forked from lijiext/lammps
866 lines
63 KiB
HTML
866 lines
63 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 ave/chunk 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 ave/correlate command" href="fix_ave_correlate.html"/>
|
|
<link rel="prev" title="fix ave/atom command" href="fix_ave_atom.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 current"><a class="current reference internal" href="#">fix ave/chunk command</a><ul>
|
|
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
|
|
<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_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"><a class="reference internal" href="fix_viscosity.html">fix viscosity command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_viscous.html">fix viscous command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall_piston.html">fix wall/piston command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html#fix-wall-reflect-kk-command">fix wall/reflect/kk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</a></li>
|
|
</ul>
|
|
</li>
|
|
<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
|
</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 ave/chunk 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_ave_correlate.html" class="btn btn-neutral float-right" title="fix ave/correlate command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="fix_ave_atom.html" class="btn btn-neutral" title="fix ave/atom 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-ave-chunk-command">
|
|
<span id="index-0"></span><h1>fix ave/chunk command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="n">Nevery</span> <span class="n">Nrepeat</span> <span class="n">Nfreq</span> <span class="n">chunkID</span> <span class="n">value1</span> <span class="n">value2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</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">ave/chunk = style name of this fix command</p>
|
|
</li>
|
|
<li><p class="first">Nevery = use input values every this many timesteps</p>
|
|
</li>
|
|
<li><p class="first">Nrepeat = # of times to use input values for calculating averages</p>
|
|
</li>
|
|
<li><p class="first">Nfreq = calculate averages every this many timesteps</p>
|
|
</li>
|
|
<li><p class="first">chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</p>
|
|
</li>
|
|
<li><p class="first">one or more input values can be listed</p>
|
|
</li>
|
|
<li><p class="first">value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name</p>
|
|
<pre class="literal-block">
|
|
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
|
density/number, density/mass = number or mass density
|
|
temp = temperature
|
|
c_ID = per-atom vector calculated by a compute with ID
|
|
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
|
f_ID = per-atom vector calculated by a fix with ID
|
|
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
|
|
v_name = per-atom vector calculated by an atom-style variable with name
|
|
</pre>
|
|
</li>
|
|
<li><p class="first">zero or more keyword/arg pairs may be appended</p>
|
|
</li>
|
|
<li><p class="first">keyword = <em>norm</em> or <em>ave</em> or <em>bias</em> or <em>adof</em> or <em>cdof</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></p>
|
|
<pre class="literal-block">
|
|
<em>norm</em> arg = <em>all</em> or <em>sample</em> or <em>none</em> = how output on <em>Nfreq</em> steps is normalized
|
|
all = output is sum of atoms across all <em>Nrepeat</em> samples, divided by atom count
|
|
sample = output is sum of <em>Nrepeat</em> sample averages, divided by <em>Nrepeat</em>
|
|
none = output is sum of <em>Nrepeat</em> sample sums, divided by <em>Nrepeat</em>
|
|
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
|
one = output new average value every Nfreq steps
|
|
running = output cumulative average of all previous Nfreq steps
|
|
window M = output average of M most recent Nfreq steps
|
|
<em>bias</em> arg = bias-ID
|
|
bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
|
|
<em>adof</em> value = dof_per_atom
|
|
dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
|
|
<em>cdof</em> value = dof_per_chunk
|
|
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
|
|
<em>file</em> arg = filename
|
|
filename = file to write results to
|
|
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
|
<em>format</em> arg = string
|
|
string = C-style format string
|
|
<em>title1</em> arg = string
|
|
string = text to print as 1st line of output file
|
|
<em>title2</em> arg = string
|
|
string = text to print as 2nd line of output file
|
|
<em>title3</em> arg = string
|
|
string = text to print as 3rd line of output file
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
|
|
fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
|
|
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
|
|
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
|
|
</pre>
|
|
<p><strong>NOTE:</strong></p>
|
|
<p>If you are trying to replace a deprectated fix ave/spatial command
|
|
with the newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
|
|
the fix ave/spatial arguments across the two new commands. For
|
|
example, this command:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>could be replaced by:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="n">flow</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">y</span> <span class="mf">0.0</span> <span class="mf">1.0</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</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">cc1</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Use one or more per-atom vectors as inputs every few timesteps, sum
|
|
the values over the atoms in each chunk at each timestep, then average
|
|
the per-chunk values over longer timescales. The resulting chunk
|
|
averages can be used by other <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> such as <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a>, and can also be written to a file.</p>
|
|
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command, which assigns each atom
|
|
to a single chunk (or no chunk). The ID for this command is specified
|
|
as chunkID. For example, a single chunk could be the atoms in a
|
|
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> doc page and <a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section 6.23</span></a> for details of how chunks can be
|
|
defined and examples of how they can be used to measure properties of
|
|
a system.</p>
|
|
<p>Note that only atoms in the specified group contribute to the summing
|
|
and averaging calculations. The <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command defines its own group as
|
|
well as an optional region. Atoms will have a chunk ID = 0, meaning
|
|
they belong to no chunk, if they are not in that group or region.
