665 lines
52 KiB
HTML
665 lines
52 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>compute fep 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/compute_fep.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="compute fep/ta command" href="compute_fep_ta.html" />
|
||
<link rel="prev" title="compute fabric command" href="compute_fabric.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"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
|
||
<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Compute Styles</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_adf.html">compute adf 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_ave_sphere_atom.html">compute ave/sphere/atom 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"><a class="reference internal" href="compute_born_matrix.html">compute born/matrix command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></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_chunk_spread_atom.html">compute chunk/spread/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_cluster_atom.html#compute-fragment-atom-command">compute fragment/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html#compute-aggregate-atom-command">compute aggregate/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_cnp_atom.html">compute cnp/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_composition_atom.html">compute composition/atom 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_count_type.html">compute count/type 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.html">compute dipole command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_dipole.html#compute-dipole-tip4p-command">compute dipole/tip4p 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_dipole_chunk.html#compute-dipole-tip4p-chunk-command">compute dipole/tip4p/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_edpd_temp_atom.html">compute edpd/temp/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_efield_atom.html">compute efield/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_efield_wolf_atom.html">compute efield/wolf/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_entropy_atom.html">compute entropy/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_fabric.html">compute fabric command</a></li>
|
||
<li class="toctree-l2 current"><a class="current reference internal" href="#">compute fep 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="#output-info">Output info</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_fep_ta.html">compute fep/ta command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_global_atom.html">compute global/atom 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_gyration_shape.html">compute gyration/shape command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_shape_chunk.html">compute gyration/shape/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_hma.html">compute hma 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_mliap.html">compute mliap command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_momentum.html">compute momentum 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_nbond_atom.html">compute nbond/atom 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_pace.html">compute pace 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_pod_atom.html">compute pod/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-podd-atom-command">compute podd/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-local-command">compute pod/local command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_pod_atom.html#compute-pod-global-command">compute pod/global 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_pressure_alchemy.html">compute pressure/alchemy command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_pressure_uef.html">compute pressure/uef 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_grid.html">compute property/grid 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_ptm_atom.html">compute ptm/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_rattlers_atom.html">compute rattlers/atom 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_reaxff_atom.html">compute reaxff/atom 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_reduce_chunk.html">compute reduce/chunk command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_rheo_property_atom.html">compute rheo/property/atom 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_slcsa_atom.html">compute slcsa/atom 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_vertices.html">compute smd/triangle/vertices command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_effm.html">compute smd/ulsph/effm command</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_sna_atom.html#compute-snap-command">compute snap command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-sna-grid-command">compute sna/grid command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-sna-grid-local-command">compute sna/grid/local command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sph_e_atom.html">compute sph/e/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sph_rho_atom.html">compute sph/rho/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_sph_t_atom.html">compute sph/t/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_spin.html">compute spin 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_stress_atom.html#compute-centroid-stress-atom-command">compute centroid/stress/atom command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_cartesian.html">compute stress/cartesian command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html">compute stress/cylinder command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_curvilinear.html#compute-stress-spherical-command">compute stress/spherical command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html">compute stress/mop command</a></li>
