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<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 current"><a class="current reference internal" href="#">fix atc command</a><ul>
<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="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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<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"><a class="reference internal" href="fix_gle.html">fix gle command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html">fix gravity command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_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>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring.html">fix spring command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_berendsen.html">fix temp/berendsen command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_csvr.html#fix-temp-csld-command">fix temp/csld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_viscosity.html">fix viscosity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html">fix wall/lj93 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_gran.html">fix wall/gran command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html#fix-wall-reflect-kk-command">fix wall/reflect/kk command</a></li>
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<div class="section" id="fix-atc-command">
<span id="index-0"></span><h1>fix atc command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;
</pre>
<ul class="simple">
<li>fixID = name of fix</li>
<li>group = name of group fix is to be applied</li>
<li>type = <em>thermal</em> or <em>two_temperature</em> or <em>hardy</em> or <em>field</em></li>
</ul>
<pre class="literal-block">
<em>thermal</em> = thermal coupling with fields: temperature
<em>two_temperature</em> = electron-phonon coupling with field: temperature and electron_temperature
<em>hardy</em> = on-the-fly post-processing using kernel localization functions (see &quot;related&quot; section for possible fields)
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see &quot;related&quot; section for possible fields)
</pre>
<ul class="simple">
<li>parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix AtC internal atc thermal Ar_thermal.dat
fix AtC internal atc two_temperature Ar_ttm.mat
fix AtC internal atc hardy
fix AtC internal atc field
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
<img alt="_images/atc_nanotube.jpg" class="align-center" src="_images/atc_nanotube.jpg" />
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">The</span> <span class="n">following</span> <span class="n">coupling</span> <span class="n">example</span> <span class="ow">is</span> <span class="n">typical</span><span class="p">,</span> <span class="n">but</span> <span class="n">non</span><span class="o">-</span><span class="n">exhaustive</span><span class="p">:</span>
<span class="c1"># ... commands to create and initialize the MD system</span>
</pre></div>
</div>
<pre class="literal-block">
# initial fix to designate coupling type and group to apply it to
# tag group physics material_file
fix AtC internal atc thermal Ar_thermal.mat
</pre>
<pre class="literal-block">
# create a uniform 12 x 2 x 2 mesh that covers region contain the group
# nx ny nz region periodicity
fix_modify AtC mesh create 12 2 2 mdRegion f p p
</pre>
<pre class="literal-block">
# specify the control method for the type of coupling
# physics control_type
fix_modify AtC thermal control flux
</pre>
<pre class="literal-block">
# specify the initial values for the empirical field &quot;temperature&quot;
# field node_group value
fix_modify AtC initial temperature all 30
</pre>
<pre class="literal-block">
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC output atc_fe_output 100
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
</pre></div>
</div>
<p>likewise for this post-processing example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># ... commands to create and initialize the MD system</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># initial fix to designate post-processing and the group to apply it to</span>
<span class="c1"># no material file is allowed nor required</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
</pre></div>
</div>
<pre class="literal-block">
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
fix AtC kernel quartic_sphere 10.0
</pre>
<pre class="literal-block">
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
# with periodicity this effectively creats a system average
fix_modify AtC mesh create 1 1 1 box p p p
</pre>
<pre class="literal-block">
# change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100
</pre>
<pre class="literal-block">
# start with no field defined
# add mass density, potential energy density, stress and temperature
fix_modify AtC fields add density energy stress temperature
</pre>
<pre class="literal-block">
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC output nvtFE 100 text
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
</pre></div>
</div>
<dl class="docutils">
<dt>the mesh&#8217;s linear interpolation functions can be used as the localization function</dt>
