forked from lijiext/lammps
617 lines
38 KiB
HTML
617 lines
38 KiB
HTML
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<title>compute fep command — LAMMPS documentation</title>
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<link rel="next" title="compute group/group command" href="compute_group_group.html"/>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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<p class="caption"><span class="caption-text">Index</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
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<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
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<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Computes</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">compute fep command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_e_atom.html">compute meso/e/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_rho_atom.html">compute meso/rho/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_meso_t_atom.html">compute meso/t/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd.html">compute msd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pair.html">compute pair command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_saed.html">compute saed command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_slice.html">compute slice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_contact_radius.html">compute smd/contact/radius command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_damage.html">compute smd/damage command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_hourglass_error.html">compute smd/hourglass/error command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_internal_energy.html">compute smd/internal/energy command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain.html">compute smd/plastic/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain_rate.html">compute smd/plastic/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_rho.html">compute smd/rho command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_defgrad.html">compute smd/tlsph/defgrad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_dt.html">compute smd/tlsph/dt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_num_neighs.html">compute smd/tlsph/num/neighs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_shape.html">compute smd/tlsph/shape command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain.html">compute smd/tlsph/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain_rate.html">compute smd/tlsph/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_stress.html">compute smd/tlsph/stress command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_triangle_mesh_vertices.html">compute smd/triangle/mesh/vertices</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_num_neighs.html">compute smd/ulsph/num/neighs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain.html">compute smd/ulsph/strain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain_rate.html">compute smd/ulsph/strain/rate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_stress.html">compute smd/ulsph/stress command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snav-atom-command">compute snav/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp.html#compute-temp-kk-command">compute temp/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd command</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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</ul>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<div class="section" id="compute-fep-command">
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<span id="index-0"></span><h1>compute fep command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<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">fep</span> <span class="n">temp</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p class="first">ID, group-ID are documented in the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p>
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</li>
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<li><p class="first">fep = name of this compute command</p>
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</li>
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<li><p class="first">temp = external temperature (as specified for constant-temperature run)</p>
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</li>
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<li><p class="first">one or more attributes with args may be appended</p>
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</li>
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<li><p class="first">attribute = <em>pair</em> or <em>atom</em></p>
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<pre class="literal-block">
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<em>pair</em> args = pstyle pparam I J v_delta
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pstyle = pair style name, e.g. lj/cut
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pparam = parameter to perturb
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I,J = type pair(s) to set parameter for
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v_delta = variable with perturbation to apply (in the units of the parameter)
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<em>atom</em> args = aparam I v_delta
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aparam = parameter to perturb
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I = type to set parameter for
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v_delta = variable with perturbation to apply (in the units of the parameter)
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</pre>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>tail</em> or <em>volume</em></p>
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<pre class="literal-block">
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<em>tail</em> value = <em>no</em> or <em>yes</em>
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<em>no</em> = ignore tail correction to pair energies (usually small in fep)
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<em>yes</em> = include tail correction to pair energies
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<em>volume</em> value = <em>no</em> or <em>yes</em>
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<em>no</em> = ignore volume changes (e.g. in <em>NVE</em> or <em>NVT</em> trajectories)
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<em>yes</em> = include volume changes (e.g. in <em>NpT</em> trajectories)
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</pre>
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</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<pre class="literal-block">
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compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
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compute 1 all fep 300 atom charge 2 v_delta
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</pre>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Apply a perturbation to parameters of the interaction potential and
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recalculate the pair potential energy without changing the atomic
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coordinates from those of the reference, unperturbed system. This
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compute can be used to calculate free energy differences using several
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methods, such as free-energy perturbation (FEP), finite-difference
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thermodynamic integration (FDTI) or Bennet’s acceptance ratio method
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(BAR).</p>
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<p>The potential energy of the system is decomposed in three terms: a
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background term corresponding to interaction sites whose parameters
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remain constant, a reference term <span class="math">\(U_0\)</span> corresponding to the
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initial interactions of the atoms that will undergo perturbation, and
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a term <span class="math">\(U_1\)</span> corresponding to the final interactions of
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these atoms:</p>
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<img alt="_images/compute_fep_u.jpg" class="align-center" src="_images/compute_fep_u.jpg" />
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<p>A coupling parameter <span class="math">\(\lambda\)</span> varying from 0 to 1 connects the
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reference and perturbed systems:</p>
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<img alt="_images/compute_fep_lambda.jpg" class="align-center" src="_images/compute_fep_lambda.jpg" />
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<p>It is possible but not necessary that the coupling parameter (or a
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function thereof) appears as a multiplication factor of the potential
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energy. Therefore, this compute can apply perturbations to interaction
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parameters that are not directly proportional to the potential energy
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(e.g. <span class="math">\(\sigma\)</span> in Lennard-Jones potentials).</p>
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<p>This command can be combined with <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> to
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perform multistage free-energy perturbation calculations along
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stepwise alchemical transformations during a simulation run:</p>
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<img alt="_images/compute_fep_fep.jpg" class="align-center" src="_images/compute_fep_fep.jpg" />
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<p>This compute is suitable for the finite-difference thermodynamic
