forked from lijiext/lammps
595 lines
42 KiB
HTML
595 lines
42 KiB
HTML
|
|
|
|
<!DOCTYPE html>
|
|
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
|
|
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
|
|
<head>
|
|
<meta charset="utf-8">
|
|
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
|
|
<title>fix viscosity command — LAMMPS documentation</title>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
|
|
|
|
|
|
|
|
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
|
|
|
|
|
|
|
|
<link rel="top" title="LAMMPS documentation" href="index.html"/>
|
|
<link rel="up" title="Fixes" href="fixes.html"/>
|
|
<link rel="next" title="fix viscous command" href="fix_viscous.html"/>
|
|
<link rel="prev" title="fix vector command" href="fix_vector.html"/>
|
|
|
|
|
|
<script src="_static/js/modernizr.min.js"></script>
|
|
|
|
</head>
|
|
|
|
<body class="wy-body-for-nav" role="document">
|
|
|
|
<div class="wy-grid-for-nav">
|
|
|
|
|
|
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
|
|
<div class="wy-side-nav-search">
|
|
|
|
|
|
|
|
<a href="Manual.html" class="icon icon-home"> LAMMPS
|
|
|
|
|
|
|
|
</a>
|
|
|
|
|
|
<div role="search">
|
|
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
|
|
<input type="text" name="q" placeholder="Search docs" />
|
|
<input type="hidden" name="check_keywords" value="yes" />
|
|
<input type="hidden" name="area" value="default" />
|
|
</form>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
|
|
|
|
|
|
|
|
<p class="caption"><span class="caption-text">User Documentation</span></p>
|
|
<ul>
|
|
<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>
|
|
</ul>
|
|
<p class="caption"><span class="caption-text">Index</span></p>
|
|
<ul class="current">
|
|
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
|
|
<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"><a class="reference internal" href="fix_spring_rg.html">fix spring/rg command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_spring_self.html">fix spring/self command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_srd.html">fix srd command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_store_force.html">fix store/force command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_store_state.html">fix store/state command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_temp_berendsen.html">fix temp/berendsen command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html">fix temp/csvr command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html#fix-temp-csld-command">fix temp/csld command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale.html">fix temp/rescale command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
|
|
<li class="toctree-l2 current"><a class="current reference internal" href="#">fix viscosity 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>
|
|
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
|
|
</ul>
|
|
</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>
|
|
</ul>
|
|
|
|
|
|
|
|
</div>
|
|
|
|
</nav>
|
|
|
|
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
|
|
|
|
|
|
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
|
|
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
|
|
<a href="Manual.html">LAMMPS</a>
|
|
</nav>
|
|
|
|
|
|
|
|
<div class="wy-nav-content">
|
|
<div class="rst-content">
|
|
<div role="navigation" aria-label="breadcrumbs navigation">
|
|
<ul class="wy-breadcrumbs">
|
|
<li><a href="Manual.html">Docs</a> »</li>
|
|
|
|
<li><a href="fixes.html">Fixes</a> »</li>
|
|
|
|
<li>fix viscosity command</li>
|
|
<li class="wy-breadcrumbs-aside">
|
|
|
|
|
|
<a href="http://lammps.sandia.gov">Website</a>
|
|
<a href="Section_commands.html#comm">Commands</a>
|
|
|
|
</li>
|
|
</ul>
|
|
<hr/>
|
|
|
|
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
|
|
|
|
<a href="fix_viscous.html" class="btn btn-neutral float-right" title="fix viscous command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="fix_vector.html" class="btn btn-neutral" title="fix vector command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
|
|
|
</div>
|
|
|
|
</div>
|
|
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
|
<div itemprop="articleBody">
|
|
|
|
<div class="section" id="fix-viscosity-command">
|
|
<span id="index-0"></span><h1>fix viscosity 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">viscosity</span> <span class="n">N</span> <span class="n">vdim</span> <span class="n">pdim</span> <span class="n">Nbin</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul>
|
|
<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>
|
|
</li>
|
|
<li><p class="first">viscosity = style name of this fix command</p>
|
|
</li>
|
|
<li><p class="first">N = perform momentum exchange every N steps</p>
|
|
</li>
|
|
<li><p class="first">vdim = <em>x</em> or <em>y</em> or <em>z</em> = which momentum component to exchange</p>
