diff --git a/doc/Manual.html b/doc/Manual.html
index 5a7436319e..a8a9bcd529 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -32,7 +32,8 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="1. Introduction" href="Section_intro.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,16 +72,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">LAMMPS Documentation</a><ul>
-<li><a class="reference internal" href="#jul-2015-version">27 Jul 2015 version</a></li>
-<li><a class="reference internal" href="#version-info">Version info:</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
-</ul>
-</div>
+
           
         
       </div>
@@ -165,13 +172,192 @@ we can improve the LAMMPS documentation.</p>
 it gives quick access to documentation for all LAMMPS commands.</p>
 <p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
 <a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.12. USER-INTEL package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.13. USER-LB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.14. USER-MISC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.15. USER-MOLFILE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.16. USER-OMP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.17. USER-PHONON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.18. USER-QMMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.19. USER-QTB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.20. USER-REAXC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.21. USER-SPH package</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
+</ul>
+</li>
+</ul>
+</div>
 </div>
 </div>
 <div class="section" id="indices-and-tables">
 <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
 <ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span>Index</span></a> // comment</li>
-<li><a class="reference internal" href="search.html"><span>Search Page</span></a> // comment</li>
+<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
 </ul>
 </BODY></div>
 
@@ -180,6 +366,13 @@ it gives quick access to documentation for all LAMMPS commands.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html
index 22a4831671..a8c7da001a 100644
--- a/doc/Section_accelerate.html
+++ b/doc/Section_accelerate.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Accelerating LAMMPS performance &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>5. Accelerating LAMMPS performance &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="6. How-to discussions" href="Section_howto.html"/>
+        <link rel="prev" title="4. Packages" href="Section_packages.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,20 +73,31 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Accelerating LAMMPS performance</a><ul>
-<li><a class="reference internal" href="#measuring-performance">Measuring performance</a></li>
-<li><a class="reference internal" href="#general-strategies">General strategies</a></li>
-<li><a class="reference internal" href="#packages-with-optimized-styles">Packages with optimized styles</a></li>
-<li><a class="reference internal" href="#comparison-of-various-accelerator-packages">Comparison of various accelerator packages</a><ul>
-<li><a class="reference internal" href="#examples">Examples</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">5. Accelerating LAMMPS performance</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#examples">5.4.1. Examples</a></li>
 </ul>
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -107,7 +120,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Accelerating LAMMPS performance</li>
+    <li>5. Accelerating LAMMPS performance</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -122,7 +135,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="accelerating-lammps-performance">
-<h1>Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline">¶</a></h1>
+<h1>5. Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline">¶</a></h1>
 <p>This section describes various methods for improving LAMMPS
 performance for different classes of problems running on different
 kinds of machines.</p>
@@ -150,7 +163,7 @@ packages discussed in Section 5.2, for several of the standard LAMMPS
 benchmark problems, as a function of problem size and number of
 compute nodes, on different hardware platforms.</p>
 <div class="section" id="measuring-performance">
-<span id="acc-1"></span><h2>Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline">¶</a></h2>
+<span id="acc-1"></span><h2>5.1. Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline">¶</a></h2>
 <p>Before trying to make your simulation run faster, you should
 understand how it currently performs and where the bottlenecks are.</p>
 <p>The best way to do this is run the your system (actual number of
@@ -191,7 +204,7 @@ LAMMPS, to obtain synchronized timings.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="general-strategies">
-<span id="acc-2"></span><h2>General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline">¶</a></h2>
+<span id="acc-2"></span><h2>5.2. General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline">¶</a></h2>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">this section 5.2 is still a work in progress</p>
@@ -244,7 +257,7 @@ such as when using a barostat.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="packages-with-optimized-styles">
-<span id="acc-3"></span><h2>Packages with optimized styles<a class="headerlink" href="#packages-with-optimized-styles" title="Permalink to this headline">¶</a></h2>
+<span id="acc-3"></span><h2>5.3. Packages with optimized styles<a class="headerlink" href="#packages-with-optimized-styles" title="Permalink to this headline">¶</a></h2>
 <p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>,
