625 lines
55 KiB
HTML
625 lines
55 KiB
HTML
<!DOCTYPE html>
|
||
<html class="writer-html5" lang="en" >
|
||
<head>
|
||
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
|
||
|
||
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
|
||
<title>fix rx command — LAMMPS documentation</title>
|
||
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/sphinx-design.min.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/css/lammps.css" type="text/css" />
|
||
<link rel="shortcut icon" href="_static/lammps.ico"/>
|
||
<link rel="canonical" href="https://docs.lammps.org/fix_rx.html" />
|
||
<!--[if lt IE 9]>
|
||
<script src="_static/js/html5shiv.min.js"></script>
|
||
<![endif]-->
|
||
|
||
<script src="_static/jquery.js?v=5d32c60e"></script>
|
||
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
|
||
<script src="_static/documentation_options.js?v=5929fcd5"></script>
|
||
<script src="_static/doctools.js?v=9bcbadda"></script>
|
||
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
|
||
<script src="_static/design-tabs.js?v=f930bc37"></script>
|
||
<script async="async" src="_static/mathjax/es5/tex-mml-chtml.js?v=cadf963e"></script>
|
||
<script src="_static/js/theme.js"></script>
|
||
<link rel="index" title="Index" href="genindex.html" />
|
||
<link rel="search" title="Search" href="search.html" />
|
||
<link rel="next" title="fix saed/vtk command" href="fix_saed_vtk.html" />
|
||
<link rel="prev" title="fix rigid/meso command" href="fix_rigid_meso.html" />
|
||
</head>
|
||
|
||
<body class="wy-body-for-nav">
|
||
<div class="wy-grid-for-nav">
|
||
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
|
||
<div class="wy-side-scroll">
|
||
<div class="wy-side-nav-search" >
|
||
|
||
|
||
|
||
<a href="Manual.html">
|
||
|
||
<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
|
||
</a>
|
||
<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
|
||
<div class="lammps_release">git info: </div>
|
||
<div role="search">
|
||
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
|
||
<input type="text" name="q" placeholder="Search docs" aria-label="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="Navigation menu">
|
||
<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
|
||
<ul>
|
||
<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
|
||
</ul>
|
||
<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
|
||
<ul>
|
||
<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
|
||
</ul>
|
||
<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
|
||
<ul class="current">
|
||
<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
|
||
<li class="toctree-l1 current"><a class="reference internal" href="fixes.html">Fix Styles</a><ul class="current">
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_accelerate_cos.html">fix accelerate/cos command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_acks2_reaxff.html">fix acks2/reaxff command</a></li>
|
||
<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_add_heat.html">fix add/heat 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_alchemy.html">fix alchemy command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_bitorsion.html">fix amoeba/bitorsion command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_amoeba_pitorsion.html">fix amoeba/pitorsion 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_grid.html">fix ave/grid 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_spatial.html">fix ave/spatial command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_ave_spatial_sphere.html">fix ave/spatial/sphere 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_bocs.html">fix bocs 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_create.html#fix-bond-create-angle-command">fix bond/create/angle command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_bond_react.html">fix bond/react 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_brownian.html">fix brownian command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-sphere-command">fix brownian/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_brownian.html#fix-brownian-asphere-command">fix brownian/asphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_charge_regulation.html">fix charge/regulation command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_cmap.html">fix cmap 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_damping_cundall.html">fix damping/cundall 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_pressure.html">fix deform/pressure 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_dpd_energy.html">fix dpd/energy command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html">fix edpd/source command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_dpd_source.html#fix-tdpd-source-command">fix tdpd/source 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_efield.html#fix-efield-tip4p-command">fix efield/tip4p 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_electrode.html">fix electrode/conp command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html#fix-electrode-conq-command">fix electrode/conq command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_electrode.html#fix-electrode-thermo-command">fix electrode/thermo command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_electron_stopping.html">fix electron/stopping command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_electron_stopping.html#fix-electron-stopping-fit-command">fix electron/stopping/fit 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_ffl.html">fix ffl command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_filter_corotate.html">fix filter/corotate 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_grem.html">fix grem command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_halt.html">fix halt 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_heat_flow.html">fix heat/flow command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_hyper_global.html">fix hyper/global command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_hyper_local.html">fix hyper/local 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_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_langevin_spin.html">fix langevin/spin 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_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_mdi_qm.html">fix mdi/qm command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mdi_qmmm.html">fix mdi/qmmm command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_meso_move.html">fix meso/move command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mol_swap.html">fix mol/swap 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_momentum.html#fix-momentum-chunk-command">fix momentum/chunk 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_mvv_dpd.html">fix