lammps/doc/html/fix_gle.html

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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending 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="tutorials.html">Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="fixes.html">Fixes</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="fix_adapt.html">fix adapt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_adapt_fep.html">fix adapt/fep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_addforce.html">fix addforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_addtorque.html">fix addtorque command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_append_atoms.html">fix append/atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_atc.html">fix atc command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_atom_swap.html">fix atom/swap command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_atom.html">fix ave/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_chunk.html">fix ave/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate.html">fix ave/correlate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate_long.html">fix ave/correlate/long command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html">fix ave/histo command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html#fix-ave-histo-weight-command">fix ave/histo/weight command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ave_time.html">fix ave/time command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_aveforce.html">fix aveforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_balance.html">fix balance command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_bond_break.html">fix bond/break command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html">fix bond/create command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_bond_swap.html">fix bond/swap command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_box_relax.html">fix box/relax command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_colvars.html">fix colvars command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_controller.html">fix controller command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_deform.html">fix deform command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_deform.html#fix-deform-kk-command">fix deform/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_deposit.html">fix deposit command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_drag.html">fix drag command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_drude.html">fix drude command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html">fix drude/transform/direct command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html#fix-drude-transform-inverse-command">fix drude/transform/inverse command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_dt_reset.html">fix dt/reset command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_efield.html">fix efield command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ehex.html">fix ehex command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_enforce2d.html">fix enforce2d command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_eos_cv.html">fix eos/cv command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_eos_table.html">fix eos/table command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_eos_table_rx.html">fix eos/table/rx command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_evaporate.html">fix evaporate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_external.html">fix external command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_flow_gauss.html">fix flow/gauss command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_freeze.html">fix freeze command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_gcmc.html">fix gcmc command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_gld.html">fix gld command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">fix gle command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html">fix gravity command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html#fix-gravity-omp-command">fix gravity/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_heat.html">fix heat command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_imd.html">fix imd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_indent.html">fix indent command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ipi.html">fix ipi command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html">fix langevin command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html#fix-langevin-kk-command">fix langevin/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_langevin_drude.html">fix langevin/drude command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_langevin_eff.html">fix langevin/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_lb_fluid.html">fix lb/fluid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_lb_momentum.html">fix lb/momentum command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_lb_pc.html">fix lb/pc command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_lb_rigid_pc_sphere.html">fix lb/rigid/pc/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_meso.html">fix meso command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_meso_stationary.html">fix meso/stationary command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html">fix momentum command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_move.html">fix move command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-intel-command">fix nvt/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-kk-command">fix nvt/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-omp-command">fix nvt/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-intel-command">fix npt/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-kk-command">fix npt/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-omp-command">fix npt/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-kk-command">fix nph/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-omp-command">fix nph/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html#fix-nph-asphere-omp-command">fix nph/asphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html#fix-nph-sphere-omp-command">fix nph/sphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html#fix-nphug-omp-command">fix nphug/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html#fix-npt-asphere-omp-command">fix npt/asphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html">fix npt/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html#fix-npt-sphere-omp-command">fix