forked from lijiext/lammps
599 lines
41 KiB
HTML
599 lines
41 KiB
HTML
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<!DOCTYPE html>
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<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>fix pimd command — LAMMPS documentation</title>
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<link rel="top" title="LAMMPS documentation" href="index.html"/>
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<link rel="up" title="Fixes" href="fixes.html"/>
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<link rel="next" title="fix planeforce command" href="fix_planeforce.html"/>
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<link rel="prev" title="fix phonon command" href="fix_phonon.html"/>
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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 current"><a class="reference internal" href="fixes.html">Fixes</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt.html">fix adapt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt_fep.html">fix adapt/fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addforce.html">fix addforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addtorque.html">fix addtorque command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_append_atoms.html">fix append/atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atc.html">fix atc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atom_swap.html">fix atom/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_atom.html">fix ave/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_chunk.html">fix ave/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate.html">fix ave/correlate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate_long.html">fix ave/correlate/long command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html">fix ave/histo command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_time.html">fix ave/time command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_aveforce.html">fix aveforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_balance.html">fix balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_break.html">fix bond/break command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html">fix bond/create command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_swap.html">fix bond/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_box_relax.html">fix box/relax command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_colvars.html">fix colvars command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_controller.html">fix controller command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html">fix deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html#fix-deform-kk-command">fix deform/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deposit.html">fix deposit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drag.html">fix drag command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude.html">fix drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html">fix drude/transform/direct command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_dt_reset.html">fix dt/reset command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html">fix efield command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ehex.html">fix ehex command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_enforce2d.html">fix enforce2d command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_cv.html">fix eos/cv command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table.html">fix eos/table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table_rx.html">fix eos/table/rx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_evaporate.html">fix evaporate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_external.html">fix external command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_flow_gauss.html">fix flow/gauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_freeze.html">fix freeze command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gcmc.html">fix gcmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gld.html">fix gld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gle.html">fix gle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html">fix gravity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html#fix-gravity-omp-command">fix gravity/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_heat.html">fix heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_imd.html">fix imd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_indent.html">fix indent command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ipi.html">fix ipi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html">fix langevin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html#fix-langevin-kk-command">fix langevin/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_drude.html">fix langevin/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_eff.html">fix langevin/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_fluid.html">fix lb/fluid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_momentum.html">fix lb/momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_pc.html">fix lb/pc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_rigid_pc_sphere.html">fix lb/rigid/pc/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso.html">fix meso command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso_stationary.html">fix meso/stationary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html">fix momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_move.html">fix move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-intel-command">fix nvt/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-kk-command">fix nvt/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-omp-command">fix nvt/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-intel-command">fix npt/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-kk-command">fix npt/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-omp-command">fix npt/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-kk-command">fix nph/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-omp-command">fix nph/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html#fix-nphug-omp-command">fix nphug/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html">fix npt/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-intel-command">fix nve/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-kk-command">fix nve/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-omp-command">fix nve/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_body.html">fix nve/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_eff.html">fix nve/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_limit.html">fix nve/limit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_line.html">fix nve/line command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_manifold_rattle.html">fix nve/manifold/rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_noforce.html">fix nve/noforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html">fix nve/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_tri.html">fix nve/tri command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html">fix nvt/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_body.html">fix nvt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html">fix nvt/sllod command</a></li>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod_eff.html">fix nvt/sllod/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html">fix nvt/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_oneway.html">fix oneway command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html">fix orient/fcc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_phonon.html">fix phonon command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">fix pimd 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="#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="fix_planeforce.html">fix planeforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_pour.html">fix pour command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_press_berendsen.html">fix press/berendsen command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_print.html">fix print command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_property_atom.html">fix property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qbmsst.html">fix qbmsst command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html">fix qeq/point command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-shielded-command">fix qeq/shielded command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-slater-command">fix qeq/slater command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-dynamic-command">fix qeq/dynamic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-fire-command">fix qeq/fire command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html">fix qeq/comb command</a></li>