mvv/dpd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-edpd-command">fix mvv/edpd command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_mvv_dpd.html#fix-mvv-tdpd-command">fix mvv/tdpd 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_neb_spin.html">fix neb/spin 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-npt-command">fix npt 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_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_nh_uef.html">fix nvt/uef command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nh_uef.html#fix-npt-uef-command">fix npt/uef command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nonaffine_displacement.html">fix nonaffine/displacement 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_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_nphug.html">fix nphug 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_body.html">fix npt/body command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_npt_cauchy.html">fix npt/cauchy 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_numdiff.html">fix numdiff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_numdiff_virial.html">fix numdiff/virial 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_asphere.html">fix nve/asphere 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_awpmd.html">fix nve/awpmd 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_bpm_sphere.html">fix nve/bpm/sphere command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_dot.html">fix nve/dot command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_nve_dotc_langevin.html">fix nve/dotc/langevin 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_spin.html">fix nve/spin 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_nvk.html">fix nvk 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_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_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_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_orient_eco.html">fix orient/eco command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pafi.html">fix pafi command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pair.html">fix pair 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/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html#fix-pimd-nvt-command">fix pimd/nvt command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimdb.html">fix pimdb/langevin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_pimdb.html#fix-pimdb-nvt-command">fix pimdb/nvt 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_plumed.html">fix plumed command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html">fix polarize/bem/gmres command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html#fix-polarize-bem-icc-command">fix polarize/bem/icc command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_polarize.html#fix-polarize-functional-command">fix polarize/functional command</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_precession_spin.html">fix precession/spin 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_press_langevin.html">fix press/langevin 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_propel_self.html">fix propel/self 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_python_invoke.html">fix python/invoke command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_python_move.html">fix python/move 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-ctip-command">fix qeq/ctip 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_reaxff.html">fix qeq/reaxff 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_qtpie_reaxff.html">fix qtpie/reaxff command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_reaxff_bonds.html">fix reaxff/bonds command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_reaxff_species.html">fix reaxff/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_rheo.html">fix rheo command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_oxidation.html">fix rheo/oxidation command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_pressure.html">fix rheo/pressure command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_thermal.html">fix rheo/thermal command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rheo_viscosity.html">fix rheo/viscosity command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_rhok.html">fix rhok 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_rigid_meso.html">fix rigid/meso command</a></li>
|
||
<li class="toctree-l2 current"><a class="current reference internal" href="#">fix rx 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_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-spin-command">fix setforce/spin command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sgcmc.html">fix sgcmc 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_sph.html">fix sph command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_sph_stationary.html">fix sph/stationary 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_tgnh_drude.html">fix tgnvt/drude command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_tgnh_drude.html#fix-tgnpt-drude-command">fix tgnpt/drude 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_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-grid-command">fix ttm/grid 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_viscous_sphere.html">fix viscous/sphere 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.html#fix-wall-lepton-command">fix wall/lepton command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-morse-command">fix wall/morse command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-table-command">fix wall/table command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polygon.html">fix wall/body/polygon command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_body_polyhedron.html">fix wall/body/polyhedron command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_ees.html">fix wall/ees command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_ees.html#fix-wall-region-ees-command">fix wall/region/ees command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_wall_flow.html">fix wall/flow 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_gran_region.html">fix wall/gran/region 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_stochastic.html">fix wall/reflect/stochastic 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>
|
||
<li class="toctree-l2"><a class="reference internal" href="fix_widom.html">fix widom command</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</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">Bond Styles</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>
|
||
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
</div>
|
||
</nav>
|
||
|
||
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
|
||