|
|
Thus you can specify the “all” group for this command if you simply
|
|
want to use the chunk definitions provided by chunkID.</p>
|
|
<p>Each specified per-atom value can be an atom attribute (position,
|
|
velocity, force component), a mass or number density, or the result of
|
|
a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> or the evaluation of an
|
|
atom-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>. In the latter cases, the
|
|
compute, fix, or variable must produce a per-atom quantity, not a
|
|
global quantity. Note that the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command provides access to
|
|
any attribute defined and stored by atoms. If you wish to
|
|
time-average global quantities from a compute, fix, or variable, then
|
|
see the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command.</p>
|
|
<p>The per-atom values of each input vector are summed and averaged
|
|
independently of the per-atom values in other input vectors.</p>
|
|
<p><a class="reference internal" href="compute.html"><span class="doc">Computes</span></a> that produce per-atom quantities are those
|
|
which have the word <em>atom</em> in their style name. See the doc pages for
|
|
individual <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> to determine which ones produce per-atom
|
|
quantities. <a class="reference internal" href="variable.html"><span class="doc">Variables</span></a> of style <em>atom</em> are the only
|
|
ones that can be used with this fix since all other styles of variable
|
|
produce global quantities.</p>
|
|
<p>Note that for values from a compute or fix, the bracketed index I can
|
|
be specified using a wildcard asterisk with the index to effectively
|
|
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
|
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
|
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
|
with no numeric values means all indices from 1 to N. A leading
|
|
asterisk means all indices from 1 to n (inclusive). A trailing
|
|
asterisk means all indices from n to N (inclusive). A middle asterisk
|
|
means all indices from m to n (inclusive).</p>
|
|
<p>Using a wildcard is the same as if the individual columns of the array
|
|
had been listed one by one. E.g. these 2 fix ave/chunk commands are
|
|
equivalent, since the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command creates, in this
|
|
case, a per-atom array with 3 columns:</p>
|
|
<pre class="literal-block">
|
|
compute myAng all property/atom angmomx angmomy angmomz
|
|
fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
|
|
fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
|
|
</pre>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues
|
|
on each processor. <em>Nchunk</em> is the number of chunks which is defined
|
|
by the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.
|
|
Nvalues is the number of input values specified. Each processor loops
|
|
over its atoms, tallying its values to the appropriate chunk. Then
|
|
the entire array is summed across all processors. This means that
|
|
using a large number of chunks will incur an overhead in memory and
|
|
computational cost (summing across processors), so be careful to
|
|
define a reasonable number of chunks.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
|
timesteps the input values will be accessed and contribute to the
|
|
average. The final averaged quantities are generated on timesteps
|
|
that are a multiples of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
|
|
quantities, computed in the preceding portion of the simulation every
|
|
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
|
|
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
|
|
contributing to the average value cannot overlap, i.e. Nrepeat*Nevery
|
|
can not exceed Nfreq.</p>
|
|
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
|
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
|
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
|
|
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
|
averaging is done; values are simply generated on timesteps
|
|
100,200,etc.</p>
|
|
<p>Each input value can also be averaged over the atoms in each chunk.