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reax.html">fix qeq/reax command</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qmmm.html">fix qmmm command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qtb.html">fix qtb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_reax_bonds.html">fix reax/bonds command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_reaxc_species.html">fix reax/c/species command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_recenter.html">fix recenter command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_restrain.html">fix restrain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html">fix rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-command">fix rigid/nve command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-command">fix rigid/npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-command">fix rigid/nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-small-command">fix rigid/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-small-command">fix rigid/nph/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rx.html">fix rx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_saed_vtk.html">fix saed/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html">fix setforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html#fix-setforce-kk-command">fix setforce/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shake.html#fix-rattle-command">fix rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd.html">fix smd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_adjust_dt.html">fix smd/adjust_dt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_tlsph.html">fix smd/integrate_tlsph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_move_triangulated_surface.html">fix smd/move_tri_surf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_setvel.html">fix smd/setvel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_wall_surface.html">fix smd/wall_surface command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_chunk.html">fix spring/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_rg.html">fix spring/rg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_self.html">fix spring/self command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_srd.html">fix srd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_store_force.html">fix store/force command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_store_state.html">fix store/state command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_berendsen.html">fix temp/berendsen command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html">fix temp/csvr command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html#fix-temp-csld-command">fix temp/csld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale.html">fix temp/rescale command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_viscosity.html">fix viscosity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_viscous.html">fix viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_piston.html">fix wall/piston command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</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>fix pimd command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="fix-pimd-command">
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<span id="index-0"></span><h1>fix pimd 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">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pimd</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="fix.html"><span class="doc">fix</span></a> command</p>
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</li>
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<li><p class="first">pimd = style name of this fix command</p>
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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>method</em> or <em>fmass</em> or <em>sp</em> or <em>temp</em> or <em>nhc</em></p>
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<pre class="literal-block">
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<em>method</em> value = <em>pimd</em> or <em>nmpimd</em> or <em>cmd</em>
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<em>fmass</em> value = scaling factor on mass
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<em>sp</em> value = scaling factor on Planck constant
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<em>temp</em> value = temperature (temperarate units)
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<em>nhc</em> value = Nc = number of chains in Nose-Hoover thermostat
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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">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pimd</span> <span class="n">method</span> <span class="n">nmpimd</span> <span class="n">fmass</span> <span class="mf">1.0</span> <span class="n">sp</span> <span class="mf">2.0</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="n">nhc</span> <span class="mi">4</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>This command performs quantum molecular dynamics simulations based on
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the Feynman path integral to include effects of tunneling and
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zero-point motion. In this formalism, the isomorphism of a quantum
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partition function for the original system to a classical partition
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function for a ring-polymer system is exploited, to efficiently sample
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configurations from the canonical ensemble <a class="reference internal" href="#feynman"><span class="std std-ref">(Feynman)</span></a>.
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The classical partition function and its components are given
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by the following equations:</p>
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<img alt="_images/fix_pimd.jpg" class="align-center" src="_images/fix_pimd.jpg" />
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<p>The interested user is referred to any of the numerous references on
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this methodology, but briefly, each quantum particle in a path
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integral simulation is represented by a ring-polymer of P quasi-beads,
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labeled from 1 to P. During the simulation, each quasi-bead interacts
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with beads on the other ring-polymers with the same imaginary time
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index (the second term in the effective potential above). The
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quasi-beads also interact with the two neighboring quasi-beads through
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|
the spring potential in imaginary-time space (first term in effective
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|
potential). To sample the canonical ensemble, a Nose-Hoover massive
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chain thermostat is applied <a class="reference internal" href="#pimd-tuckerman"><span class="std std-ref">(Tuckerman)</span></a>. With the
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massive chain algorithm, a chain of NH thermostats is coupled to each
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degree of freedom for each quasi-bead. The keyword <em>temp</em> sets the
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|
target temperature for the system and the keyword <em>nhc</em> sets the
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|
number <em>Nc</em> of thermostats in each chain. For example, for a
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|
simulation of N particles with P beads in each ring-polymer, the total
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number of NH thermostats would be 3 x N x P x Nc.</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">This fix implements a complete velocity-verlet integrator
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combined with NH massive chain thermostat, so no other time
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integration fix should be used.</p>
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</div>
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<p>The <em>method</em> keyword determines what style of PIMD is performed. A
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value of <em>pimd</em> is standard PIMD. A value of <em>nmpimd</em> is for