<dd>by using the field option:</dd>
</dl>
<p>fix AtC internal atc field</p>
<p>fix_modify AtC mesh create 1 1 1 box p p p</p>
<p>...</p>
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes.</p>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
<ul class="simple">
<li>Currently,</li>
<li><ul class="first">
<li>the coupling is restricted to thermal physics</li>
</ul>
</li>
<li><ul class="first">
<li>the FE computations are done in serial on each processor.</li>
</ul>
</li>
</ul>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p>After specifying this fix in your input script, several other <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
<p>fix_modify commands for setup:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_mesh_create.html">fix_modify AtC mesh create</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_read.html">fix_modify AtC mesh read</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_write.html">fix_modify AtC mesh write</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li>
<li><a class="reference external" href="USER/atc/man_boundary.html">fix_modify AtC boundary</a></li>
<li><a class="reference external" href="USER/atc/man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li>
<li><a class="reference external" href="USER/atc/man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li>
<li><a class="reference external" href="USER/atc/man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li>
<li><a class="reference external" href="USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li>
<li><a class="reference external" href="USER/atc/man_internal_element_set.html">fix_modify AtC internal_element_set</a></li>
<li><a class="reference external" href="USER/atc/man_decomposition.html">fix_modify AtC decomposition</a></li>
</ul>
<p>fix_modify commands for boundary and initial conditions:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_initial.html">fix_modify AtC initial</a></li>
<li><a class="reference external" href="USER/atc/man_fix_nodes.html">fix_modify AtC fix</a></li>
<li><a class="reference external" href="USER/atc/man_unfix_nodes.html">fix_modify AtC unfix</a></li>
<li><a class="reference external" href="USER/atc/man_fix_flux.html">fix_modify AtC fix_flux</a></li>
<li><a class="reference external" href="USER/atc/man_unfix_flux.html">fix_modify AtC unfix_flux</a></li>
<li><a class="reference external" href="USER/atc/man_source.html">fix_modify AtC source</a></li>
<li><a class="reference external" href="USER/atc/man_remove_source.html">fix_modify AtC remove_source</a></li>
</ul>
<p>fix_modify commands for control and filtering:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_control.html">fix_modify AtC control</a></li>
<li><a class="reference external" href="USER/atc/man_control_thermal.html">fix_modify AtC control thermal</a></li>
<li><a class="reference external" href="USER/atc/man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li>
<li><a class="reference external" href="USER/atc/man_control_momentum.html">fix_modify AtC control momentum</a></li>
<li><a class="reference external" href="USER/atc/man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li>
<li><a class="reference external" href="USER/atc/man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li>
<li><a class="reference external" href="USER/atc/man_mask_direction.html">fix_modify AtC control mask_direction</a> control</li>
<li><a class="reference external" href="USER/atc/man_time_filter.html">fix_modify AtC filter</a></li>
<li><a class="reference external" href="USER/atc/man_filter_scale.html">fix_modify AtC filter scale</a></li>
<li><a class="reference external" href="USER/atc/man_filter_type.html">fix_modify AtC filter type</a></li>
<li><a class="reference external" href="USER/atc/man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li>
<li><a class="reference external" href="USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li>
<li><a class="reference external" href="USER/atc/man_poisson_solver.html">fix_modify AtC poisson_solver</a></li>
</ul>
<p>fix_modify commands for output:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_output.html">fix_modify AtC output</a></li>
<li><a class="reference external" href="USER/atc/man_output_nodeset.html">fix_modify AtC output nodeset</a></li>
<li><a class="reference external" href="USER/atc/man_output_elementset.html">fix_modify AtC output elementset</a></li>
<li><a class="reference external" href="USER/atc/man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li>
<li><a class="reference external" href="USER/atc/man_contour_integral.html">fix_modify AtC output contour_integral</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_output.html">fix_modify AtC mesh output</a></li>
<li><a class="reference external" href="USER/atc/man_write_restart.html">fix_modify AtC write_restart</a></li>
<li><a class="reference external" href="USER/atc/man_read_restart.html">fix_modify AtC read_restart</a></li>
</ul>
