forked from lijiext/lammps
493 lines
32 KiB
HTML
493 lines
32 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>compute centro/atom 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="Computes" href="computes.html"/>
|
|
<link rel="next" title="compute chunk/atom command" href="compute_chunk_atom.html"/>
|
|
<link rel="prev" title="compute bond/local command" href="compute_bond_local.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"><a class="reference internal" href="fixes.html">Fixes</a></li>
|
|
<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Computes</a><ul class="current">
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
|
|
<li class="toctree-l2 current"><a class="current reference internal" href="#">compute centro/atom 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="compute_chunk_atom.html">compute chunk/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_meso_e_atom.html">compute meso/e/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_meso_rho_atom.html">compute meso/rho/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_meso_t_atom.html">compute meso/t/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_msd.html">compute msd command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_pair.html">compute pair command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_saed.html">compute saed command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_slice.html">compute slice command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_contact_radius.html">compute smd/contact/radius command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_damage.html">compute smd/damage command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_hourglass_error.html">compute smd/hourglass/error command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_internal_energy.html">compute smd/internal/energy command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain.html">compute smd/plastic/strain command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain_rate.html">compute smd/plastic/strain/rate command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_rho.html">compute smd/rho command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_defgrad.html">compute smd/tlsph/defgrad command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_dt.html">compute smd/tlsph/dt command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_num_neighs.html">compute smd/tlsph/num/neighs command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_shape.html">compute smd/tlsph/shape command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain.html">compute smd/tlsph/strain command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain_rate.html">compute smd/tlsph/strain/rate command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_stress.html">compute smd/tlsph/stress command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_triangle_mesh_vertices.html">compute smd/triangle/mesh/vertices</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_num_neighs.html">compute smd/ulsph/num/neighs command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain.html">compute smd/ulsph/strain command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain_rate.html">compute smd/ulsph/strain/rate command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_stress.html">compute smd/ulsph/stress command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snav-atom-command">compute snav/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp.html#compute-temp-kk-command">compute temp/kk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd command</a></li>
|
|
</ul>
|
|
</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="computes.html">Computes</a> »</li>
|
|
|
|
<li>compute centro/atom 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="compute_chunk_atom.html" class="btn btn-neutral float-right" title="compute chunk/atom command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="compute_bond_local.html" class="btn btn-neutral" title="compute bond/local 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="compute-centro-atom-command">
|
|
<span id="index-0"></span><h1>compute centro/atom command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">centro</span><span class="o">/</span><span class="n">atom</span> <span class="n">lattice</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command
|
|
centro/atom = style name of this compute command
|
|
lattice = <em>fcc</em> or <em>bcc</em> or N = # of neighbors per atom to include</li>
|
|
<li>zero or more keyword/value pairs may be appended</li>
|
|
<li>keyword = <em>axes</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>axes</em> value = <em>no</em> or <em>yes</em>
|
|
<em>no</em> = do not calulate 3 symmetry axes
|
|
<em>yes</em> = calulate 3 symmetry axes
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">centro</span><span class="o">/</span><span class="n">atom</span> <span class="n">fcc</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">centro</span><span class="o">/</span><span class="n">atom</span> <span class="mi">8</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Define a computation that calculates the centro-symmetry parameter for
|
|
each atom in the group, for either FCC or BCC lattices, depending on
|
|
the choice of the <em>lattice</em> argument. In solid-state systems the
|
|
centro-symmetry parameter is a useful measure of the local lattice
|
|
disorder around an atom and can be used to characterize whether the
|
|
atom is part of a perfect lattice, a local defect (e.g. a dislocation
|
|
or stacking fault), or at a surface.</p>
|
|
<p>The value of the centro-symmetry parameter will be 0.0 for atoms not
|
|
in the specified compute group.</p>
|
|
<p>This parameter is computed using the following formula from
|
|
<a class="reference internal" href="#kelchner"><span class="std std-ref">(Kelchner)</span></a></p>
|
|
<img alt="_images/centro_symmetry.jpg" class="align-center" src="_images/centro_symmetry.jpg" />