 <a class="reference internal" href="fix.html"><em>fixes</em></a>, <a class="reference internal" href="compute.html"><em>computes</em></a>, and other commands have
 been added to LAMMPS, which will typically run faster than the
@@ -436,7 +449,7 @@ CPU.</li>
 <hr class="docutils" />
 </div>
 <div class="section" id="comparison-of-various-accelerator-packages">
-<span id="acc-4"></span><h2>Comparison of various accelerator packages<a class="headerlink" href="#comparison-of-various-accelerator-packages" title="Permalink to this headline">¶</a></h2>
+<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages<a class="headerlink" href="#comparison-of-various-accelerator-packages" title="Permalink to this headline">¶</a></h2>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">this section still needs to be re-worked with additional KOKKOS
@@ -507,7 +520,7 @@ is generally not a problem since typical runs are computation-limited
 rather than memory-limited.</li>
 </ul>
 <div class="section" id="examples">
-<h3>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<h3>5.4.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
 <p>The LAMMPS distribution has two directories with sample input scripts
 for the GPU and USER-CUDA packages.</p>
 <ul class="simple">
@@ -525,6 +538,15 @@ to benchmark the performance of both packages on your system.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_howto.html" class="btn btn-neutral float-right" title="6. How-to discussions" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 224017192d..77c9c68bf5 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Commands &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>3. Commands &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="4. Packages" href="Section_packages.html"/>
+        <link rel="prev" title="2. Getting Started" href="Section_start.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,26 +73,37 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Commands</a><ul>
-<li><a class="reference internal" href="#lammps-input-script">LAMMPS input script</a></li>
-<li><a class="reference internal" href="#parsing-rules">Parsing rules</a></li>
-<li><a class="reference internal" href="#input-script-structure">Input script structure</a></li>
-<li><a class="reference internal" href="#commands-listed-by-category">Commands listed by category</a></li>
-<li><a class="reference internal" href="#individual-commands">Individual commands</a></li>
-<li><a class="reference internal" href="#fix-styles">Fix styles</a></li>
-<li><a class="reference internal" href="#compute-styles">Compute styles</a></li>
-<li><a class="reference internal" href="#pair-style-potentials">Pair_style potentials</a></li>
-<li><a class="reference internal" href="#bond-style-potentials">Bond_style potentials</a></li>
-<li><a class="reference internal" href="#angle-style-potentials">Angle_style potentials</a></li>
-<li><a class="reference internal" href="#dihedral-style-potentials">Dihedral_style potentials</a></li>
-<li><a class="reference internal" href="#improper-style-potentials">Improper_style potentials</a></li>
-<li><a class="reference internal" href="#kspace-solvers">Kspace solvers</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">3. Commands</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#lammps-input-script">3.1. LAMMPS input script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#parsing-rules">3.2. Parsing rules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#input-script-structure">3.3. Input script structure</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#commands-listed-by-category">3.4. Commands listed by category</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#individual-commands">3.5. Individual commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#fix-styles">3.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#compute-styles">3.7. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pair-style-potentials">3.8. Pair_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#bond-style-potentials">3.9. Bond_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#angle-style-potentials">3.10. Angle_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#improper-style-potentials">3.12. Improper_style potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#kspace-solvers">3.13. Kspace solvers</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -113,7 +126,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Commands</li>
+    <li>3. Commands</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -128,7 +141,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="commands">
-<h1>Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h1>
+<h1>3. Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h1>
 <p>This section describes how a LAMMPS input script is formatted and the
 input script commands used to define a LAMMPS simulation.</p>
 <div class="line-block">
@@ -140,7 +153,7 @@ input script commands used to define a LAMMPS simulation.</p>
 <div class="line"><br /></div>
 </div>
 <div class="section" id="lammps-input-script">
-<span id="cmd-1"></span><h2>LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-1"></span><h2>3.1. LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS executes by reading commands from a input script (text file),
 one line at a time.  When the input script ends, LAMMPS exits.  Each
 command causes LAMMPS to take some action.  It may set an internal
@@ -187,7 +200,7 @@ command lists restrictions on how the command can be used.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="parsing-rules">
-<span id="cmd-2"></span><h2>Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-2"></span><h2>3.2. Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline">¶</a></h2>
 <p>Each non-blank line in the input script is treated as a command.