|
|
</li>
|
|
<li><p class="first">pdim = <em>x</em> or <em>y</em> or <em>z</em> = direction of momentum transfer</p>
|
|
</li>
|
|
<li><p class="first">Nbin = # of layers in pdim direction (must be even number)</p>
|
|
</li>
|
|
<li><p class="first">zero or more keyword/value pairs may be appended</p>
|
|
</li>
|
|
<li><p class="first">keyword = <em>swap</em> or <em>target</em></p>
|
|
<pre class="literal-block">
|
|
<em>swap</em> value = Nswap = number of swaps to perform every N steps
|
|
<em>vtarget</em> value = V or INF = target velocity of swap partners (velocity units)
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">viscosity</span> <span class="mi">100</span> <span class="n">x</span> <span class="n">z</span> <span class="mi">20</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">viscosity</span> <span class="mi">50</span> <span class="n">x</span> <span class="n">z</span> <span class="mi">20</span> <span class="n">swap</span> <span class="mi">2</span> <span class="n">vtarget</span> <span class="mf">1.5</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Use the Muller-Plathe algorithm described in <a class="reference internal" href="#muller-plathe"><span class="std std-ref">this paper</span></a> to exchange momenta between two particles in
|
|
different regions of the simulation box every N steps. This induces a
|
|
shear velocity profile in the system. As described below this enables
|
|
a viscosity of the fluid to be calculated. This algorithm is
|
|
sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
|
|
to computing viscosity. This is because the usual NEMD approach is to
|
|
impose a shear velocity profile on the system and measure the response
|
|
via an off-diagonal component of the stress tensor, which is
|
|
proportional to the momentum flux. In the Muller-Plathe method, the
|
|
momentum flux is imposed, and the shear velocity profile is the
|
|
system’s response.</p>
|
|
<p>The simulation box is divided into <em>Nbin</em> layers in the <em>pdim</em>
|
|
direction, where the layer 1 is at the low end of that dimension and
|
|
the layer <em>Nbin</em> is at the high end. Every N steps, Nswap pairs of
|
|
atoms are chosen in the following manner. Only atoms in the fix group
|
|
are considered. Nswap atoms in layer 1 with positive velocity
|
|
components in the <em>vdim</em> direction closest to the target value <em>V</em> are
|
|
selected. Similarly, Nswap atoms in the “middle” layer (see below) with
|
|
negative velocity components in the <em>vdim</em> direction closest to the
|
|
negative of the target value <em>V</em> are selected. The two sets of Nswap
|
|
atoms are paired up and their <em>vdim</em> momenta components are swapped
|
|
within each pair. This resets their velocities, typically in opposite
|
|
directions. Over time, this induces a shear velocity profile in the
|
|
system which can be measured using commands such as the following,
|
|
which writes the profile to the file tmp.profile:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
|
|
<span class="n">fix</span> <span class="n">f1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">vx</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>Note that by default, Nswap = 1 and vtarget = INF, though this can be
|
|
changed by the optional <em>swap</em> and <em>vtarget</em> keywords. When vtarget =
|
|
INF, one or more atoms with the most positive and negative velocity
|
|
components are selected. Setting these parameters appropriately, in
|
|
conjunction with the swap rate N, allows the momentum flux rate to be
|
|
adjusted across a wide range of values, and the momenta to be
|
|
exchanged in large chunks or more smoothly.</p>
|
|
<p>The “middle” layer for momenta swapping is defined as the <em>Nbin</em>/2 + 1
|
|
layer. Thus if <em>Nbin</em> = 20, the two swapping layers are 1 and 11.
|
|
This should lead to a symmetric velocity profile since the two layers
|
|
are separated by the same distance in both directions in a periodic
|
|
sense. This is why <em>Nbin</em> is restricted to being an even number.</p>
|
|
<p>As described below, the total momentum transferred by these velocity
|
|
swaps is computed by the fix and can be output. Dividing this
|
|
quantity by time and the cross-sectional area of the simulation box
|
|
yields a momentum flux. The ratio of momentum flux to the slope of
|
|
the shear velocity profile is proportional to the viscosity of the
|
|
fluid, in appropriate units. See the <a class="reference internal" href="#muller-plathe"><span class="std std-ref">Muller-Plathe paper</span></a> for details.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If your system is periodic in the direction of the momentum
|
|
flux, then the flux is going in 2 directions. This means the
|
|
effective momentum flux in one direction is reduced by a factor of 2.