|
|
The way the averaging is done across the <em>Nrepeat</em> timesteps to
|
|
produce output on the <em>Nfreq</em> timesteps, and across multiple <em>Nfreq</em>
|
|
outputs, is determined by the <em>norm</em> and <em>ave</em> keyword settings, as
|
|
discussed below.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">To perform per-chunk averaging within a <em>Nfreq</em> time window, the
|
|
number of chunks <em>Nchunk</em> defined by the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command must remain constant. If
|
|
the <em>ave</em> keyword is set to <em>running</em> or <em>window</em> then <em>Nchunk</em> must
|
|
remain constant for the duration of the simulation. This fix forces
|
|
the chunk/atom compute specified by chunkID to hold <em>Nchunk</em> constant
|
|
for the appropriate time windows, by not allowing it to re-calcualte
|
|
<em>Nchunk</em>, which can also affect how it assigns chunk IDs to atoms.
|
|
More details are given on the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> doc page.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
|
|
As noted above, any other atom attributes can be used as input values
|
|
to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
|
|
an input value from that compute.</p>
|
|
<p>The <em>density/number</em> value means the number density is computed for
|
|
each chunk, i.e. number/volume. The <em>density/mass</em> value means the
|
|
mass density is computed for each chunk, i.e. total-mass/volume. The
|
|
output values are in units of 1/volume or density (mass/volume). See
|
|
the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command doc page for the definition of density
|
|
for each choice of units, e.g. gram/cm^3. If the chunks defined by
|
|
the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command are spatial
|
|
bins, the volume is the bin volume. Otherwise it is the volume of the
|
|
entire simulation box.</p>
|
|
<p>The <em>temp</em> value means the temperature is computed for each chunk, by
|
|
the formula KE = DOF/2 k T, where KE = total kinetic energy of the
|
|
chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees
|
|
of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
|
|
temperature.</p>
|
|
<p>The DOF is calculated as N*adof + cdof, where N = number of atoms in
|
|
the chunk, adof = degrees of freedom per atom, and cdof = degrees of
|
|
freedom per chunk. By default adof = 2 or 3 = dimensionality of
|
|
system, as set via the <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a> command, and cdof =
|
|
0.0. This gives the usual formula for temperature.</p>
|
|
<p>Note that currently this temperature only includes translational
|
|
degrees of freedom for each atom. No rotational degrees of freedom
|
|
are included for finite-size particles. Also no degrees of freedom
|
|
are subtracted for any velocity bias or constraints that are applied,
|
|
such as <a class="reference internal" href="compute_temp_partial.html"><span class="doc">compute temp/partial</span></a>, or <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>. This is because
|
|
those degrees of freedom (e.g. a constrained bond) could apply to sets
|
|
of atoms that are both included and excluded from a specific chunk,
|
|
and hence the concept is somewhat ill-defined. In some cases, you can
|
|
use the <em>adof</em> and <em>cdof</em> keywords to adjust the calculated degress of
|
|
freedom appropriately, as explained below.</p>
|
|
<p>Also note that a bias can be subtracted from atom velocities before
|
|
they are used in the above formula for KE, by using the <em>bias</em>
|
|
keyword. This allows, for example, a thermal temperature to be
|
|
computed after removal of a flow velocity profile.</p>
|
|
<p>Note that the per-chunk temperature calculated by this fix and the
|
|
<a class="reference internal" href="compute_temp_chunk.html"><span class="doc">compute temp/chunk</span></a> command can be different.
