2016-05-10 01:33:12 +08:00
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2016-09-14 08:22:17 +08:00
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2016-05-10 01:33:12 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_packages.html" > 4. Packages< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_howto.html" > 6. How-to discussions< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_example.html" > 7. Example problems< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_errors.html" > 12. Errors< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_history.html" > 13. Future and history< / a > < / li >
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2016-09-14 08:22:17 +08:00
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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 current" > < a class = "reference internal" href = "fixes.html" > Fixes< / a > < ul class = "current" >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_adapt.html" > fix adapt command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_adapt_fep.html" > fix adapt/fep command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_addforce.html" > fix addforce command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_addtorque.html" > fix addtorque command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_append_atoms.html" > fix append/atoms command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_atc.html" > fix atc command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_atom_swap.html" > fix atom/swap command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_atom.html" > fix ave/atom command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_chunk.html" > fix ave/chunk command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_correlate.html" > fix ave/correlate command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_correlate_long.html" > fix ave/correlate/long command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_histo.html" > fix ave/histo command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_histo.html#fix-ave-histo-weight-command" > fix ave/histo/weight command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ave_time.html" > fix ave/time command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_aveforce.html" > fix aveforce command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_balance.html" > fix balance command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_bond_break.html" > fix bond/break command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_bond_create.html" > fix bond/create command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_bond_swap.html" > fix bond/swap command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_box_relax.html" > fix box/relax command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_colvars.html" > fix colvars command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_controller.html" > fix controller command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_deform.html" > fix deform command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_deform.html#fix-deform-kk-command" > fix deform/kk command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_deposit.html" > fix deposit command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_drag.html" > fix drag command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_drude.html" > fix drude command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_drude_transform.html" > fix drude/transform/direct command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_drude_transform.html#fix-drude-transform-inverse-command" > fix drude/transform/inverse command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_dt_reset.html" > fix dt/reset command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_efield.html" > fix efield command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_ehex.html" > fix ehex command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_enforce2d.html" > fix enforce2d command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_eos_cv.html" > fix eos/cv command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_eos_table.html" > fix eos/table command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_eos_table_rx.html" > fix eos/table/rx command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_evaporate.html" > fix evaporate command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_external.html" > fix external command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_flow_gauss.html" > fix flow/gauss command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_freeze.html" > fix freeze command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_gcmc.html" > fix gcmc command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_gld.html" > fix gld command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_gle.html" > fix gle command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_gravity.html" > fix gravity command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_gravity.html#fix-gravity-omp-command" > fix gravity/omp command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" href = "fix_heat.html" > fix heat command< / a > < / li >
< li class = "toctree-l2" > < a class = "reference internal" 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 = "reference internal" 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" > < a class = "reference internal" href = "fix_spring_chunk.html" > fix spring/chunk command< / a > < / li >
< li class = "toctree-l2 current" > < a class = "current reference internal" href = "#" > fix spring/rg 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_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 >
< li class = "toctree-l1" > < a class = "reference internal" href = "pairs.html" > Pair Styles< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "bonds.html" > Bonds< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "angles.html" > Angle Styles< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "dihedrals.html" > Dihedral Styles< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "impropers.html" > Improper Styles< / a > < / li >
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2016-05-10 01:33:12 +08:00
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2016-09-14 08:22:17 +08:00
< li > < a href = "fixes.html" > Fixes< / a > » < / li >
2016-05-10 01:33:12 +08:00
< li > fix spring/rg command< / li >
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< div class = "section" id = "fix-spring-rg-command" >
< span id = "index-0" > < / span > < h1 > fix spring/rg 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" > rg< / span > < span class = "n" > K< / span > < span class = "n" > RG0< / 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/rg = style name of this fix command< / li >
< li > K = harmonic force constant (force/distance units)< / li >
< li > RG0 = target radius of gyration to constrain to (distance units)< / li >
< / ul >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "k" > if< / span > < span class = "n" > RG0< / span > < span class = "o" > =< / span > < span class = "n" > NULL< / span > < span class = "p" > ,< / span > < span class = "n" > use< / span > < span class = "n" > the< / span > < span class = "n" > current< / span > < span class = "n" > RG< / span > < span class = "k" > as< / span > < span class = "n" > the< / span > < span class = "n" > target< / span > < span class = "n" > value< / span >
< / pre > < / div >
< / div >
< / 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 = "mi" > 1< / span > < span class = "n" > protein< / span > < span class = "n" > spring< / span > < span class = "o" > /< / span > < span class = "n" > rg< / span > < span class = "mf" > 5.0< / span > < span class = "mf" > 10.0< / span >
< span class = "n" > fix< / span > < span class = "mi" > 2< / span > < span class = "n" > micelle< / span > < span class = "n" > spring< / span > < span class = "o" > /< / span > < span class = "n" > rg< / span > < span class = "mf" > 5.0< / span > < span class = "n" > NULL< / span >
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Apply a harmonic restraining force to atoms in the group to affect
their central moment about the center of mass (radius of gyration).
This fix is useful to encourage a protein or polymer to fold/unfold
and also when sampling along the radius of gyration as a reaction
coordinate (i.e. for protein folding).< / p >
< p > The radius of gyration is defined as RG in the first formula. The
energy of the constraint and associated force on each atom is given by
the second and third formulas, when the group is at a different RG
than the target value RG0.< / p >
< img alt = "_images/fix_spring_rg.jpg" class = "align-center" src = "_images/fix_spring_rg.jpg" / >
< p > The (xi - center-of-mass) term is computed taking into account
periodic boundary conditions, m_i is the mass of the atom, and M is
the mass of the entire group. Note that K is thus a force constant
for the aggregate force on the group of atoms, not a per-atom force.< / p >
< p > If RG0 is specified as NULL, then the RG of the group is computed at
the time the fix is specified, and that value is used as the target.< / p >
2016-09-07 22:09:53 +08:00
< p > < strong > Restart, fix_modify, output, run start/stop, minimize info:< / strong > < / p >
2016-05-10 01:33:12 +08:00
< p > No information about this fix is written to < a class = "reference internal" href = "restart.html" > < span class = "doc" > binary restart files< / span > < / a > . None of the < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various < a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > output commands< / span > < / a > . 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.
This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < span class = "doc" > energy minimization< / span > < / a > .< / p >
2016-06-18 07:24:05 +08:00
< 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 >
2016-05-10 01:33:12 +08:00
< / 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_drag.html" > < span class = "doc" > fix drag< / span > < / a > , < a class = "reference internal" href = "fix_smd.html" > < span class = "doc" > fix smd< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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