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normal-mode PIMD. A value of <em>cmd</em> is for centroid molecular dynamics
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|
(CMD). The difference between the styles is as follows.</p>
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<p>In standard PIMD, the value used for a bead’s fictitious mass is
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arbitrary. A common choice is to use Mi = m/P, which results in the
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mass of the entire ring-polymer being equal to the real quantum
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particle. But it can be difficult to efficiently integrate the
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equations of motion for the stiff harmonic interactions in the ring
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polymers.</p>
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<p>A useful way to resolve this issue is to integrate the equations of
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motion in a normal mode representation, using Normal Mode
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Path-Integral Molecular Dynamics (NMPIMD) <a class="reference internal" href="#cao1"><span class="std std-ref">(Cao1)</span></a>. In NMPIMD,
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|
the NH chains are attached to each normal mode of the ring-polymer and
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the fictitious mass of each mode is chosen as Mk = the eigenvalue of
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the Kth normal mode for k > 0. The k = 0 mode, referred to as the
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zero-frequency mode or centroid, corresponds to overall translation of
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the ring-polymer and is assigned the mass of the real particle.</p>
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|
<p>Motion of the centroid can be effectively uncoupled from the other
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normal modes by scaling the fictitious masses to achieve a partial
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adiabatic separation. This is called a Centroid Molecular Dynamics
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|
(CMD) approximation <a class="reference internal" href="#cao2"><span class="std std-ref">(Cao2)</span></a>. The time-evolution (and resulting
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dynamics) of the quantum particles can be used to obtain centroid time
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correlation functions, which can be further used to obtain the true
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quantum correlation function for the original system. The CMD method
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|
also uses normal modes to evolve the system, except only the k > 0
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modes are thermostatted, not the centroid degrees of freedom.</p>
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|
<p>The keyword <em>fmass</em> sets a further scaling factor for the fictitious
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|
masses of beads, which can be used for the Partial Adiabatic CMD
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|
<a class="reference internal" href="#hone"><span class="std std-ref">(Hone)</span></a>, or to be set as P, which results in the fictitious
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masses to be equal to the real particle masses.</p>
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|
<p>The keyword <em>sp</em> is a scaling factor on Planck’s constant, which can
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|
be useful for debugging or other purposes. The default value of 1.0
|
|
is appropriate for most situations.</p>
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|
<p>The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
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|
as described in <a class="reference internal" href="#calhoun"><span class="std std-ref">(Calhoun)</span></a>. In LAMMPS this is done by using
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|
<a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">multi-replica feature</span></a> in LAMMPS, where
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each quasi-particle system is stored and simulated on a separate
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|
partition of processors. The following diagram illustrates this
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|
approach. The original system with 2 ring polymers is shown in red.
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|
Since each ring has 4 quasi-beads (imaginary time slices), there are 4
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|
replicas of the system, each running on one of the 4 partitions of
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processors. Each replica (shown in green) owns one quasi-bead in each
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ring.</p>
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|
<img alt="_images/pimd.jpg" class="align-center" src="_images/pimd.jpg" />
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|
<p>To run a PIMD simulation with M quasi-beads in each ring polymer using
|
|
N MPI tasks for each partition’s domain-decomposition, you would use P
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|
= MxN processors (cores) and run the simulation as follows:</p>
|
|
<pre class="literal-block">
|
|
mpirun -np P lmp_mpi -partition MxN -in script
|
|
</pre>
|
|
<p>Note that in the LAMMPS input script for a multi-partition simulation,
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|
it is often very useful to define a <a class="reference internal" href="variable.html"><span class="doc">uloop-style variable</span></a> such as</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ibead</span> <span class="n">uloop</span> <span class="n">M</span> <span class="n">pad</span>
|
|
</pre></div>
|
|
</div>
|
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<p>where M is the number of quasi-beads (partitions) used in the
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|
calculation. The uloop variable can then be used to manage I/O
|
|
related tasks for each of the partitions, e.g.</p>
|
|
<pre class="literal-block">
|
|
dump dcd all dcd 10 system_${ibead}.dcd
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|
restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
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|
read_restart system_${ibead}.restart2
|
|
</pre>
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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>This fix is part of the USER-MISC package. It is only enabled if
|
|
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>A PIMD simulation can be initialized with a single data file read via
|
|
the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. However, this means all
|
|
quasi-beads in a ring polymer will have identical positions and
|
|
velocities, resulting in identical trajectories for all quasi-beads.
|
|
To avoid this, users can simply initialize velocities with different
|
|
random number seeds assigned to each partition, as defined by the
|
|
uloop variable, e.g.</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span>velocity all create 300.0 1234${ibead} rot yes dist gaussian
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</pre></div>
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</div>
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</div>
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<div class="section" id="default">
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<h2>Default</h2>
|
|
<p>The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0,
|
|
and nhc = 2.</p>
|
|
<hr class="docutils" />
|
|
<p id="feynman"><strong>(Feynman)</strong> R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
|
|
Path Integrals, McGraw-Hill, New York (1965).</p>
|
|
<p id="pimd-tuckerman"><strong>(Tuckerman)</strong> M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).</p>
|
|
<p id="cao1"><strong>(Cao1)</strong> J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993).</p>
|
|
<p id="cao2"><strong>(Cao2)</strong> J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994).</p>
|
|
<p id="hone"><strong>(Hone)</strong> T. Hone, P. Rossky, G. Voth, J Chem Phys, 124,
|
|
154103 (2006).</p>
|
|
<p id="calhoun"><strong>(Calhoun)</strong> A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262,
|
|
415 (1996).</p>
|
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