|
|
The compute calculates the temperature for each chunk for a single
|
|
snapshot. This fix can do that but can also time average those values
|
|
over many snapshots, or it can compute a temperature as if the atoms
|
|
in the chunk on different timesteps were collected together as one set
|
|
of atoms to calculate their temperature. The compute allows the
|
|
center-of-mass velocity of each chunk to be subtracted before
|
|
calculating the temperature; this fix does not.</p>
|
|
<p>If a value begins with “c_”, a compute ID must follow which has been
|
|
previously defined in the input script. If no bracketed integer is
|
|
appended, the per-atom vector calculated by the compute is used. If a
|
|
bracketed integer is appended, the Ith column of the per-atom array
|
|
calculated by the compute is used. Users can also write code for
|
|
their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.
|
|
See the discussion above for how I can be specified with a wildcard
|
|
asterisk to effectively specify multiple values.</p>
|
|
<p>If a value begins with “f_”, a fix ID must follow which has been
|
|
previously defined in the input script. If no bracketed integer is
|
|
appended, the per-atom vector calculated by the fix is used. If a
|
|
bracketed integer is appended, the Ith column of the per-atom array
|
|
calculated by the fix is used. Note that some fixes only produce
|
|
their values on certain timesteps, which must be compatible with
|
|
<em>Nevery</em>, else an error results. Users can also write code for their
|
|
own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
|
|
discussion above for how I can be specified with a wildcard asterisk
|
|
to effectively specify multiple values.</p>
|
|
<p>If a value begins with “v_”, a variable name must follow which has
|
|
been previously defined in the input script. Variables of style
|
|
<em>atom</em> can reference thermodynamic keywords and various per-atom
|
|
attributes, or invoke other computes, fixes, or variables when they
|
|
are evaluated, so this is a very general means of generating per-atom
|
|
quantities to average within chunks.</p>
|
|
<hr class="docutils" />
|
|
<p>Additional optional keywords also affect the operation of this fix
|
|
and its outputs.</p>
|
|
<p>The <em>norm</em> keyword affects how averaging is done for the per-chunk
|
|
values that are output every <em>Nfreq</em> timesteps.</p>
|
|
<p>It the <em>norm</em> setting is <em>all</em>, which is the default, a chunk value is
|
|
summed over all atoms in all <em>Nrepeat</em> samples, as is the count of
|
|
atoms in the chunk. The averaged output value for the chunk on the
|
|
<em>Nfreq</em> timesteps is Total-sum / Total-count. In other words it is an
|
|
average over atoms across the entire <em>Nfreq</em> timescale.</p>
|
|
<p>If the <em>norm</em> setting is <em>sample</em>, the chunk value is summed over atoms
|
|
for each sample, as is the count, and an “average sample value” is
|
|
computed for each sample, i.e. Sample-sum / Sample-count. The output
|
|
value for the chunk on the <em>Nfreq</em> timesteps is the average of the
|
|
<em>Nrepeat</em> “average sample values”, i.e. the sum of <em>Nrepeat</em> “average
|
|
sample values” divided by <em>Nrepeat</em>. In other words it is an average
|
|
of an average.</p>
|
|
<p>If the <em>norm</em> setting is <em>none</em>, a similar computation as for the
|
|
<em>sample</em> seting is done, except the individual “average sample values”
|
|
are “summed sample values”. A summed sample value is simply the chunk
|
|
value summed over atoms in the sample, without dividing by the number
|
|
of atoms in the sample. The output value for the chunk on the
|
|
<em>Nfreq</em> timesteps is the average of the <em>Nrepeat</em> “summed sample
|
|
values”, i.e. the sum of <em>Nrepeat</em> “summed sample values” divided by
|
|
<em>Nrepeat</em>.</p>
|
|
<p>The <em>ave</em> keyword determines how the per-chunk values produced every
|
|
<em>Nfreq</em> steps are averaged with values produced on previous steps that
|
|
were multiples of <em>Nfreq</em>, before they are accessed by another output
|
|
command or written to a file.</p>
|
|
<p>If the <em>ave</em> setting is <em>one</em>, which is the default, then the chunk
|
|
values produced on timesteps that are multiples of <em>Nfreq</em> are
|
|
independent of each other; they are output as-is without further
|
|
averaging.</p>
|
|