<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 style-external-links">
|
||
<div role="navigation" aria-label="Page navigation">
|
||
<ul class="wy-breadcrumbs">
|
||
<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
|
||
<li class="breadcrumb-item"><a href="fixes.html">Fix Styles</a></li>
|
||
<li class="breadcrumb-item active">fix rx command</li>
|
||
<li class="wy-breadcrumbs-aside">
|
||
<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
|
||
</li>
|
||
</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
|
||
<a href="fix_rigid_meso.html" class="btn btn-neutral float-left" title="fix rigid/meso command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="fix_saed_vtk.html" class="btn btn-neutral float-right" title="fix saed/vtk command" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
<hr/>
|
||
</div>
|
||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||
<div itemprop="articleBody">
|
||
|
||
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
||
<section id="fix-rx-command">
|
||
<span id="index-1"></span><span id="index-0"></span><h1>fix rx command<a class="headerlink" href="#fix-rx-command" title="Link to this heading"></a></h1>
|
||
<p>Accelerator Variants: <em>rx/kk</em></p>
|
||
<section id="syntax">
|
||
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">rx</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">localTemp</span><span class="w"> </span><span class="n">matrix</span><span class="w"> </span><span class="n">solver</span><span class="w"> </span><span class="n">minSteps</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul class="simple">
|
||
<li><p>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p></li>
|
||
<li><p>rx = style name of this fix command</p></li>
|
||
<li><p>file = filename containing the reaction kinetic equations and Arrhenius parameters</p></li>
|
||
<li><p>localTemp = <em>none,lucy</em> = no local temperature averaging or local temperature defined through Lucy weighting function</p></li>
|
||
<li><p>matrix = <em>sparse, dense</em> format for the stoichiometric matrix</p></li>
|
||
<li><p>solver = <em>lammps_rk4,rkf45</em> = rk4 is an explicit fourth order Runge-Kutta method; rkf45 is an adaptive fourth-order Runge-Kutta-Fehlberg method</p></li>
|
||
<li><p>minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)</p></li>
|
||
<li><p>maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)</p></li>
|
||
<li><p>relTol = relative tolerance for the rkf45 solver (rkf45 only)</p></li>
|
||
<li><p>absTol = absolute tolerance for the rkf45 solver (rkf45 only)</p></li>
|
||
<li><p>diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only)</p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">rx</span><span class="w"> </span><span class="n">kinetics.rx</span><span class="w"> </span><span class="n">none</span><span class="w"> </span><span class="n">dense</span><span class="w"> </span><span class="n">lammps_rk4</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">rx</span><span class="w"> </span><span class="n">kinetics.rx</span><span class="w"> </span><span class="n">none</span><span class="w"> </span><span class="n">sparse</span><span class="w"> </span><span class="n">lammps_rk4</span><span class="w"> </span><span class="m">1</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">rx</span><span class="w"> </span><span class="n">kinetics.rx</span><span class="w"> </span><span class="n">lucy</span><span class="w"> </span><span class="n">sparse</span><span class="w"> </span><span class="n">lammps_rk4</span><span class="w"> </span><span class="m">10</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">rx</span><span class="w"> </span><span class="n">kinetics.rx</span><span class="w"> </span><span class="n">none</span><span class="w"> </span><span class="n">dense</span><span class="w"> </span><span class="n">rkf45</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">1e-6</span><span class="w"> </span><span class="m">1e-8</span>
|
||
<span class="k">fix </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">rx</span><span class="w"> </span><span class="n">kinetics.rx</span><span class="w"> </span><span class="n">none</span><span class="w"> </span><span class="n">dense</span><span class="w"> </span><span class="n">rkf45</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="m">1e-6</span><span class="w"> </span><span class="m">1e-8</span><span class="w"> </span><span class="o">-</span><span class="m">1</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Fix <em>rx</em> solves the reaction kinetic ODEs for a given reaction set that is
|
||
defined within the file associated with this command.</p>
|
||
<p>For a general reaction such that</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\nu_{A}A + \nu_{B}B \rightarrow \nu_{C}C\]</div>
|
||
<p>the reaction rate equation is defined to be of the form</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[r = k(T)[A]^{\nu_{A}}[B]^{\nu_{B}}\]</div>
|
||
<p>In the current implementation, the exponents are defined to be equal
|
||
to the stoichiometric coefficients. A given reaction set consisting
|
||
of <em>n</em> reaction equations will contain a total of <em>m</em> species. A set
|
||
of <em>m</em> ordinary differential equations (ODEs) that describe the change
|
||
in concentration of a given species as a function of time are then
|
||
constructed based on the <em>n</em> reaction rate equations.</p>
|
||
<p>The ODE systems are solved over the full DPD timestep <em>dt</em> using either a fourth
|
||
order Runge-Kutta <em>rk4</em> method with a fixed step-size <em>h</em>, specified
|
||
by the <em>lammps_rk4</em> keyword, or a fourth order Runge-Kutta-Fehlberg (rkf45) method
|
||
with an adaptive step-size for <em>h</em>. The number of ODE steps per DPD timestep
|
||
for the rk4 method is optionally specified immediately after the rk4
|
||
keyword. The ODE step-size is set as <em>dt/num_steps</em>. Smaller
|
||
step-sizes tend to yield more accurate results but there is not
|
||
control on the error. For error control, use the rkf45 ODE solver.</p>
|
||
<p>The rkf45 method adjusts the step-size so that the local truncation error is held
|
||
within the specified absolute and relative tolerances. The initial step-size <em>h0</em>
|
||
can be specified by the user or estimated internally. It is recommended that the user
|
||
specify <em>h0</em> since this will generally reduced the number of ODE integration steps
|
||
required. <em>h0</em> is defined as <em>dt / min_steps</em> if min_steps >= 1. If min_steps == 0,
|
||
<em>h0</em> is estimated such that an explicit Euler method would likely produce
|
||
an acceptable solution. This is generally overly conservative for the fourth-order
|
||
method and users are advised to specify <em>h0</em> as some fraction of the DPD timestep.