<p>fix_modify commands for post-processing:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_hardy_kernel.html">fix_modify AtC kernel</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_fields.html">fix_modify AtC fields</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_gradients.html">fix_modify AtC grdients</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_rates.html">fix_modify AtC rates</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_computes.html">fix_modify AtC computes</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li>
<li><a class="reference external" href="USER/atc/man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li>
<li><a class="reference external" href="USER/atc/man_sample_frequency.html">fix_modify AtC sample_frequency</a></li>
<li><a class="reference external" href="USER/atc/man_set.html">fix_modify AtC set</a></li>
</ul>
<p>miscellaneous fix_modify commands:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_atom_element_map.html">fix_modify AtC atom_element_map</a></li>
<li><a class="reference external" href="USER/atc/man_atom_weight.html">fix_modify AtC atom_weight</a></li>
<li><a class="reference external" href="USER/atc/man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li>
<li><a class="reference external" href="USER/atc/man_reset_time.html">fix_modify AtC reset_time</a></li>
<li><a class="reference external" href="USER/atc/man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li>
<li><a class="reference external" href="USER/atc/man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li>
<li><a class="reference external" href="USER/atc/man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li>
<li><a class="reference external" href="USER/atc/man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li>
<li><a class="reference external" href="USER/atc/man_mass_matrix.html">fix_modify AtC mass_matrix</a></li>
<li><a class="reference external" href="USER/atc/man_material.html">fix_modify AtC material</a></li>
<li><a class="reference external" href="USER/atc/man_atomic_charge.html">fix_modify AtC atomic_charge</a></li>
<li><a class="reference external" href="USER/atc/man_source_integration.html">fix_modify AtC source_integration</a></li>
<li><a class="reference external" href="USER/atc/man_temperature_definition.html">fix_modify AtC temperature_definition</a></li>
<li><a class="reference external" href="USER/atc/man_track_displacement.html">fix_modify AtC track_displacement</a></li>
<li><a class="reference external" href="USER/atc/man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li>
<li><a class="reference external" href="USER/atc/man_add_species.html">fix_modify AtC add_species</a></li>
<li><a class="reference external" href="USER/atc/man_add_molecule.html">fix_modify AtC add_molecule</a></li>
<li><a class="reference external" href="USER/atc/man_remove_species.html">fix_modify AtC remove_species</a></li>
<li><a class="reference external" href="USER/atc/man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
</ul>
<p>Note: a set of example input files with the attendant material files are included with this package</p>
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<div class="section" id="default">
<h2>Default</h2>
<p>None</p>
<hr class="docutils" />
<p>For detailed exposition of the theory and algorithms please see:</p>
<p id="wagner"><strong>(Wagner)</strong> Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, &#8220;An atomistic-to-continuum coupling method for heat transfer in solids.&#8221; Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.</p>
<p id="zimmeman2004"><strong>(Zimmerman2004)</strong> Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, &#8220;Calculation of stress in atomistic simulation.&#8221; Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.</p>
<p id="zimmerman2010"><strong>(Zimmerman2010)</strong> Zimmerman, JA; Jones, RE; Templeton, JA, &#8220;A material frame approach for evaluating continuum variables in atomistic simulations.&#8221; Journal of Computational Physics (2010), 229:2364.</p>
<p id="templeton2010"><strong>(Templeton2010)</strong> Templeton, JA; Jones, RE; Wagner, GJ, &#8220;Application of a field-based method to spatially varying thermal transport problems in molecular dynamics.&#8221; Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.</p>
<p id="jones"><strong>(Jones)</strong> Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, &#8220;Electron transport enhanced molecular dynamics for metals and semi-metals.&#8221; International Journal for Numerical Methods in Engineering (2010), 83:940.</p>
<p id="templeton2011"><strong>(Templeton2011)</strong> Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, &#8220;A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling.&#8221; Journal of Chemical Theory and Computation (2011), 7:1736.</p>
<p id="mandadapu"><strong>(Mandadapu)</strong> Mandadapu, KK; Templeton, JA; Lee, JW, &#8220;Polarization as a field variable from molecular dynamics simulations.&#8221; Journal of Chemical Physics (2013), 139:054115.</p>
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes &#8221; The finite element method &#8221;, Dover 2003, for the basics of FE simulation.</p>
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