|
||
<li class="toctree-l2"><a class="reference internal" href="compute_stress_mop.html#compute-stress-mop-profile-command">compute stress/mop/profile 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-heat-flux-virial-tally-command">compute heat/flux/virial/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_tdpd_cc_atom.html">compute tdpd/cc/atom 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_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_temp_uef.html">compute temp/uef 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_viscosity_cos.html">compute viscosity/cos 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">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="computes.html">Compute Styles</a></li>
|
||
<li class="breadcrumb-item active">compute fep 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="compute_fabric.html" class="btn btn-neutral float-left" title="compute fabric command" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="compute_fep_ta.html" class="btn btn-neutral float-right" title="compute fep/ta 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="compute-fep-command">
|
||
<span id="index-0"></span><h1>compute fep command<a class="headerlink" href="#compute-fep-command" title="Link to this heading"></a></h1>
|
||
<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">compute </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">fep</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="n">attribute</span><span class="w"> </span><span class="n">args</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">value</span><span class="w"> </span><span class="n">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul>
|
||
<li><p>ID, group-ID are documented in the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p></li>
|
||
<li><p>fep = name of this compute command</p></li>
|
||
<li><p>temp = external temperature (as specified for constant-temperature run)</p></li>
|
||
<li><p>one or more attributes with args may be appended</p></li>
|
||
<li><p>attribute = <em>pair</em> or <em>atom</em></p>
|
||
<pre class="literal-block"><em>pair</em> args = pstyle pparam I J v_delta
|
||
pstyle = pair style name (e.g., <em>lj/cut</em>)
|
||
pparam = parameter to perturb
|
||
I,J = type pair(s) to set parameter for
|
||
v_delta = variable with perturbation to apply (in the units of the parameter)
|
||
<em>atom</em> args = aparam I v_delta
|
||
aparam = <em>charge</em> = parameter to perturb
|
||
I = type to set parameter for
|
||
v_delta = variable with perturbation to apply (in the units of the parameter)</pre>
|
||
</li>
|
||
<li><p>zero or more keyword/value pairs may be appended</p></li>
|
||
<li><p>keyword = <em>tail</em> or <em>volume</em></p>
|
||
<pre class="literal-block"><em>tail</em> value = <em>no</em> or <em>yes</em>
|
||
<em>no</em> = ignore tail correction to pair energies (usually small in fep)
|
||
<em>yes</em> = include tail correction to pair energies
|
||
<em>volume</em> value = <em>no</em> or <em>yes</em>
|
||
<em>no</em> = ignore volume changes (e.g., in <em>NVE</em> or <em>NVT</em> trajectories)
|
||
<em>yes</em> = include volume changes (e.g., in <em>NPT</em> trajectories)</pre>
|
||
</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">compute </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">fep</span><span class="w"> </span><span class="m">298</span><span class="w"> </span><span class="n">pair</span><span class="w"> </span><span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="w"> </span><span class="n">epsilon</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">v_delta</span><span class="w"> </span><span class="n">pair</span><span class="w"> </span><span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="w"> </span><span class="n">sigma</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">v_delta</span><span class="w"> </span><span class="n">volume</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">compute </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">fep</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="n">charge</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="n">v_delta</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Example input scripts available: examples/PACKAGES/fep</p>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Apply a perturbation to parameters of the interaction potential and
|
||
recalculate the pair potential energy without changing the atomic
|
||
coordinates from those of the reference, unperturbed system. This
|
||
compute can be used to calculate free energy differences using several
|
||
methods, such as free-energy perturbation (FEP), finite-difference
|
||
thermodynamic integration (FDTI) or Bennet’s acceptance ratio method
|
||
(BAR).</p>
|
||
<p>The potential energy of the system is decomposed in three terms: a
|
||
background term corresponding to interaction sites whose parameters