|
||
For small DPD timesteps, only one step may be necessary depending upon the tolerances.
|
||
Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness
|
||
but no more than max_steps will be taken. If max_steps is reached, an error warning
|
||
is printed and the simulation is stopped.</p>
|
||
<p>After each ODE step, the solution error <em>e</em> is tested and weighted using the absTol
|
||
and relTol values. The error vector is weighted as <em>e</em> / (relTol * |<em>u</em>| + absTol)
|
||
where <em>u</em> is the solution vector. If the norm of the error is <= 1, the solution is
|
||
accepted, <em>h</em> is increased by a proportional amount, and the next ODE step is begun.
|
||
Otherwise, <em>h</em> is shrunk and the ODE step is repeated.</p>
|
||
<p>Run-time diagnostics are available for the rkf45 ODE solver. The frequency
|
||
(in timesteps) that diagnostics are reported is controlled by the last (optional)
|
||
12th argument. A negative frequency means that diagnostics are reported once at the
|
||
end of each run. A positive value N means that the diagnostics are reported once
|
||
per N timesteps.</p>
|
||
<p>The diagnostics report the average # of integrator steps and RHS function evaluations
|
||
and run-time per ODE as well as the average/RMS/min/max per process. If the
|
||
reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
|
||
statistics can be used to adjust the tolerance and min/max step parameters. The
|
||
statistics per MPI process can be useful to examine any load imbalance caused by the
|
||
adaptive ODE solver. (Some DPD particles can take longer to solve than others. This
|
||
can lead to an imbalance across the MPI processes.)</p>
|
||
<hr class="docutils" />
|
||
<p>The filename specifies a file that contains the entire set of reaction
|
||
kinetic equations and corresponding Arrhenius parameters. The format of
|
||
this file is described below.</p>
|
||
<p>There is no restriction on the total number or reaction equations that
|
||
are specified. The species names are arbitrary string names that are
|
||
associated with the species concentrations. Each species in a given
|
||
reaction must be preceded by it’s stoichiometric coefficient. The
|
||
only delimiters that are recognized between the species are either a
|
||
<em>+</em> or <em>=</em> character. The <em>=</em> character corresponds to an
|
||
irreversible reaction. After specifying the reaction, the reaction
|
||
rate constant is determined through the temperature dependent
|
||
Arrhenius equation:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}\]</div>
|
||
<p>where <em>A</em> is the Arrhenius factor in time units or concentration/time
|
||
units, <em>n</em> is the unitless exponent of the temperature dependence, and
|
||
<span class="math notranslate nohighlight">\(E_a\)</span> is the activation energy in energy units. The temperature
|
||
dependence can be removed by specifying the exponent as zero.</p>
|
||
<p>The internal temperature of the coarse-grained particles can be used
|
||
in constructing the reaction rate constants at every DPD timestep by
|
||
specifying the keyword <em>none</em>. Alternatively, the keyword <em>lucy</em> can
|
||
be specified to compute a local-average particle internal temperature
|
||
for use in the reaction rate constant expressions. The local-average
|
||
particle internal temperature is defined as:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\theta_i^{-1} = \frac{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)\theta_j^{-1}}{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)}\]</div>
|
||
<p>where the Lucy function is expressed as:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\omega_{Lucy}\left(r_{ij}\right) = \left( 1 + \frac{3r_{ij}}{r_c} \right) \left( 1 - \frac{r_{ij}}{r_c} \right)^3\]</div>
|
||
<p>The self-particle interaction is included in the above equation.</p>
|
||
<p>The stoichiometric coefficients for the reaction mechanism are stored
|
||
in either a sparse or dense matrix format. The dense matrix should only be
|
||
used for small reaction mechanisms. The sparse matrix should be used when there
|
||
are many reactions (e.g., more than 5). This allows the number of reactions and
|
||
species to grow while keeping the computational cost tractable. The matrix
|
||
format can be specified as using either the <em>sparse</em> or <em>dense</em> keywords.