npt/sphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-intel-command">fix nve/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-kk-command">fix nve/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-omp-command">fix nve/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html#fix-nve-asphere-intel-command">fix nve/asphere/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_body.html">fix nve/body command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_eff.html">fix nve/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_limit.html">fix nve/limit command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_line.html">fix nve/line command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_manifold_rattle.html">fix nve/manifold/rattle command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_noforce.html">fix nve/noforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html">fix nve/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html#fix-nve-sphere-omp-command">fix nve/sphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nve_tri.html">fix nve/tri command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html">fix nvt/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html#fix-nvt-asphere-omp-command">fix nvt/asphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_body.html">fix nvt/body command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html">fix nvt/sllod command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html#fix-nvt-sllod-intel-command">fix nvt/sllod/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html#fix-nvt-sllod-omp-command">fix nvt/sllod/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod_eff.html">fix nvt/sllod/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html">fix nvt/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html#fix-nvt-sphere-omp-command">fix nvt/sphere/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_oneway.html">fix oneway command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_orient.html">fix orient/fcc command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_phonon.html">fix phonon command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html">fix pimd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_planeforce.html">fix planeforce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_pour.html">fix pour command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_press_berendsen.html">fix press/berendsen command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_print.html">fix print command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_property_atom.html">fix property/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qbmsst.html">fix qbmsst command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html">fix qeq/point command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-shielded-command">fix qeq/shielded command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-slater-command">fix qeq/slater command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-dynamic-command">fix qeq/dynamic command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-fire-command">fix qeq/fire command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html">fix qeq/comb command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_comb.html#fix-qeq-comb-omp-command">fix qeq/comb/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reax.html">fix qeq/reax command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reax.html#fix-qeq-reax-kk-command">fix qeq/reax/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qmmm.html">fix qmmm command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_qtb.html">fix qtb command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_reax_bonds.html">fix reax/bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_reax_bonds.html#fix-reax-c-bonds-command">fix reax/c/bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_reaxc_species.html">fix reax/c/species command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_recenter.html">fix recenter command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_restrain.html">fix restrain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html">fix rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-command">fix rigid/nve command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-command">fix rigid/npt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-command">fix rigid/nph command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-small-command">fix rigid/small command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-small-command">fix rigid/nph/small command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_rx.html">fix rx command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_saed_vtk.html">fix saed/vtk command</a></li>
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<div class="section" id="fix-gle-command">
<span id="index-0"></span><h1>fix gle command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="nb">id</span><span class="o">-</span><span class="n">group</span> <span class="n">gle</span> <span class="n">Ns</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">seed</span> <span class="n">Amatrix</span> <span class="p">[</span><span class="n">noneq</span> <span class="n">Cmatrix</span><span class="p">]</span> <span class="p">[</span><span class="n">every</span> <span class="n">stride</span><span class="p">]</span>
</pre></div>
</div>
<ul>
<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
</li>
<li><p class="first">gle = style name of this fix command</p>
</li>
<li><p class="first">Ns = number of additional fictitious momenta</p>
</li>
<li><p class="first">Tstart, Tstop = temperature ramp during the run</p>
</li>
<li><p class="first">Amatrix = file to read the drift matrix A from</p>
</li>
<li><p class="first">seed = random number seed to use for generating noise (positive integer)</p>
</li>
<li><p class="first">zero or more keyword/value pairs may be appended</p>
<pre class="literal-block">
keyword = <em>noneq</em> or <em>every</em>
<em>noneq</em> Cmatrix = file to read the non-equilibrium covariance matrix from
<em>every</em> stride = apply the GLE once every time steps. Reduces the accuracy
of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
sampling. It might change sampling properties when used together with <em>noneq</em>.
</pre>