|
||
remain constant, a reference term <span class="math notranslate nohighlight">\(U_0\)</span> corresponding to the
|
||
initial interactions of the atoms that will undergo perturbation, and
|
||
a term <span class="math notranslate nohighlight">\(U_1\)</span> corresponding to the final interactions of
|
||
these atoms:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda)\]</div>
|
||
<p>A coupling parameter <span class="math notranslate nohighlight">\(\lambda\)</span> varying from 0 to 1 connects the
|
||
reference and perturbed systems:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\begin{split}\lambda &= 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
|
||
\lambda &= 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1\end{split}\]</div>
|
||
<p>It is possible but not necessary that the coupling parameter (or a
|
||
function thereof) appears as a multiplication factor of the potential
|
||
energy. Therefore, this compute can apply perturbations to interaction
|
||
parameters that are not directly proportional to the potential energy
|
||
(e.g., <span class="math notranslate nohighlight">\(\sigma\)</span> in Lennard-Jones potentials).</p>
|
||
<p>This command can be combined with <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> to
|
||
perform multistage free-energy perturbation calculations along
|
||
stepwise alchemical transformations during a simulation run:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A = - k_B T
|
||
\sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
|
||
U(\lambda_i)}{k_B T} \right) \right>_{\lambda_i}\]</div>
|
||
<p>This compute is suitable for the finite-difference thermodynamic
|
||
integration (FDTI) method <a class="reference internal" href="#mezei"><span class="std std-ref">(Mezei)</span></a>, which is based on an
|
||
evaluation of the numerical derivative of the free energy by a
|
||
perturbation method using a very small <span class="math notranslate nohighlight">\(\delta\)</span>:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
|
||
A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda \approx
|
||
\sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) - A(\lambda_i)}{\delta}\]</div>
|
||
<p>where <span class="math notranslate nohighlight">\(w_i\)</span> are weights of a numerical quadrature. The
|
||
<a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> command can be used to define the stages of
|
||
<span class="math notranslate nohighlight">\(\lambda\)</span> at which the derivative is calculated and averaged.</p>
|
||
<p>The compute fep calculates the exponential Boltzmann term and also the
|
||
potential energy difference <span class="math notranslate nohighlight">\(U_1 -U_0\)</span>. By
|
||
choosing a very small perturbation <span class="math notranslate nohighlight">\(\delta\)</span> the thermodynamic
|
||
integration method can be implemented using a numerical evaluation of
|
||
the derivative of the potential energy with respect to <span class="math notranslate nohighlight">\(\lambda\)</span>:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
|
||
U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda \approx
|
||
\sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
|
||
U(\lambda_i)}{\delta} \right>_{\lambda_i}\]</div>
|
||
<p>Another technique to calculate free energy differences is the
|
||
acceptance ratio method <a class="reference internal" href="#bennet"><span class="std std-ref">(Bennet)</span></a>, which can be implemented
|
||
by calculating the potential energy differences with <span class="math notranslate nohighlight">\(\delta = 1.0\)</span> on
|
||
both the forward and reverse routes:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /k_B T
|
||
\right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 +
|
||
\Delta_0^1A \right) /k_B T \right]} \right>_1\]</div>
|
||
<p>The value of the free energy difference is determined by numerical
|
||
root finding to establish the equality.</p>
|
||
<p>Concerning the choice of how the atomic parameters are perturbed in
|
||
order to setup an alchemical transformation route, several strategies
|
||
are available, such as single-topology or double-topology strategies
|
||
<a class="reference internal" href="#pearlman"><span class="std std-ref">(Pearlman)</span></a>. The latter does not require modification of
|
||
bond lengths, angles or other internal coordinates.</p>
|
||
<p>NOTES: This compute command does not take kinetic energy into account,
|
||
therefore the masses of the particles should not be modified between
|
||
the reference and perturbed states, or along the alchemical
|
||
transformation route. This compute command does not change bond
|
||
lengths or other internal coordinates <a class="reference internal" href="#boreschkarplus"><span class="std std-ref">(Boresch, Karplus)</span></a>.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>pair</em> attribute enables various parameters of potentials defined
|
||
by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>
|
||
commands to be changed, if the pair style supports it.</p>
|
||
<p>The <em>pstyle</em> argument is the name of the pair style. For example,
|
||
<em>pstyle</em> could be specified as “lj/cut”. The <em>pparam</em> argument is the
|
||
name of the parameter to change. This is a list of
|
||
pair styles and parameters that can be used with this compute. See
|
||
