forked from lijiext/lammps
611 lines
44 KiB
HTML
611 lines
44 KiB
HTML
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<!DOCTYPE html>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>fix rx command — LAMMPS documentation</title>
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<link rel="top" title="LAMMPS documentation" href="index.html"/>
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<link rel="up" title="Fixes" href="fixes.html"/>
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<link rel="next" title="fix saed/vtk command" href="fix_saed_vtk.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 current"><a class="reference internal" href="fixes.html">Fixes</a><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt.html">fix adapt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_adapt_fep.html">fix adapt/fep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addforce.html">fix addforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_addtorque.html">fix addtorque command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_append_atoms.html">fix append/atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_atc.html">fix atc command</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>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_atom.html">fix ave/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_chunk.html">fix ave/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate.html">fix ave/correlate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_correlate_long.html">fix ave/correlate/long command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_histo.html">fix ave/histo command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_ave_time.html">fix ave/time command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_aveforce.html">fix aveforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_balance.html">fix balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_break.html">fix bond/break command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_create.html">fix bond/create command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_bond_swap.html">fix bond/swap command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_box_relax.html">fix box/relax command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_colvars.html">fix colvars command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_controller.html">fix controller command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html">fix deform command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deform.html#fix-deform-kk-command">fix deform/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_deposit.html">fix deposit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drag.html">fix drag command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude.html">fix drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_drude_transform.html">fix drude/transform/direct command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_dt_reset.html">fix dt/reset command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_efield.html">fix efield command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ehex.html">fix ehex command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_enforce2d.html">fix enforce2d command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_cv.html">fix eos/cv command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table.html">fix eos/table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_eos_table_rx.html">fix eos/table/rx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_evaporate.html">fix evaporate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_external.html">fix external command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_flow_gauss.html">fix flow/gauss command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_freeze.html">fix freeze command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gcmc.html">fix gcmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gld.html">fix gld command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gle.html">fix gle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html">fix gravity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_gravity.html#fix-gravity-omp-command">fix gravity/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_heat.html">fix heat command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_imd.html">fix imd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_indent.html">fix indent command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ipi.html">fix ipi command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html">fix langevin command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin.html#fix-langevin-kk-command">fix langevin/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_drude.html">fix langevin/drude command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_langevin_eff.html">fix langevin/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_fluid.html">fix lb/fluid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_momentum.html">fix lb/momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_pc.html">fix lb/pc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_rigid_pc_sphere.html">fix lb/rigid/pc/sphere command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lb_viscous.html">fix lb/viscous command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_lineforce.html">fix lineforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_manifoldforce.html">fix manifoldforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso.html">fix meso command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_meso_stationary.html">fix meso/stationary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_momentum.html">fix momentum command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_move.html">fix move command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_msst.html">fix msst command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_neb.html">fix neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html">fix nvt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-intel-command">fix nvt/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-kk-command">fix nvt/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nvt-omp-command">fix nvt/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-command">fix npt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-intel-command">fix npt/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-kk-command">fix npt/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-npt-omp-command">fix npt/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-command">fix nph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-kk-command">fix nph/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh.html#fix-nph-omp-command">fix nph/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html">fix nvt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-npt-eff-command">fix npt/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nh_eff.html#fix-nph-eff-command">fix nph/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_asphere.html">fix nph/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_body.html">fix nph/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nph_sphere.html">fix nph/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html">fix nphug command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nphug.html#fix-nphug-omp-command">fix nphug/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_asphere.html">fix npt/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_body.html">fix npt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_npt_sphere.html">fix npt/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html">fix nve command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-intel-command">fix nve/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-kk-command">fix nve/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve.html#fix-nve-omp-command">fix nve/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere.html">fix nve/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_asphere_noforce.html">fix nve/asphere/noforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_body.html">fix nve/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_eff.html">fix nve/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_limit.html">fix nve/limit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_line.html">fix nve/line command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_manifold_rattle.html">fix nve/manifold/rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_noforce.html">fix nve/noforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_sphere.html">fix nve/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nve_tri.html">fix nve/tri command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_asphere.html">fix nvt/asphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_body.html">fix nvt/body command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_manifold_rattle.html">fix