<p>If the <em>ave</em> setting is <em>running</em>, then the chunk values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged in a
|
|
cumulative sense before being output. Each output chunk value is thus
|
|
the average of the chunk value produced on that timestep with all
|
|
preceding values for the same chunk. This running average begins when
|
|
the fix is defined; it can only be restarted by deleting the fix via
|
|
the <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command, or re-defining the fix by
|
|
re-specifying it.</p>
|
|
<p>If the <em>ave</em> setting is <em>window</em>, then the chunk values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged within
|
|
a moving “window” of time, so that the last M values for the same
|
|
chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
|
|
then the output on step 10000 will be the average of the individual
|
|
chunk values on steps 8000,9000,10000. Outputs on early steps will
|
|
average over less than M values if they are not available.</p>
|
|
<p>The <em>bias</em> keyword specifies the ID of a temperature compute that
|
|
removes a “bias” velocity from each atom, specified as <em>bias-ID</em>. It
|
|
is only used when the <em>temp</em> value is calculated, to compute the
|
|
thermal temperature of each chunk after the translational kinetic
|
|
energy components have been altered in a prescribed way, e.g. to
|
|
remove a flow velocity profile. See the doc pages for individual
|
|
computes that calculate a temperature to see which ones implement a
|
|
bias.</p>
|
|
<p>The <em>adof</em> and <em>cdof</em> keywords define the values used in the degree of
|
|
freedom (DOF) formula described above for for temperature calculation
|
|
for each chunk. They are only used when the <em>temp</em> value is
|
|
calculated. They can be used to calculate a more appropriate
|
|
temperature for some kinds of chunks. Here are 3 examples:</p>
|
|
<p>If spatially binned chunks contain some number of water molecules and
|
|
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> is used to make each molecule rigid, then
|
|
you could calculate a temperature with 6 degrees of freedom (DOF) (3
|
|
translational, 3 rotational) per molecule by setting <em>adof</em> to 2.0.</p>
|
|
<p>If <a class="reference internal" href="compute_temp_partial.html"><span class="doc">compute temp/partial</span></a> is used with the
|
|
<em>bias</em> keyword to only allow the x component of velocity to contribute
|
|
to the temperature, then <em>adof</em> = 1.0 would be appropriate.</p>
|
|
<p>If each chunk consists of a large molecule, with some number of its
|
|
bonds constrained by <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or the entire molecule
|
|
by <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a>, <em>adof</em> = 0.0 and <em>cdof</em> could be
|
|
set to the remaining degrees of freedom for the entire molecule
|
|
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
|
|
molecule.</p>
|
|
<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
|
|
timesteps, a section of chunk info will be written to a text file in
|
|
the following format. A line with the timestep and number of chunks
|
|
is written. Then one line per chunk is written, containing the chunk
|
|
ID (1-Nchunk), an optional original ID value, optional coordinate
|
|
values for chunks that represent spatial bins, the number of atoms in
|
|
the chunk, and one or more calculated values. More explanation of the
|
|
optional values is given below. The number of values in each line
|
|
corresponds to the number of values specified in the fix ave/chunk
|
|
command. The number of atoms and the value(s) are summed or average
|
|
quantities, as explained above.</p>
|
|
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
|
|
with the latest output, so that it only contains one timestep worth of
|
|
output. This option can only be used with the <em>ave running</em> setting.</p>
|
|
<p>The <em>format</em> keyword sets the numeric format of each value when it is
|
|
printed to a file via the <em>file</em> keyword. Note that all values are
|
|
floating point quantities. The default format is %g. You can specify
|
|
a higher precision if desired, e.g. %20.16g.</p>
|
|
<p>The <em>title1</em> and <em>title2</em> and <em>title3</em> keywords allow specification of
|
|
the strings that will be printed as the first 3 lines of the output
|
|
file, assuming the <em>file</em> keyword was used. LAMMPS uses default