|
||
If all stoichiometric coefficients for a reaction are small integers (whole
|
||
numbers <= 3), a fast exponential function is used. This can save significant
|
||
computational time so users are encouraged to use integer coefficients
|
||
where possible.</p>
|
||
<hr class="docutils" />
|
||
<p>The format of a tabulated file is as follows (without the
|
||
parenthesized comments):</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span># Rxn equations and parameters (one or more comment or blank lines)
|
||
|
||
1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49E+01 0.0 1.34 (rxn equation, A, n, Ea)
|
||
1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 2.16E+00 0.0 1.52
|
||
...
|
||
1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69
|
||
</pre></div>
|
||
</div>
|
||
<p>A section begins with a non-blank line whose first character is not a
|
||
“#”; blank lines or lines starting with “#” can be used as comments
|
||
between sections.</p>
|
||
<p>Following a blank line, the next N lines list the N reaction
|
||
equations. Each species within the reaction equation is specified
|
||
through its stoichiometric coefficient and a species tag. Reactant
|
||
species are specified on the left-hand side of the equation and
|
||
product species are specified on the right-hand side of the equation.
|
||
After specifying the reactant and product species, the final three
|
||
arguments of each line represent the Arrhenius parameter <em>A</em>, the
|
||
temperature exponent <em>n</em>, and the activation energy <em>Ea</em>.</p>
|
||
<p>Note that the species tags that are defined in the reaction equations
|
||
are used by the <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> command to
|
||
define the thermodynamic properties of each species. Furthermore, the
|
||
number of species molecules (i.e., concentration) can be specified
|
||
either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the “d_” prefix or by
|
||
reading directly the concentrations from a data file. For the latter
|
||
case, the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command with the fix keyword
|
||
should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g.</p>
|
||
<p>fix foo all rx reaction.file …
|
||
read_data data.dpd fix foo_SPECIES NULL Species</p>
|
||
<hr class="docutils" />
|
||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||
functionally the same as the corresponding style without the suffix.
|
||
They have been optimized to run faster, depending on your available
|
||
hardware, as discussed on the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a>
|
||
page. The accelerated styles take the same arguments and should
|
||
produce the same results, except for round-off and precision issues.</p>
|
||
<p>These accelerated styles are part of the GPU, INTEL, KOKKOS,
|
||
OPENMP, and OPT packages, respectively. They are only enabled if
|
||
LAMMPS was built with those packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
<p>You can specify the accelerated styles explicitly in your input script
|
||
by including their suffix, or you can use the <a class="reference internal" href="Run_options.html"><span class="doc">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can use the
|
||
<a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
||
<p>See the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a> page for more
|
||
instructions on how to use the accelerated styles effectively.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This command is part of the DPD-REACT package. It is only enabled if
|
||
LAMMPS was built with that package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
|
||
command.</p>
|
||
<p>This command can only be used with a constant energy or constant
|
||
enthalpy DPD simulation.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a>,
|
||
<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>,
|
||
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>none</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="fix_rigid_meso.html" class="btn btn-neutral float-left" title="fix rigid/meso command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="fix_saed_vtk.html" class="btn btn-neutral float-right" title="fix saed/vtk command" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
|
||
<hr/>
|
||
|
||
<div role="contentinfo">
|
||
<p>© Copyright 2003-2025 Sandia Corporation.</p>
|
||
</div>
|
||
|
||
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
|
||
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
|
||
provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
||
|
||
|
||
</footer>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</div>
|
||
<script>
|
||
jQuery(function () {
|
||
SphinxRtdTheme.Navigation.enable(false);
|
||
});
|
||
</script>
|
||
|
||
</body>
|
||
</html> |