the doc pages for individual pair styles and their energy formulas for
|
||
the meaning of these parameters:</p>
|
||
<table class="docutils align-default">
|
||
<tbody>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_born.html"><span class="doc">born</span></a></p></td>
|
||
<td><p>a,b,c</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_buck.html"><span class="doc">buck, buck/coul/cut, buck/coul/long, buck/coul/msm</span></a></p></td>
|
||
<td><p>a,c</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_mdf.html"><span class="doc">buck/mdf</span></a></p></td>
|
||
<td><p>a,c</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_coul.html"><span class="doc">coul/cut</span></a></p></td>
|
||
<td><p>scale</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_fep_soft.html"><span class="doc">coul/cut/soft</span></a></p></td>
|
||
<td><p>lambda</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_coul.html"><span class="doc">coul/long, coul/msm</span></a></p></td>
|
||
<td><p>scale</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_fep_soft.html"><span class="doc">coul/long/soft</span></a></p></td>
|
||
<td><p>scale, lambda</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_eam.html"><span class="doc">eam</span></a></p></td>
|
||
<td><p>scale</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss</span></a></p></td>
|
||
<td><p>a</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_mdf.html"><span class="doc">lennard/mdf</span></a></p></td>
|
||
<td><p>a,b</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_class2.html"><span class="doc">lj/class2</span></a></p></td>
|
||
<td><p>epsilon,sigma</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_class2.html"><span class="doc">lj/class2/coul/cut, lj/class2/coul/long</span></a></p></td>
|
||
<td><p>epsilon,sigma</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a></p></td>
|
||
<td><p>epsilon,sigma</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_fep_soft.html"><span class="doc">lj/cut/soft</span></a></p></td>
|
||
<td><p>epsilon,sigma,lambda</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm</span></a></p></td>
|
||
<td><p>epsilon,sigma</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_fep_soft.html"><span class="doc">lj/cut/coul/cut/soft, lj/cut/coul/long/soft</span></a></p></td>
|
||
<td><p>epsilon,sigma,lambda</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_lj_cut_tip4p.html"><span class="doc">lj/cut/tip4p/cut, lj/cut/tip4p/long</span></a></p></td>
|
||
<td><p>epsilon,sigma</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_fep_soft.html"><span class="doc">lj/cut/tip4p/long/soft</span></a></p></td>
|
||
<td><p>epsilon,sigma,lambda</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_lj_expand.html"><span class="doc">lj/expand</span></a></p></td>
|
||
<td><p>epsilon,sigma,delta</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_mdf.html"><span class="doc">lj/mdf</span></a></p></td>
|
||
<td><p>epsilon,sigma</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/sf/dipole/sf</span></a></p></td>
|
||
<td><p>epsilon,sigma,scale</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_mie.html"><span class="doc">mie/cut</span></a></p></td>
|
||
<td><p>epsilon,sigma,gamR,gamA</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_morse.html"><span class="doc">morse, morse/smooth/linear</span></a></p></td>
|
||
<td><p>d0,r0,alpha</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_morse.html"><span class="doc">morse/soft</span></a></p></td>
|
||
<td><p>d0,r0,alpha,lambda</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_nm.html"><span class="doc">nm/cut</span></a></p></td>
|
||
<td><p>e0,r0,nn,mm</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_nm.html"><span class="doc">nm/cut/coul/cut, nm/cut/coul/long</span></a></p></td>
|
||
<td><p>e0,r0,nn,mm</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p><a class="reference internal" href="pair_ufm.html"><span class="doc">ufm</span></a></p></td>
|
||
<td><p>epsilon,sigma,scale</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p><a class="reference internal" href="pair_soft.html"><span class="doc">soft</span></a></p></td>
|
||
<td><p>a</p></td>
|
||
<td><p>type pairs</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Note that it is easy to add new potentials and their parameters to
|
||
this list. All it typically takes is adding an extract() method to
|
||
the pair_*.cpp file associated with the potential.</p>
|
||
<p>Similar to the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command, I and J can be
|
||
specified in one of two ways. Explicit numeric values can be used for
|
||
each, as in the first example above. I <span class="math notranslate nohighlight">\(\le\)</span> J is required. LAMMPS sets
|
||
the coefficients for the symmetric J,I interaction to the same
|
||
values. A wild-card asterisk can be used in place of or in conjunction
|
||
with the I,J arguments to set the coefficients for multiple pairs of
|
||
atom types. This takes the form “*” or “*n” or “m*” or “m*n”. If
|
||
<span class="math notranslate nohighlight">\(N\)</span> is the number of atom types, then an asterisk with no numeric values
|
||
means all types from 1 to <span class="math notranslate nohighlight">\(N\)</span>. A leading asterisk means all types from
|
||
1 to n (inclusive). A trailing asterisk means all types from m to N
|
||
(inclusive). A middle asterisk means all types from m to n