 LAMMPS commands are case sensitive.  Command names are lower-case, as
 are specified command arguments.  Upper case letters may be used in
@@ -291,7 +304,7 @@ allowed, but that should be sufficient for most use cases.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="input-script-structure">
-<span id="cmd-3"></span><h2>Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-3"></span><h2>3.3. Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline">¶</a></h2>
 <p>This section describes the structure of a typical LAMMPS input script.
 The &#8220;examples&#8221; directory in the LAMMPS distribution contains many
 sample input scripts; the corresponding problems are discussed in
@@ -370,7 +383,7 @@ the <a class="reference internal" href="minimize.html"><em>minimize</em></a> com
 <hr class="docutils" />
 </div>
 <div class="section" id="commands-listed-by-category">
-<span id="cmd-4"></span><h2>Commands listed by category<a class="headerlink" href="#commands-listed-by-category" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-4"></span><h2>3.4. Commands listed by category<a class="headerlink" href="#commands-listed-by-category" title="Permalink to this headline">¶</a></h2>
 <p>This section lists all LAMMPS commands, grouped by category.  The
 <a class="reference internal" href="#cmd-5"><span>next section</span></a> lists the same commands alphabetically.  Note
 that some style options for some commands are part of specific LAMMPS
@@ -429,7 +442,7 @@ in the command&#8217;s documentation.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="individual-commands">
-<span id="comm"></span><span id="cmd-5"></span><h2>Individual commands<a class="headerlink" href="#individual-commands" title="Permalink to this headline">¶</a></h2>
+<span id="comm"></span><span id="cmd-5"></span><h2>3.5. Individual commands<a class="headerlink" href="#individual-commands" title="Permalink to this headline">¶</a></h2>
 <p>This section lists all LAMMPS commands alphabetically, with a separate
 listing below of styles within certain commands.  The <a class="reference internal" href="#cmd-4"><span>previous section</span></a> lists the same commands, grouped by category.  Note
 that some style options for some commands are part of specific LAMMPS
@@ -575,7 +588,7 @@ in the command&#8217;s documentation.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="fix-styles">
-<h2>Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
+<h2>3.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="fix.html"><em>fix</em></a> command for one-line descriptions of each style
 or click on the style itself for a full description.  Some of the
 styles have accelerated versions, which can be used if LAMMPS is built
@@ -797,7 +810,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="compute-styles">
-<h2>Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
+<h2>3.7. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="compute.html"><em>compute</em></a> command for one-line descriptions of
 each style or click on the style itself for a full description.  Some
 of the styles have accelerated versions, which can be used if LAMMPS
@@ -931,7 +944,7 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
 </div>
 <hr class="docutils" />
 <div class="section" id="pair-style-potentials">
-<h2>Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>3.8. Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command for an overview of pair
 potentials.  Click on the style itself for a full description.  Many
 of the styles have accelerated versions, which can be used if LAMMPS
@@ -1143,7 +1156,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
 </div>
 <hr class="docutils" />
 <div class="section" id="bond-style-potentials">
-<h2>Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>3.9. Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command for an overview of bond
 potentials.  Click on the style itself for a full description.  Some
 of the styles have accelerated versions, which can be used if LAMMPS
@@ -1191,7 +1204,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
 </div>
 <hr class="docutils" />
 <div class="section" id="angle-style-potentials">
-<h2>Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>3.10. Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="angle_style.html"><em>angle_style</em></a> command for an overview of
 angle potentials.  Click on the style itself for a full description.