nvt/manifold/rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod.html">fix nvt/sllod command</a></li>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sllod_eff.html">fix nvt/sllod/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_nvt_sphere.html">fix nvt/sphere command</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="fix_oneway.html">fix oneway command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html">fix orient/fcc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_orient.html#fix-orient-bcc-command">fix orient/bcc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_phonon.html">fix phonon command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_pimd.html">fix pimd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_planeforce.html">fix planeforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_poems.html">fix poems</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_pour.html">fix pour command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_press_berendsen.html">fix press/berendsen command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_print.html">fix print command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_property_atom.html">fix property/atom command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qbmsst.html">fix qbmsst command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html">fix qeq/point command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-shielded-command">fix qeq/shielded command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-slater-command">fix qeq/slater command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq.html#fix-qeq-dynamic-command">fix qeq/dynamic command</a></li>
|
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<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>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qeq_reax.html">fix qeq/reax command</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qmmm.html">fix qmmm command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_qtb.html">fix qtb command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_reax_bonds.html">fix reax/bonds command</a></li>
|
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<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>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_reaxc_species.html">fix reax/c/species command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_recenter.html">fix recenter command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_restrain.html">fix restrain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html">fix rigid command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-command">fix rigid/nve command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-command">fix rigid/npt command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nph-command">fix rigid/nph command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-small-command">fix rigid/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="fix_rigid.html#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
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<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 current"><a class="current reference internal" href="#">fix rx 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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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="fix_saed_vtk.html">fix saed/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html">fix setforce command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_setforce.html#fix-setforce-kk-command">fix setforce/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shake.html">fix shake command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shake.html#fix-rattle-command">fix rattle command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_shardlow.html">fix shardlow command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd.html">fix smd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_adjust_dt.html">fix smd/adjust_dt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_integrate_tlsph.html">fix smd/integrate_tlsph command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_move_triangulated_surface.html">fix smd/move_tri_surf command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_smd_setvel.html">fix smd/setvel 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_spring_chunk.html">fix spring/chunk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_rg.html">fix spring/rg command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_spring_self.html">fix spring/self command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_srd.html">fix srd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_store_force.html">fix store/force command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_store_state.html">fix store/state 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/csvr 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_temp_rescale.html">fix temp/rescale command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_ttm.html#fix-ttm-mod-command">fix ttm/mod command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_tune_kspace.html">fix tune/kspace command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_vector.html">fix vector command</a></li>
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<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_viscous.html">fix viscous 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.html#fix-wall-lj126-command">fix wall/lj126 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-colloid-command">fix wall/colloid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall.html#fix-wall-harmonic-command">fix wall/harmonic 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_piston.html">fix wall/piston command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_reflect.html">fix wall/reflect 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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<li class="toctree-l2"><a class="reference internal" href="fix_wall_region.html">fix wall/region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_wall_srd.html">fix wall/srd command</a></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">Bond Styles</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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<li>fix rx command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="fix-rx-command">
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<span id="index-0"></span><h1>fix rx 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">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">rx</span> <span class="n">file</span> <span class="n">localTemp</span> <span class="n">matrix</span> <span class="n">solver</span> <span class="n">minSteps</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
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<li>rx = style name of this fix command</li>
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<li>file = filename containing the reaction kinetic equations and Arrhenius parameters</li>
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<li>localTemp = <em>none,lucy</em> = no local temperature averaging or local temperature defined through Lucy weighting function</li>
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<li>matrix = <em>sparse, dense</em> format for the stoichiometric matrix</li>
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<li>solver = <em>lammps_rk4,rkf45</em> = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method</li>
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<li>minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)</li>
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<li>maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)</li>
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<li>relTol = relative tolerance for the rkf45 solver (rkf45 only)</li>
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<li>absTol = absolute tolernace for the rkf45 solver (rkf45 only)</li>
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<li>diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only)</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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fix 1 all rx kinetics.rx none dense lammps_rk4
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fix 1 all rx kinetics.rx none sparse lammps_rk4 1
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fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10
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fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8
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fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1
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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>Fix <em>rx</em> solves the reaction kinetic ODEs for a given reaction set that is
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defined within the file associated with this command.</p>