|
||
(inclusive). Note that only type pairs with I <span class="math notranslate nohighlight">\(\le\)</span> J are considered; if
|
||
asterisks imply type pairs where J <span class="math notranslate nohighlight">\(<\)</span> I, they are ignored.</p>
|
||
<p>If <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid or hybrid/overlay</span></a> is being
|
||
used, then the <em>pstyle</em> will be a sub-style name. You must specify
|
||
I,J arguments that correspond to type pair values defined (via the
|
||
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command) for that sub-style.</p>
|
||
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
|
||
<a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> which will be evaluated each time
|
||
this compute is invoked. It should be specified as v_name, where name
|
||
is the variable name.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>atom</em> attribute enables atom properties to be changed. The
|
||
<em>aparam</em> argument is the name of the parameter to change. This is the
|
||
current list of atom parameters that can be used with this compute:</p>
|
||
<ul class="simple">
|
||
<li><p>charge = charge on particle</p></li>
|
||
</ul>
|
||
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
|
||
<a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> which will be evaluated each time
|
||
this compute is invoked. It should be specified as v_name, where name
|
||
is the variable name.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>tail</em> keyword controls the calculation of the tail correction to
|
||
“van der Waals” pair energies beyond the cutoff, if this has been
|
||
activated via the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> command. If the
|
||
perturbation is small, the tail contribution to the energy difference
|
||
between the reference and perturbed systems should be negligible.</p>
|
||
<p>If the keyword <em>volume</em> = <em>yes</em>, then the Boltzmann term is multiplied
|
||
by the volume so that correct ensemble averaging can be performed over
|
||
trajectories during which the volume fluctuates or changes <a class="reference internal" href="#allentildesley"><span class="std std-ref">(Allen and Tildesley)</span></a>:</p>
|
||
<div class="math notranslate nohighlight">
|
||
\[\Delta_0^1 A = - k_B T \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
|
||
\frac{U(\lambda_{i+1}) - U(\lambda_i)}{k_B T} \right)
|
||
\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}}\]</div>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="output-info">
|
||
<h2>Output info<a class="headerlink" href="#output-info" title="Link to this heading"></a></h2>
|
||
<p>This compute calculates a global vector of length 3 which contains the
|
||
energy difference ( <span class="math notranslate nohighlight">\(U_1-U_0\)</span> ) as c_ID[1], the
|
||
Boltzmann factor <span class="math notranslate nohighlight">\(\exp(-(U_1-U_0)/k_B T)\)</span>, or
|
||
<span class="math notranslate nohighlight">\(V \exp(-(U_1-U_0)/k_B T)\)</span>, as c_ID[2] and the
|
||
volume of the simulation box <span class="math notranslate nohighlight">\(V\)</span> as c_ID[3]. <span class="math notranslate nohighlight">\(U_1\)</span> is the
|
||
pair potential energy obtained with the perturbed parameters and
|
||
<span class="math notranslate nohighlight">\(U_0\)</span> is the pair potential energy obtained with the
|
||
unperturbed parameters. The energies include kspace terms if these
|
||
are used in the simulation.</p>
|
||
<p>These output results can be used by any command that uses a global
|
||
scalar or vector from a compute as input. See the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> page for an overview of LAMMPS output
|
||
options. For example, the computed values can be averaged using <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>.</p>
|
||
<p>The values calculated by this compute are “extensive”.</p>
|
||
</section>
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>This compute is distributed as the FEP 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>
|
||
</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_adapt_fep.html"><span class="doc">fix adapt/fep</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
|
||
<a class="reference internal" href="pair_fep_soft.html"><span class="doc">pair_style …/soft</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The option defaults are <em>tail</em> = <em>no</em>, <em>volume</em> = <em>no</em>.</p>
|
||
<hr class="docutils" />
|
||
<p id="pearlman"><strong>(Pearlman)</strong> Pearlman, J Chem Phys, 98, 1487 (1994)</p>
|
||
<p id="mezei"><strong>(Mezei)</strong> Mezei, J Chem Phys, 86, 7084 (1987)</p>
|
||
<p id="bennet"><strong>(Bennet)</strong> Bennet, J Comput Phys, 22, 245 (1976)</p>
|
||
<p id="boreschkarplus"><strong>(BoreschKarplus)</strong> Boresch and Karplus, J Phys Chem A, 103, 103 (1999)</p>
|
||
<p id="allentildesley"><strong>(AllenTildesley)</strong> Allen and Tildesley, Computer Simulation of
|
||
Liquids, Oxford University Press (1987)</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="compute_fabric.html" class="btn btn-neutral float-left" title="compute fabric command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="compute_fep_ta.html" class="btn btn-neutral float-right" title="compute fep/ta 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> |