 Some of the styles have accelerated versions, which can be used if
@@ -1248,7 +1261,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
 </div>
 <hr class="docutils" />
 <div class="section" id="dihedral-style-potentials">
-<h2>Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>3.11. Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a> command for an overview
 of dihedral potentials.  Click on the style itself for a full
 description.  Some of the styles have accelerated versions, which can
@@ -1300,7 +1313,7 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
 </div>
 <hr class="docutils" />
 <div class="section" id="improper-style-potentials">
-<h2>Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>3.12. Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="improper_style.html"><em>improper_style</em></a> command for an overview
 of improper potentials.  Click on the style itself for a full
 description.  Some of the styles have accelerated versions, which can
@@ -1345,7 +1358,7 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
 </div>
 <hr class="docutils" />
 <div class="section" id="kspace-solvers">
-<h2>Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline">¶</a></h2>
+<h2>3.13. Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command for an overview of
 Kspace solvers.  Click on the style itself for a full description.
 Some of the styles have accelerated versions, which can be used if
@@ -1385,6 +1398,15 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_packages.html" class="btn btn-neutral float-right" title="4. Packages" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_start.html" class="btn btn-neutral" title="2. Getting Started" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_errors.html b/doc/Section_errors.html
index b8565e9977..037ce3b819 100644
--- a/doc/Section_errors.html
+++ b/doc/Section_errors.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Errors &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>12. Errors &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="13. Future and history" href="Section_history.html"/>
+        <link rel="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,18 +73,29 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Errors</a><ul>
-<li><a class="reference internal" href="#common-problems">Common problems</a></li>
-<li><a class="reference internal" href="#reporting-bugs">Reporting bugs</a></li>
-<li><a class="reference internal" href="#error-warning-messages">Error &amp; warning messages</a></li>
-<li><a class="reference internal" href="#error">Errors:</a></li>
-<li><a class="reference internal" href="#warnings">Warnings:</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">12. Errors</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#common-problems">12.1. Common problems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#reporting-bugs">12.2. Reporting bugs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#error-warning-messages">12.3. Error &amp; warning messages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#error">12.4. Errors:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#warnings">12.5. Warnings:</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -105,7 +118,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Errors</li>
+    <li>12. Errors</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -120,7 +133,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="errors">
-<h1>Errors<a class="headerlink" href="#errors" title="Permalink to this headline">¶</a></h1>
+<h1>12. Errors<a class="headerlink" href="#errors" title="Permalink to this headline">¶</a></h1>
 <p>This section describes the errors you can encounter when using LAMMPS,
 either conceptually, or as printed out by the program.</p>
 <div class="line-block">
@@ -130,7 +143,7 @@ either conceptually, or as printed out by the program.</p>
 <div class="line"><br /></div>
 </div>
 <div class="section" id="common-problems">
-<span id="err-1"></span><h2>Common problems<a class="headerlink" href="#common-problems" title="Permalink to this headline">¶</a></h2>
+<span id="err-1"></span><h2>12.1. Common problems<a class="headerlink" href="#common-problems" title="Permalink to this headline">¶</a></h2>
 <p>If two LAMMPS runs do not produce the same answer on different
 machines or different numbers of processors, this is typically not a
 bug.  In theory you should get identical answers on any number of
@@ -219,7 +232,7 @@ buffering or boost the sizes of messages that can be buffered.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="reporting-bugs">
-<span id="err-2"></span><h2>Reporting bugs<a class="headerlink" href="#reporting-bugs" title="Permalink to this headline">¶</a></h2>
+<span id="err-2"></span><h2>12.2. Reporting bugs<a class="headerlink" href="#reporting-bugs" title="Permalink to this headline">¶</a></h2>
 <p>If you are confident that you have found a bug in LAMMPS, follow these
 steps.</p>