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<p>For a general reaction such that</p>
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<img alt="_images/fix_rx_reaction.jpg" class="align-center" src="_images/fix_rx_reaction.jpg" />
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<p>the reaction rate equation is defined to be of the form</p>
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<img alt="_images/fix_rx_reactionRate.jpg" class="align-center" src="_images/fix_rx_reactionRate.jpg" />
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<p>In the current implementation, the exponents are defined to be equal
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to the stoichiometric coefficients. A given reaction set consisting
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|
of <em>n</em> reaction equations will contain a total of <em>m</em> species. A set
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of <em>m</em> ordinary differential equations (ODEs) that describe the change
|
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in concentration of a given species as a function of time are then
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constructed based on the <em>n</em> reaction rate equations.</p>
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<p>The ODE systems are solved over the full DPD timestep <em>dt</em> using either a 4th
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|
order Runge-Kutta <em>rk4</em> method with a fixed step-size <em>h</em>, specified
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|
by the <em>lammps_rk4</em> keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method
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|
with an adaptive step-size for <em>h</em>. The number of ODE steps per DPD timestep
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|
for the rk4 method is optionally specified immediately after the rk4
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|
keyword. The ODE step-size is set as <em>dt/num_steps</em>. Smaller
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|
step-sizes tend to yield more accurate results but there is not
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|
control on the error. For error control, use the rkf45 ODE solver.</p>
|
|
<p>The rkf45 method adjusts the step-size so that the local truncation error is held
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|
within the specified absolute and relative tolerances. The initial step-size <em>h0</em>
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|
can be specified by the user or estimated internally. It is recommeded that the user
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|
specify <em>h0</em> since this will generally reduced the number of ODE integration steps
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|
required. <em>h0</em> is defined as <em>dt / min_steps</em> if min_steps >= 1. If min_steps == 0,
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|
<em>h0</em> is estimated such that an explicit Euler method would likely produce
|
|
an acceptable solution. This is generally overly conservative for the 4th-order
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|
method and users are advised to specify <em>h0</em> as some fraction of the DPD timestep.
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|
For small DPD timesteps, only one step may be necessary depending upon the tolerances.
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Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness
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|
but no more than max_steps will be taken. If max_steps is reached, an error warning
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is printed and the simulation is stopped.</p>
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<p>After each ODE step, the solution error <em>e</em> is tested and weighted using the absTol
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|
and relTol values. The error vector is weighted as <em>e</em> / (relTol * | <em>u</em> | + absTol)
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where <em>u</em> is the solution vector. If the norm of the error is <= 1, the solution is
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|
accepted, <em>h</em> is increased by a proportional amount, and the next ODE step is begun.
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Otherwise, <em>h</em> is shrunk and the ODE step is repeated.</p>
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|
<p>Run-time diagnostics are available for the rkf45 ODE solver. The frequency
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|
(in time-steps) that diagnostics are reported is controlled by the last (optional)
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|
12th argument. A negative frequency means that diagnostics are reported once at the
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|
end of each run. A positive value N means that the diagnostics are reported once
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|
per N time-steps.</p>
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|
<p>The diagnostics report the average # of integrator steps and RHS function evaluations
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|
and run-time per ODE as well as the the average/RMS/min/max per process. If the
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|
reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
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|
statistics can be used to adjust the tolerance and min/max step parameters. The
|
|
statistics per MPI process can be useful to examine any load imbalance caused by the
|
|
adaptive ODE solver. (Some DPD particles can take longer to solve than others. This
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|
can lead to an imbalance across the MPI processes.)</p>
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|
<hr class="docutils" />
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<p>The filename specifies a file that contains the entire set of reaction
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|
kinetic equations and corresponding Arrhenius parameters. The format of
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|
this file is described below.</p>
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|
<p>There is no restriction on the total number or reaction equations that
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|
are specified. The species names are arbitrary string names that are
|
|
associated with the species concentrations. Each species in a given
|
|
reaction must be preceded by it’s stoichiometric coefficient. The
|
|
only delimiters that are recognized between the species are either a
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|
<em>+</em> or <em>=</em> character. The <em>=</em> character corresponds to an
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|
irreversible reaction. After specifying the reaction, the reaction
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|
rate constant is determined through the temperature dependent
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|
Arrhenius equation:</p>
|
|
<img alt="_images/fix_rx.jpg" class="align-center" src="_images/fix_rx.jpg" />
|
|
<p>where <em>A</em> is the Arrhenius factor in time units or concentration/time
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|
units, <em>n</em> is the unitless exponent of the temperature dependence, and
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|
<em>E_a</em> is the activation energy in energy units. The temperature
|
|
dependence can be removed by specifying the exponent as zero.</p>
|
|
<p>The internal temperature of the coarse-grained particles can be used
|
|
in constructing the reaction rate constants at every DPD timestep by
|
|
specifying the keyword <em>none</em>. Alternatively, the keyword <em>lucy</em> can
|
|
be specified to compute a local-average particle internal temperature
|
|
for use in the reaction rate constant expressions. The local-average
|
|
particle internal temperature is defined as:</p>
|
|
<img alt="_images/fix_rx_localTemp.jpg" class="align-center" src="_images/fix_rx_localTemp.jpg" />
|
|
<p>where the Lucy function is expressed as:</p>
|
|
<img alt="_images/fix_rx_localTemp2.jpg" class="align-center" src="_images/fix_rx_localTemp2.jpg" />
|
|
<p>The self-particle interaction is included in the above equation.</p>
|
|
<p>The stoichiometric coefficients for the reaction mechanism are stored
|
|
in either a sparse or dense matrix format. The dense matrix should only be
|
|
used for small reaction mechanisms. The sparse matrix should be used when there
|
|
are many reactions (e.g., more than 5). This allows the number of reactions and
|
|
species to grow while keeping the computational cost tractable. The matrix
|
|
format can be specified as using either the <em>sparse</em> or <em>dense</em> keywords.