|
|
<p>where the <em>N</em> nearest neighbors of each atom are identified and Ri and
|
|
Ri+N/2 are vectors from the central atom to a particular pair of
|
|
nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that
|
|
can contribute to this formula. The quantity in the sum is computed
|
|
for each, and the N/2 smallest are used. This will typically be for
|
|
pairs of atoms in symmetrically opposite positions with respect to the
|
|
central atom; hence the i+N/2 notation.</p>
|
|
<p><em>N</em> is an input parameter, which should be set to correspond to the
|
|
number of nearest neighbors in the underlying lattice of atoms. If
|
|
the keyword <em>fcc</em> or <em>bcc</em> is used, <em>N</em> is set to 12 and 8
|
|
respectively. More generally, <em>N</em> can be set to a positive, even
|
|
integer.</p>
|
|
<p>For an atom on a lattice site, surrounded by atoms on a perfect
|
|
lattice, the centro-symmetry parameter will be 0. It will be near 0
|
|
for small thermal perturbations of a perfect lattice. If a point
|
|
defect exists, the symmetry is broken, and the parameter will be a
|
|
larger positive value. An atom at a surface will have a large
|
|
positive parameter. If the atom does not have <em>N</em> neighbors (within
|
|
the potential cutoff), then its centro-symmetry parameter is set to
|
|
0.0.</p>
|
|
<p>If the keyword <em>axes</em> has the setting <em>yes</em>, then this compute also
|
|
estimates three symmetry axes for each atom’s local neighborhood. The
|
|
first two of these are the vectors joining the two pairs of neighbor
|
|
atoms with smallest contributions to the centrosymmetry parameter,
|
|
i.e. the two most symmetric pairs of atoms. The third vector is
|
|
normal to the first two by the right-hand rule. All three vectors are
|
|
normalized to unit length. For FCC crystals, the first two vectors
|
|
will lie along a <110> direction, while the third vector will lie
|
|
along either a <100> or <111> direction. For HCP crystals, the first
|
|
two vectors will lie along <1000> directions, while the third vector
|
|
will lie along <0001>. This provides a simple way to measure local
|
|
orientation in HCP structures. In general, the <em>axes</em> keyword can be
|
|
used to estimate the orientation of symmetry axes in the neighborhood
|
|
of any atom.</p>
|
|
<p>Only atoms within the cutoff of the pairwise neighbor list are
|
|
considered as possible neighbors. Atoms not in the compute group are
|
|
included in the <em>N</em> neighbors used in this calculation.</p>
|
|
<p>The neighbor list needed to compute this quantity is constructed each
|
|
time the calculation is performed (e.g. each time a snapshot of atoms
|
|
is dumped). Thus it can be inefficient to compute/dump this quantity
|
|
too frequently or to have multiple compute/dump commands, each with a
|
|
<em>centro/atom</em> style.</p>
|
|
<p><strong>Output info:</strong></p>
|
|
<p>By default, this compute calculates the centrosymmetry value for each
|
|
atom as a per-atom vector, which can be accessed by any command that
|
|
uses per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section 6.15</span></a> for an overview of LAMMPS output
|
|
options.</p>
|
|
<p>If the <em>axes</em> keyword setting is <em>yes</em>, then a per-atom array is
|
|
calculated. The first column is the centrosymmetry parameter. The
|
|
next three columns are the x, y, and z components of the first
|
|
symmetry axis, followed by the second, and third symmetry axes in
|
|
columns 5-7 and 8-10.</p>
|
|
<p>The centrosymmetry values are unitless values >= 0.0. Their magnitude
|
|
depends on the lattice style due to the number of contibuting neighbor
|
|
pairs in the summation in the formula above. And it depends on the
|
|
local defects surrounding the central atom, as described above. For
|
|
the <em>axes yes</em> case, the vector components are also unitless, since
|
|
they represent spatial directions.</p>
|
|
<p>Here are typical centro-symmetry values, from a a nanoindentation
|
|
simulation into gold (FCC). These were provided by Jon Zimmerman
|
|
(Sandia):</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
|
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">1.0</span> <span class="p">(</span><span class="mf">0.5</span> <span class="n">to</span> <span class="mf">1.25</span><span class="p">)</span>
|
|
<span class="n">Stacking</span> <span class="n">faults</span> <span class="o">~</span> <span class="mf">5.0</span> <span class="p">(</span><span class="mf">4.0</span> <span class="n">to</span> <span class="mf">6.0</span><span class="p">)</span>
|
|
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>These values are *not* normalized by the square of the lattice
|
|
parameter. If they were, normalized values would be:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
|
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>
|
|
<span class="n">Stacking</span> <span class="n">faults</span> <span class="o">~</span> <span class="mf">0.3</span> <span class="p">(</span><span class="mf">0.24</span> <span class="n">to</span> <span class="mf">0.36</span><span class="p">)</span>
|
|
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">1.38</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>For BCC materials, the values for dislocation cores and free surfaces
|
|
would be somewhat different, due to their being only 8 neighbors instead
|
|
of 12.</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_cna_atom.html"><span class="doc">compute cna/atom</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The default value for the optional keyword is axes = no.</p>
|
|
<hr class="docutils" />
|
|
<p id="kelchner"><strong>(Kelchner)</strong> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
|
|
|
<a href="compute_chunk_atom.html" class="btn btn-neutral float-right" title="compute chunk/atom command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="compute_bond_local.html" class="btn btn-neutral" title="compute bond/local 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> |