|
|
values for each of these, so they do not need to be specified.</p>
|
|
<p>By default, these header lines are as follows:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Chunk-averaged data for fix ID and group name</span>
|
|
<span class="c1"># Timestep Number-of-chunks</span>
|
|
<span class="c1"># Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ...</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>In the first line, ID and name are replaced with the fix-ID and group
|
|
name. The second line describes the two values that are printed at
|
|
the first of each section of output. In the third line the values are
|
|
replaced with the appropriate value names, e.g. fx or c_myCompute<strong>2</strong>.</p>
|
|
<p>The words in parenthesis only appear with corresponding columns if the
|
|
chunk style specified for the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command supports them. The OrigID
|
|
column is only used if the <em>compress</em> keyword was set to <em>yes</em> for the
|
|
<a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. This means that
|
|
the original chunk IDs (e.g. molecule IDs) will have been compressed
|
|
to remove chunk IDs with no atoms assigned to them. Thus a compresed
|
|
chunk ID of 3 may correspond to an original chunk ID or molecule ID of
|
|
415. The OrigID column will list 415 for the 3rd chunk.</p>
|
|
<p>The CoordN columns only appear if a <em>binning</em> style was used in the
|
|
<a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. For <em>bin/1d</em>,
|
|
<em>bin/2d</em>, and <em>bin/3d</em> styles the column values are the center point
|
|
of the bin in the corresponding dimension. Just Coord1 is used for
|
|
<em>bin/1d</em>, Coord2 is added for <em>bin/2d</em>, Coord3 is added for <em>bin/3d</em>.
|
|
For <em>bin/sphere</em>, just Coord1 is used, and it is the radial
|
|
coordinate. For <em>bin/cylinder</em>, Coord1 and Coord2 are used. Coord1
|
|
is the radial coordinate (away from the cylinder axis), and coord2 is
|
|
the coordinate along the cylinder axis.</p>
|
|
<p>Note that if the value of the <em>units</em> keyword used in the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom command</span></a> is <em>box</em> or <em>lattice</em>, the
|
|
coordinate values will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>. If the
|
|
value of the <em>units</em> keyword is <em>reduced</em>, the coordinate values will
|
|
be in unitless reduced units (0-1). This is not true for the Coord1 value
|
|
of style <em>bin/sphere</em> or <em>bin/cylinder</em> which both represent radial
|
|
dimensions. Those values are always in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
|
<hr class="docutils" />
|
|
<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 array of values 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 values can
|
|
only be accessed on timesteps that are multiples of <em>Nfreq</em> since that
|
|
is when averaging is performed. The global array has # of rows =
|
|
the number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The # of columns =
|
|
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
|
|
columns for OrigID and CoordN are used, as explained above.
|
|
Following the optional columns, the next column contains the count of
|
|
atoms in the chunk, and the remaining columns are the Nvalue
|
|
quantities. When the array is accessed with a row I that exceeds the
|
|
current number of chunks, than a 0.0 is returned by the fix instead of
|
|
an error, since the number of chunks can vary as a simulation runs
|
|
depending on how that value is computed by the compute chunk/atom
|
|
command.</p>
|
|
<p>The array values calculated by this fix are treated as “intensive”,
|
|
since they are typically already normalized by the count of atoms in
|
|
each chunk.</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>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
|
|
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are norm = all, ave = one, bias = none, no file output, and
|
|
title 1,2,3 = strings as described above.</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
|
|
|
<a href="fix_ave_correlate.html" class="btn btn-neutral float-right" title="fix ave/correlate command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="fix_ave_atom.html" class="btn btn-neutral" title="fix ave/atom 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> |