 <p>Check the <a class="reference external" href="http://lammps.sandia.gov/bug.html">New features and bug fixes</a> section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a> to see if the bug has already been reported or fixed or the
@@ -241,7 +254,7 @@ causing the problem.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="error-warning-messages">
-<span id="err-3"></span><h2>Error &amp; warning messages<a class="headerlink" href="#error-warning-messages" title="Permalink to this headline">¶</a></h2>
+<span id="err-3"></span><h2>12.3. Error &amp; warning messages<a class="headerlink" href="#error-warning-messages" title="Permalink to this headline">¶</a></h2>
 <p>These are two alphabetic lists of the <a class="reference internal" href="#error"><span>ERROR</span></a> and
 <a class="reference internal" href="#warn"><span>WARNING</span></a> messages LAMMPS prints out and the reason why.  If the
 explanation here is not sufficient, the documentation for the
@@ -256,7 +269,7 @@ error occurs and is not self-explanatory, you&#8217;ll need to look in the
 source code or contact the author of the package.</p>
 </div>
 <div class="section" id="error">
-<span id="id2"></span><h2>Errors:<a class="headerlink" href="#error" title="Permalink to this headline">¶</a></h2>
+<span id="id2"></span><h2>12.4. Errors:<a class="headerlink" href="#error" title="Permalink to this headline">¶</a></h2>
 <dl class="docutils">
 <dt><em>1-3 bond count is inconsistent</em></dt>
 <dd>An inconsistency was detected when computing the number of 1-3
@@ -5775,7 +5788,7 @@ read_restart, or create_box command.</dd>
 </dl>
 </div>
 <div class="section" id="warnings">
-<span id="warn"></span><h2>Warnings:<a class="headerlink" href="#warnings" title="Permalink to this headline">¶</a></h2>
+<span id="warn"></span><h2>12.5. Warnings:<a class="headerlink" href="#warnings" title="Permalink to this headline">¶</a></h2>
 <dl class="docutils">
 <dt><em>Adjusting Coulombic cutoff for MSM, new cutoff = %g</em></dt>
 <dd>The adjust/cutoff command is turned on and the Coulombic cutoff has been
@@ -6286,6 +6299,15 @@ infinity.</dd>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_history.html" class="btn btn-neutral float-right" title="13. Future and history" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_python.html" class="btn btn-neutral" title="11. Python interface to LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_example.html b/doc/Section_example.html
index 2866e57570..d24ca83ded 100644
--- a/doc/Section_example.html
+++ b/doc/Section_example.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Example problems &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>7. Example problems &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/>
+        <link rel="prev" title="6. How-to discussions" href="Section_howto.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,11 +73,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Example problems</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -98,7 +111,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Example problems</li>
+    <li>7. Example problems</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -113,7 +126,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="example-problems">
-<h1>Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline">¶</a></h1>
+<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline">¶</a></h1>
 <p>The LAMMPS distribution includes an examples sub-directory with
 several sample problems.  Each problem is in a sub-directory of its
 own.  Most are 2d models so that they run quickly, requiring at most a
@@ -305,6 +318,15 @@ packages.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance &amp; scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_howto.html" class="btn btn-neutral" title="6. How-to discussions" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_history.html b/doc/Section_history.html
index b409943b14..3d3e00aacc 100644
--- a/doc/Section_history.html
+++ b/doc/Section_history.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Future and history &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>13. Future and history &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,8 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="prev" title="12. Errors" href="Section_errors.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,15 +72,26 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Future and history</a><ul>
-<li><a class="reference internal" href="#coming-attractions">Coming attractions</a></li>
-<li><a class="reference internal" href="#past-versions">Past versions</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">13. Future and history</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#coming-attractions">13.1. Coming attractions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#past-versions">13.2. Past versions</a></li>
 </ul>
 </li>
 </ul>
-</div>
+
           
         
