2>
Syntax
</h2>
<div
class=
"highlight-default"
><div
class=
"highlight"
><pre><span></span><span
class=
"n"
>
fix
</span>
<span
class=
"n"
>
ID
</span>
<span
class=
"n"
>
group
</span><span
class=
"o"
>
-
</span><span
class=
"n"
>
ID
</span>
<span
class=
"n"
>
spring
</span><span
class=
"o"
>
/
</span><span
class=
"n"
>
chunk
</span>
<span
class=
"n"
>
K
</span>
<span
class=
"n"
>
chunkID
</span>
<span
class=
"n"
>
comID
</span>
</pre></div>
</div>
<ul
class=
"simple"
>
<li>
ID, group-ID are documented in
<a
class=
"reference internal"
href=
"fix.html"
><span
class=
"doc"
>
fix
</span></a>
command
</li>
<li>
spring/chunk = style name of this fix command
</li>
<li>
K = spring constant for each chunk (force/distance units)
</li>
<li>
chunkID = ID of
<a
class=
"reference internal"
href=
"compute_chunk_atom.html"
><span
class=
"doc"
>
compute chunk/atom
</span></a>
command
</li>
<li>
comID = ID of
<a
class=
"reference internal"
href=
"compute_com_chunk.html"
><span
class=
"doc"
>
compute com/chunk
</span></a>
command
</li>
</ul>
</div>
<div
class=
"section"
id=
"examples"
>
<h2>
Examples
</h2>
<div
class=
"highlight-default"
><div
class=
"highlight"
><pre><span></span><span
class=
"n"
>
fix
</span>
<span
class=
"n"
>
restrain
</span>
<span
class=
"nb"
>
all
</span>
<span
class=
"n"
>
spring
</span><span
class=
"o"
>
/
</span><span
class=
"n"
>
chunk
</span>
<span
class=
"mi"
>
100
</span>
<span
class=
"n"
>
chunkID
</span>
<span
class=
"n"
>
comID
</span>
</pre></div>
</div>
</div>
<div
class=
"section"
id=
"description"
>
<h2>
Description
</h2>
<p>
Apply a spring force to the center-of-mass (COM) of chunks of atoms as
defined by the
<a
class=
"reference internal"
href=
"compute_chunk_atom.html"
><span
class=
"doc"
>
compute chunk/atom
</span></a>
command.
Chunks can be molecules or spatial bins or other groupings of atoms.
This is a way of tethering each chunk to its initial COM coordinates.
</p>
<p>
The
<em>
chunkID
</em>
is the ID of a compute chunk/atom command defined in the
input script. It is used to define the chunks. The
<em>
comID
</em>
is the ID
of a compute com/chunk command defined in the input script. It is
used to compute the COMs of each chunk.
</p>
<p>
At the beginning of the first
<a
class=
"reference internal"
href=
"run.html"
><span
class=
"doc"
>
run
</span></a>
or
<a
class=
"reference internal"
href=
"minimize.html"
><span
class=
"doc"
>
minimize
</span></a>
command after this fix is defined, the
initial COM of each chunk is calculated and stored as R0m, where M is
the chunk number. Thereafter, at every timestep (or minimization
iteration), the current COM of each chunk is calculated as Rm. A
restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
atom in each chunk where
<em>
K
</em>
is the specified spring constant, Mi is
the mass of the atom, and Mm is the total mass of all atoms in the
chunk. Note that
<em>
K
</em>
thus represents the spring constant for the
total force on each chunk of atoms, not for a spring applied to each
atom.
</p>
<p><strong>
Restart, fix_modify, output, run start/stop, minimize info:
</strong></p>
<p>
No information about this fix is written to
<a
class=
"reference internal"
href=
"restart.html"
><span
class=
"doc"
>
binary restart files
</span></a>
.
</p>
<p>
The
<a
class=
"reference internal"
href=
"fix_modify.html"
><span
class=
"doc"
>
fix_modify
</span></a>
<em>
energy
</em>
option is supported by this
fix to add the energy stored in all the springs to the system
’
s potential
energy as part of
<a
class=
"reference internal"
href=
"thermo_style.html"
><span
class=
"doc"
>
thermodynamic output
</span></a>
.
</p>
<p>
The
<a
class=
"reference internal"
href=
"fix_modify.html"
><span
class=
"doc"
>
fix_modify
</span></a>
<em>
respa
</em>
option is supported by this
fix. This allows to set at which level of the
<a
class=
"reference internal"
href=
"run_style.html"
><span
class=
"doc"
>
r-RESPA
</span></a>
integrator the fix is adding its forces. Default is the outermost level.
</p>
<p>
This fix computes a global scalar which can be accessed by various
<a
class=
"reference internal"
href=
"Section_howto.html#howto-15"
><span
class=
"std std-ref"
>
output commands
</span></a>
. The scalar is the
energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
</p>
<p>
The scalar value calculated by this fix is
“
extensive
”
.
</p>
<p>
No parameter of this fix can be used with the
<em>
start/stop
</em>
keywords of
the
<a
class=
"reference internal"
href=
"run.html"
><span
class=
"doc"
>
run
</span></a>
command.
</p>
<p>
The forces due to this fix are imposed during an energy minimization,
invoked by the
<a
class=
"reference internal"
href=
"minimize.html"
><span
class=
"doc"
>
minimize
</span></a>
command.
</p>
<div
class=
"admonition note"
>
<p
class=
"first admonition-title"
>
Note
</p>
<p
class=
"last"
>
If you want the spring energies to be included in the total
potential energy of the system (the quantity being minimized), you
MUST enable the
<a
class=
"reference internal"
href=
"fix_modify.html"
><span
class=
"doc"
>
fix_modify
</span></a>
<em>
energy
</em>
option for this
fix.
</p>
</div>
</div>
<div
class=
"section"
id=
"restrictions"
>
<h2>
Restrictions
</h2>
<blockquote>
<div>
none
</div></blockquote>
</div>
<div
class=
"section"
id=
"related-commands"
>
<h2>
Related commands
</h2>
<p><a
class=
"reference internal"
href=
"fix_spring.html"
><span
class=
"doc"
>
fix spring
</span></a>
,
<a
class=
"reference internal"
href=
"fix_spring_self.html"
><span
class=
"doc"
>
fix spring/self
</span></a>
,
<a
class=
"reference internal"
href=
"fix_spring_rg.html"
><span
class=
"doc"
>
fix spring/rg
</span></a></p>
<p><strong>
Default:
</strong>
none
</p>
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