|
|
You will see this in the equations for viscosity in the Muller-Plathe
|
|
paper. LAMMPS is simply tallying momentum which does not account for
|
|
whether or not your system is periodic; you must use the value
|
|
appropriately to yield a viscosity for your system.</p>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">After equilibration, if the velocity profile you observe is not
|
|
linear, then you are likely swapping momentum too frequently and are
|
|
not in a regime of linear response. In this case you cannot
|
|
accurately infer a viscosity and should try increasing the Nevery
|
|
parameter.</p>
|
|
</div>
|
|
<p>An alternative method for calculating a viscosity is to run a NEMD
|
|
simulation, as described in <a class="reference internal" href="Section_howto.html#howto-13"><span class="std std-ref">Section 6.13</span></a> of the manual. NEMD simulations
|
|
deform the simmulation box via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a>
|
|
command. Thus they cannot be run on a charged system using a <a class="reference internal" href="kspace_style.html"><span class="doc">PPPM solver</span></a> since PPPM does not currently support
|
|
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
|
|
thus it does not suffer from this limitation.</p>
|
|
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
|
are relevant to this fix.</p>
|
|
<p>This fix computes a global scalar which can be accessed by various
|
|
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
|
|
cummulative momentum transferred between the bottom and middle of the
|
|
simulation box (in the <em>pdim</em> direction) is stored as a scalar
|
|
quantity by this fix. This quantity is zeroed when the fix is defined
|
|
and accumlates thereafter, once every N steps. The units of the
|
|
quantity are momentum = mass*velocity. The scalar value calculated by
|
|
this fix is “intensive”.</p>
|
|
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
|
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>This fix is part of the 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>Swaps conserve both momentum and kinetic energy, even if the masses of
|
|
the swapped atoms are not equal. Thus you should not need to
|
|
thermostat the system. If you do use a thermostat, you may want to
|
|
apply it only to the non-swapped dimensions (other than <em>vdim</em>).</p>
|
|
<p>LAMMPS does not check, but you should not use this fix to swap
|
|
velocities of atoms that are in constrained molecules, e.g. via <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>. This is because
|
|
application of the constraints will alter the amount of transferred
|
|
momentum. You should, however, be able to use flexible molecules.
|
|
See the <a class="reference internal" href="#maginn"><span class="std std-ref">Maginn paper</span></a> for an example of using this algorithm
|
|
in a computation of alcohol molecule properties.</p>
|
|
<p>When running a simulation with large, massive particles or molecules
|
|
in a background solvent, you may want to only exchange momenta bewteen
|
|
solvent particles.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are swap = 1 and vtarget = INF.</p>
|
|
<hr class="docutils" />
|
|
<p id="muller-plathe"><strong>(Muller-Plathe)</strong> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).</p>
|
|
<p id="maginn"><strong>(Maginn)</strong> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
|
|
260, 218-231 (2007).</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
|
|
|
<a href="fix_viscous.html" class="btn btn-neutral float-right" title="fix viscous command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="fix_vector.html" class="btn btn-neutral" title="fix vector command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
|
|
|
</div>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© Copyright 2013 Sandia Corporation.
|
|
</p>
|
|
</div>
|
|
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
|
|
|
</footer>
|
|
|
|
</div>
|
|
</div>
|
|
|
|
</section>
|
|
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript">
|
|
var DOCUMENTATION_OPTIONS = {
|
|
URL_ROOT:'./',
|
|
VERSION:'',
|
|
COLLAPSE_INDEX:false,
|
|
FILE_SUFFIX:'.html',
|
|
HAS_SOURCE: true
|
|
};
|
|
</script>
|
|
<script type="text/javascript" src="_static/jquery.js"></script>
|
|
<script type="text/javascript" src="_static/underscore.js"></script>
|
|
<script type="text/javascript" src="_static/doctools.js"></script>
|
|
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
|
|
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
|
|
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
|
|
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
|
|
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript" src="_static/js/theme.js"></script>
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript">
|
|
jQuery(function () {
|
|
SphinxRtdTheme.StickyNav.enable();
|
|
});
|
|
</script>
|
|
|
|
|
|
</body>
|
|
</html> |