       </div>
@@ -102,7 +114,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Future and history</li>
+    <li>13. Future and history</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -117,7 +129,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="future-and-history">
-<h1>Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline">¶</a></h1>
+<h1>13. Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline">¶</a></h1>
 <p>This section lists features we plan to add to LAMMPS, features of
 previous versions of LAMMPS, and features of other parallel molecular
 dynamics codes our group has distributed.</p>
@@ -127,7 +139,7 @@ dynamics codes our group has distributed.</p>
 <div class="line"><br /></div>
 </div>
 <div class="section" id="coming-attractions">
-<span id="hist-1"></span><h2>Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline">¶</a></h2>
+<span id="hist-1"></span><h2>13.1. Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline">¶</a></h2>
 <p>The <a class="reference external" href="http://lammps.sandia.gov/future.html">Wish list link</a> on the
 LAMMPS WWW page gives a list of features we are hoping to add to
 LAMMPS in the future, including contact names of individuals you can
@@ -138,7 +150,7 @@ your wish to the list.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="past-versions">
-<span id="hist-2"></span><h2>Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline">¶</a></h2>
+<span id="hist-2"></span><h2>13.2. Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS development began in the mid 1990s under a cooperative research
 &amp; development agreement (CRADA) between two DOE labs (Sandia and LLNL)
 and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
@@ -226,6 +238,13 @@ internally.  A brief listing of their features is given here.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+      
+        <a href="Section_errors.html" class="btn btn-neutral" title="12. Errors" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_howto.html b/doc/Section_howto.html
index 752f10f1d7..a9777f52a1 100644
--- a/doc/Section_howto.html
+++ b/doc/Section_howto.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>How-to discussions &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>6. How-to discussions &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="7. Example problems" href="Section_example.html"/>
+        <link rel="prev" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,66 +73,77 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">How-to discussions</a><ul>
-<li><a class="reference internal" href="#restarting-a-simulation">Restarting a simulation</a></li>
-<li><a class="reference internal" href="#d-simulations">2d simulations</a></li>
-<li><a class="reference internal" href="#charmm-amber-and-dreiding-force-fields">CHARMM, AMBER, and DREIDING force fields</a></li>
-<li><a class="reference internal" href="#running-multiple-simulations-from-one-input-script">Running multiple simulations from one input script</a></li>
-<li><a class="reference internal" href="#multi-replica-simulations">Multi-replica simulations</a></li>
-<li><a class="reference internal" href="#granular-models">Granular models</a></li>
-<li><a class="reference internal" href="#tip3p-water-model">TIP3P water model</a></li>
-<li><a class="reference internal" href="#tip4p-water-model">TIP4P water model</a></li>
-<li><a class="reference internal" href="#spc-water-model">SPC water model</a></li>
-<li><a class="reference internal" href="#coupling-lammps-to-other-codes">Coupling LAMMPS to other codes</a></li>
-<li><a class="reference internal" href="#visualizing-lammps-snapshots">Visualizing LAMMPS snapshots</a></li>
-<li><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">Triclinic (non-orthogonal) simulation boxes</a></li>
-<li><a class="reference internal" href="#nemd-simulations">NEMD simulations</a></li>
-<li><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">Finite-size spherical and aspherical particles</a><ul>
-<li><a class="reference internal" href="#atom-styles">Atom styles</a></li>
-<li><a class="reference internal" href="#pair-potentials">Pair potentials</a></li>
-<li><a class="reference internal" href="#time-integration">Time integration</a></li>
-<li><a class="reference internal" href="#computes-thermodynamics-and-dump-output">Computes, thermodynamics, and dump output</a></li>