|
|
If all stoichiometric coefficients for a reaction are small integers (whole
|
|
numbers <= 3), a fast exponential function is used. This can save significant
|
|
computational time so users are encouraged to use integer coefficients
|
|
where possible.</p>
|
|
<hr class="docutils" />
|
|
<p>The format of a tabulated file is as follows (without the
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parenthesized comments):</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Rxn equations and parameters (one or more comment or blank lines)</span>
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</pre></div>
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</div>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mf">1.0</span> <span class="n">hcn</span> <span class="o">+</span> <span class="mf">1.0</span> <span class="n">no2</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="n">no</span> <span class="o">+</span> <span class="mf">0.5</span> <span class="n">n2</span> <span class="o">+</span> <span class="mf">0.5</span> <span class="n">h2</span> <span class="o">+</span> <span class="mf">1.0</span> <span class="n">co</span> <span class="mf">2.49E+01</span> <span class="mf">0.0</span> <span class="mf">1.34</span> <span class="p">(</span><span class="n">rxn</span> <span class="n">equation</span><span class="p">,</span> <span class="n">A</span><span class="p">,</span> <span class="n">n</span><span class="p">,</span> <span class="n">Ea</span><span class="p">)</span>
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<span class="mf">1.0</span> <span class="n">hcn</span> <span class="o">+</span> <span class="mf">1.0</span> <span class="n">no</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="n">co</span> <span class="o">+</span> <span class="mf">1.0</span> <span class="n">n2</span> <span class="o">+</span> <span class="mf">0.5</span> <span class="n">h2</span> <span class="mf">2.16E+00</span> <span class="mf">0.0</span> <span class="mf">1.52</span>
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<span class="o">...</span>
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<span class="mf">1.0</span> <span class="n">no</span> <span class="o">+</span> <span class="mf">1.0</span> <span class="n">co</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="n">n2</span> <span class="o">+</span> <span class="mf">1.0</span> <span class="n">co2</span> <span class="mf">1.66E+06</span> <span class="mf">0.0</span> <span class="mf">0.69</span>
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</pre></div>
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</div>
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<p>A section begins with a non-blank line whose 1st character is not a
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“#”; blank lines or lines starting with “#” can be used as comments
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|
between sections.</p>
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<p>Following a blank line, the next N lines list the N reaction
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equations. Each species within the reaction equation is specified
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|
through its stoichiometric coefficient and a species tag. Reactant
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species are specified on the left-hand side of the equation and
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product species are specified on the right-hand side of the equation.
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After specifying the reactant and product species, the final three
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arguments of each line represent the Arrhenius parameter <em>A</em>, the
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temperature exponent <em>n</em>, and the activation energy <em>Ea</em>.</p>
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<p>Note that the species tags that are defined in the reaction equations
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are used by the <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> command to
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|
define the thermodynamic properties of each species. Furthermore, the
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number of species molecules (i.e., concentration) can be specified
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either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the “d_” prefix or by
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|
reading directly the concentrations from a data file. For the latter
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case, the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command with the fix keyword
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|
should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g.</p>
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|
<p>fix foo all rx reaction.file ...
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|
read_data data.dpd fix foo_SPECIES NULL Species</p>
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</div>
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|
<hr class="docutils" />
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|
<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>This command is part of the USER-DPD package. It is only enabled if
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|
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>
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|
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
|
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command.</p>
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<p>This command can only be used with a constant energy or constant
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enthalpy DPD simulation.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a>,
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<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>,
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<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a></p>
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<p><strong>Default:</strong> none</p>
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