</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">3</span> <span class="n">boundary</span> <span class="n">gle</span> <span class="mi">6</span> <span class="mi">300</span> <span class="mi">300</span> <span class="mi">31415</span> <span class="n">smart</span><span class="o">.</span><span class="n">A</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gle</span> <span class="mi">6</span> <span class="mi">300</span> <span class="mi">300</span> <span class="mi">31415</span> <span class="n">qt</span><span class="o">-</span><span class="mi">300</span><span class="n">k</span><span class="o">.</span><span class="n">A</span> <span class="n">noneq</span> <span class="n">qt</span><span class="o">-</span><span class="mi">300</span><span class="n">k</span><span class="o">.</span><span class="n">C</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Apply a Generalized Langevin Equation (GLE) thermostat as described
in <a class="reference internal" href="#ceriotti"><span class="std std-ref">(Ceriotti)</span></a>. The formalism allows one to obtain a number
of different effects ranging from efficient sampling of all
vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
<a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
should not be used together with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> &#8211; at least not
on the same atom groups.</p>
<p>Each degree of freedom in the thermostatted group is supplemented
with Ns additional degrees of freedom s, and the equations of motion
become</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dq</span><span class="o">/</span><span class="n">dt</span><span class="o">=</span><span class="n">p</span><span class="o">/</span><span class="n">m</span>
<span class="n">d</span><span class="p">(</span><span class="n">p</span><span class="p">,</span><span class="n">s</span><span class="p">)</span><span class="o">/</span><span class="n">dt</span><span class="o">=</span><span class="p">(</span><span class="n">F</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span> <span class="o">-</span> <span class="n">A</span><span class="p">(</span><span class="n">p</span><span class="p">,</span><span class="n">s</span><span class="p">)</span> <span class="o">+</span> <span class="n">B</span> <span class="n">dW</span><span class="o">/</span><span class="n">dt</span>
</pre></div>
</div>
<p>where F is the physical force, A is the drift matrix (that generalizes
the friction in Langevin dynamics), B is the diffusion term and dW/dt
un-correlated Gaussian random forces. The A matrix couples the physical
(q,p) dynamics with that of the additional degrees of freedom,
and makes it possible to obtain effectively a history-dependent
noise and friction kernel.</p>
<p>The drift matrix should be given as an external file <em>Afile</em>,
as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
optimal for a given application and the system of choice can be
obtained from <a class="reference internal" href="#gle4md"><span class="std std-ref">(GLE4MD)</span></a>.</p>
<p>Equilibrium sampling a temperature T is obtained by specifiying the
target value as the <em>Tstart</em> and <em>Tstop</em> arguments, so that the diffusion
matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
can be used for instance to model inexpensively zero-point energy
effects <a class="reference internal" href="#ceriotti2"><span class="std std-ref">(Ceriotti2)</span></a>. This is achieved specifying the
<em>noneq</em> keyword followed by the name of the file that contains the
static covariance matrix for the non-equilibrium dynamics.</p>
<p>Since integrating GLE dynamics can be costly when used together with
simple potentials, one can use the <em>every</em> optional keyword to
apply the Langevin terms only once every several MD steps, in a
multiple time-step fashion. This should be used with care when doing
non-equilibrium sampling, but should have no effect on equilibrium
averages when using canonical sampling.</p>
<p>The random number <em>seed</em> must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.</p>
<p>Note also that the Generalized Langevin Dynamics scheme that is
implemented by the <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> scheme is closely related
to the present one. In fact, it should be always possible to cast the
Prony series form of the memory kernel used by GLD into an appropriate
input matrix for <a class="reference internal" href="#"><span class="doc">fix gle</span></a>. While the GLE scheme is more
general, the form used by <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> can be more directly
related to the representation of an implicit solvent environment.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<p>The instantaneous values of the extended variables are written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random
number generator is not saved in restart files, this means you cannot
do &#8220;exact&#8221; restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
Note however that you should use a different seed each time you
restart, otherwise the same sequence of random numbers will be used
each time, which might lead to stochastic synchronization and
subtle artefacts in the sampling.</p>
<p>This fix can ramp its target temperature over multiple runs, using the
<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
<a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of how to do this.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
<p>This fix computes a global scalar which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is &#8220;extensive&#8221;.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The GLE thermostat in its current implementation should not be used
with rigid bodies, SHAKE or RATTLE. It is expected that all the
thermostatted degrees of freedom are fully flexible, and the sampled
ensemble will not be correct otherwise.</p>
<p>In order to perform constant-pressure simulations please use
<a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berendsen</span></a>, rather than
<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, to avoid duplicate integration of the
equations of motion.</p>
<p>This fix is part of the USER-MISC 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_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="pair_dpd.html"><span class="doc">pair_style dpd/tstat</span></a>, <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a></p>
<hr class="docutils" />
<p id="ceriotti"><strong>(Ceriotti)</strong> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
1170-80 (2010)</p>
<p id="gle4md"><strong>(GLE4MD)</strong> <a class="reference external" href="http://epfl-cosmo.github.io/gle4md/">http://epfl-cosmo.github.io/gle4md/</a></p>
<p id="ceriotti2"><strong>(Ceriotti2)</strong> Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
030603 (2009)</p>
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