-<li><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">Rigid bodies composed of finite-size particles</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">6. How-to discussions</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#restarting-a-simulation">6.1. Restarting a simulation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#d-simulations">6.2. 2d simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#granular-models">6.6. Granular models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#tip3p-water-model">6.7. TIP3P water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#tip4p-water-model">6.8. TIP4P water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#spc-water-model">6.9. SPC water model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#nemd-simulations">6.13. NEMD simulations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#atom-styles">6.14.1. Atom styles</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pair-potentials">6.14.2. Pair potentials</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#time-integration">6.14.3. Time integration</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#computes-thermodynamics-and-dump-output">6.14.4. Computes, thermodynamics, and dump output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">6.14.5. Rigid bodies composed of finite-size particles</a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
-<li><a class="reference internal" href="#global-per-atom-local-data">Global/per-atom/local data</a></li>
-<li><a class="reference internal" href="#scalar-vector-array-data">Scalar/vector/array data</a></li>
-<li><a class="reference internal" href="#thermodynamic-output">Thermodynamic output</a></li>
-<li><a class="reference internal" href="#dump-file-output">Dump file output</a></li>
-<li><a class="reference internal" href="#fixes-that-write-output-files">Fixes that write output files</a></li>
-<li><a class="reference internal" href="#computes-that-process-output-quantities">Computes that process output quantities</a></li>
-<li><a class="reference internal" href="#fixes-that-process-output-quantities">Fixes that process output quantities</a></li>
-<li><a class="reference internal" href="#computes-that-generate-values-to-output">Computes that generate values to output</a></li>
-<li><a class="reference internal" href="#fixes-that-generate-values-to-output">Fixes that generate values to output</a></li>
-<li><a class="reference internal" href="#variables-that-generate-values-to-output">Variables that generate values to output</a></li>
-<li><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">Summary table of output options and data flow between commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#global-per-atom-local-data">6.15.1. Global/per-atom/local data</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#scalar-vector-array-data">6.15.2. Scalar/vector/array data</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#thermodynamic-output">6.15.3. Thermodynamic output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#dump-file-output">6.15.4. Dump file output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#fixes-that-write-output-files">6.15.5. Fixes that write output files</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#computes-that-process-output-quantities">6.15.6. Computes that process output quantities</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#fixes-that-process-output-quantities">6.15.7. Fixes that process output quantities</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#computes-that-generate-values-to-output">6.15.8. Computes that generate values to output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#fixes-that-generate-values-to-output">6.15.9. Fixes that generate values to output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#variables-that-generate-values-to-output">6.15.10. Variables that generate values to output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">6.15.11. Summary table of output options and data flow between commands</a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">Thermostatting, barostatting, and computing temperature</a></li>
-<li><a class="reference internal" href="#walls">Walls</a></li>
-<li><a class="reference internal" href="#elastic-constants">Elastic constants</a></li>
-<li><a class="reference internal" href="#library-interface-to-lammps">Library interface to LAMMPS</a></li>
-<li><a class="reference internal" href="#calculating-thermal-conductivity">Calculating thermal conductivity</a></li>
-<li><a class="reference internal" href="#calculating-viscosity">Calculating viscosity</a></li>
-<li><a class="reference internal" href="#calculating-a-diffusion-coefficient">Calculating a diffusion coefficient</a></li>
-<li><a class="reference internal" href="#using-chunks-to-calculate-system-properties">Using chunks to calculate system properties</a><ul>
-<li><a class="reference internal" href="#compute-chunk-atom-command">Compute chunk/atom command:</a></li>
-<li><a class="reference internal" href="#fix-ave-chunk-command">Fix ave/chunk command:</a></li>
-<li><a class="reference internal" href="#compute-chunk-commands">Compute */chunk commands:</a></li>