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integration (FDTI) method <a class="reference internal" href="#mezei"><span class="std std-ref">(Mezei)</span></a>, which is based on an
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evaluation of the numerical derivative of the free energy by a
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perturbation method using a very small <span class="math">\(\delta\)</span>:</p>
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<img alt="_images/compute_fep_fdti.jpg" class="align-center" src="_images/compute_fep_fdti.jpg" />
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<p>where <span class="math">\(w_i\)</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
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<span class="math">\(\lambda\)</span> at which the derivative is calculated and averaged.</p>
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<p>The compute fep calculates the exponential Boltzmann term and also the
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potential energy difference <span class="math">\(U_1 -U_0\)</span>. By
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choosing a very small perturbation <span class="math">\(\delta\)</span> the thermodynamic
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integration method can be implemented using a numerical evaluation of
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the derivative of the potential energy with respect to <span class="math">\(\lambda\)</span>:</p>
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<img alt="_images/compute_fep_ti.jpg" class="align-center" src="_images/compute_fep_ti.jpg" />
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<p>Another technique to calculate free energy differences is the
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acceptance ratio method <a class="reference internal" href="#bennet"><span class="std std-ref">(Bennet)</span></a>, which can be implemented
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by calculating the potential energy differences with <span class="math">\(\delta\)</span> = 1.0 on
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both the forward and reverse routes:</p>
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<img alt="_images/compute_fep_bar.jpg" class="align-center" src="_images/compute_fep_bar.jpg" />
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<p>The value of the free energy difference is determined by numerical
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root finding to establish the equality.</p>
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<p>Concerning the choice of how the atomic parameters are perturbed in
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order to setup an alchemical transformation route, several strategies
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are available, such as single-topology or double-topology strategies
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<a class="reference internal" href="#pearlman"><span class="std std-ref">(Pearlman)</span></a>. The latter does not require modification of
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bond lengths, angles or other internal coordinates.</p>
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<p>NOTES: This compute command does not take kinetic energy into account,
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therefore the masses of the particles should not be modified between
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the reference and perturbed states, or along the alchemical
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transformation route. This compute command does not change bond
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lengths or other internal coordinates <a class="reference internal" href="#boreschkarplus"><span class="std std-ref">(Boresch, Karplus)</span></a>.</p>
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<hr class="docutils" />
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<p>The <em>pair</em> attribute enables various parameters of potentials defined
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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>
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commands to be changed, if the pair style supports it.</p>
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<p>The <em>pstyle</em> argument is the name of the pair style. For example,
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|
<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 (non-exclusive) list of
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pair styles and parameters that can be used with this compute. See
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the doc pages for individual pair styles and their energy formulas for
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the meaning of these parameters:</p>
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<table border="1" class="docutils">
|
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<colgroup>
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<col width="59%" />
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<col width="27%" />
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<col width="15%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a></td>
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<td>epsilon,sigma</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut/coul/cut</span></a></td>
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<td>epsilon,sigma</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut/coul/long</span></a></td>
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<td>epsilon,sigma</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/soft</span></a></td>
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<td>epsilon,sigma,lambda</td>
|
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<td>type pairs</td>
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</tr>
|
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<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">coul/cut/soft</span></a></td>
|
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<td>lambda</td>
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<td>type pairs</td>
|
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</tr>
|
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<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">coul/long/soft</span></a></td>
|
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<td>lambda</td>
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<td>type pairs</td>
|
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</tr>
|
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<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/cut/soft</span></a></td>
|
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<td>epsilon,sigma,lambda</td>
|
|
<td>type pairs</td>
|
|
</tr>
|
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<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/long/soft</span></a></td>
|
|
<td>epsilon,sigma,lambda</td>
|
|
<td>type pairs</td>
|
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</tr>
|
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<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/tip4p/long/soft</span></a></td>
|
|
<td>epsilon,sigma,lambda</td>
|
|
<td>type pairs</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">tip4p/long/soft</span></a></td>
|
|
<td>lambda</td>
|
|
<td>type pairs</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/charmm/coul/long/soft</span></a></td>
|
|
<td>epsilon,sigma,lambda</td>
|
|
<td>type pairs</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><span class="doc">born</span></a></td>
|
|
<td>a,b,c</td>
|
|
<td>type pairs</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><span class="doc">buck</span></a></td>
|
|
<td>a,c</td>
|
|
<td>type pairs</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 1st example above. I <= 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 “n*” or “m*n”. If N =
|
|
the number of atom types, then an asterisk with no numeric values
|
|
means all types from 1 to N. A leading asterisk means all types from
|
|
1 to n (inclusive). A trailing asterisk means all types from n to N
|
|
(inclusive). A middle asterisk means all types from m to n
|
|
(inclusive). Note that only type pairs with I <= J are considered; if
|
|
asterisks imply type pairs where J < 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" />
|
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<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>charge = charge on particle</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>
|
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<hr class="docutils" />
|
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<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
|
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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>
|
|
<img alt="_images/compute_fep_vol.jpg" class="align-center" src="_images/compute_fep_vol.jpg" />
|
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<hr class="docutils" />
|
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<p><strong>Output info:</strong></p>
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|
<p>This compute calculates a global vector of length 3 which contains the
|
|
energy difference ( <span class="math">\(U_1-U_0\)</span> ) as c_ID[1], the
|
|
Boltzmann factor <span class="math">\(\exp(-(U_1-U_0)/kT)\)</span>, or
|
|
<span class="math">\(V \exp(-(U_1-U_0)/kT)\)</span>, as c_ID[2] and the
|
|
volume of the simulation box <span class="math">\(V\)</span> as c_ID[3]. <span class="math">\(U_1\)</span> is the
|
|
pair potential energy obtained with the perturbed parameters and
|
|
<span class="math">\(U_0\)</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 <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. 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>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>This compute is distributed as the USER-FEP package. It is only
|
|
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</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 external" href="pair_lj_soft_coul_soft.txt">pair_lj_soft_coul_soft</a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</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>
|
|
</div>
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