-<li><a class="reference internal" href="#example-calculations-with-chunks">Example calculations with chunks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#walls">6.17. Walls</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#elastic-constants">6.18. Elastic constants</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#calculating-viscosity">6.21. Calculating viscosity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-atom-command">6.23.1. Compute chunk/atom command:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#fix-ave-chunk-command">6.23.2. Fix ave/chunk command:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-commands">6.23.3. Compute */chunk commands:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#example-calculations-with-chunks">6.23.4. Example calculations with chunks</a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#setting-parameters-for-the-kspace-style-pppm-disp-command">Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
-<li><a class="reference internal" href="#polarizable-models">Polarizable models</a></li>
-<li><a class="reference internal" href="#adiabatic-core-shell-model">Adiabatic core/shell model</a></li>
-<li><a class="reference internal" href="#drude-induced-dipoles">Drude induced dipoles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#polarizable-models">6.25. Polarizable models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -153,7 +166,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>How-to discussions</li>
+    <li>6. How-to discussions</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -168,7 +181,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="how-to-discussions">
-<h1>How-to discussions<a class="headerlink" href="#how-to-discussions" title="Permalink to this headline">¶</a></h1>
+<h1>6. How-to discussions<a class="headerlink" href="#how-to-discussions" title="Permalink to this headline">¶</a></h1>
 <p>This section describes how to perform common tasks using LAMMPS.</p>
 <div class="line-block">
 <div class="line">6.1 <a class="reference internal" href="#howto-1"><span>Restarting a simulation</span></a></div>
@@ -204,7 +217,7 @@
 highlighted in <a class="reference internal" href="Section_example.html"><em>Section_example</em></a> also show how to
 setup and run various kinds of simulations.</p>
 <div class="section" id="restarting-a-simulation">
-<span id="howto-1"></span><h2>Restarting a simulation<a class="headerlink" href="#restarting-a-simulation" title="Permalink to this headline">¶</a></h2>
+<span id="howto-1"></span><h2>6.1. Restarting a simulation<a class="headerlink" href="#restarting-a-simulation" title="Permalink to this headline">¶</a></h2>
 <p>There are 3 ways to continue a long LAMMPS simulation.  Multiple
 <a class="reference internal" href="run.html"><em>run</em></a> commands can be used in the same input script.  Each
 run will continue from where the previous run left off.  Or binary
@@ -297,7 +310,7 @@ but not in data files.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="d-simulations">
-<span id="howto-2"></span><h2>2d simulations<a class="headerlink" href="#d-simulations" title="Permalink to this headline">¶</a></h2>
+<span id="howto-2"></span><h2>6.2. 2d simulations<a class="headerlink" href="#d-simulations" title="Permalink to this headline">¶</a></h2>
 <p>Use the <a class="reference internal" href="dimension.html"><em>dimension</em></a> command to specify a 2d simulation.</p>
 <p>Make the simulation box periodic in z via the <a class="reference internal" href="boundary.html"><em>boundary</em></a>
 command.  This is the default.</p>
@@ -329,7 +342,7 @@ the same as in 3d.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="charmm-amber-and-dreiding-force-fields">
-<span id="howto-3"></span><h2>CHARMM, AMBER, and DREIDING force fields<a class="headerlink" href="#charmm-amber-and-dreiding-force-fields" title="Permalink to this headline">¶</a></h2>
+<span id="howto-3"></span><h2>6.3. CHARMM, AMBER, and DREIDING force fields<a class="headerlink" href="#charmm-amber-and-dreiding-force-fields" title="Permalink to this headline">¶</a></h2>
 <p>A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly
@@ -391,7 +404,7 @@ documentation for the formula it computes.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="running-multiple-simulations-from-one-input-script">
-<span id="howto-4"></span><h2>Running multiple simulations from one input script<a class="headerlink" href="#running-multiple-simulations-from-one-input-script" title="Permalink to this headline">¶</a></h2>
+<span id="howto-4"></span><h2>6.4. Running multiple simulations from one input script<a class="headerlink" href="#running-multiple-simulations-from-one-input-script" title="Permalink to this headline">¶</a></h2>
 <p>This can be done in several ways.  See the documentation for
 individual commands for more details on how these examples work.</p>
 <p>If &#8220;multiple simulations&#8221; means continue a previous simulation for
@@ -474,7 +487,7 @@ the 4th simulation, and so forth, until all 8 were completed.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="multi-replica-simulations">
-<span id="howto-5"></span><h2>Multi-replica simulations<a class="headerlink" href="#multi-replica-simulations" title="Permalink to this headline">¶</a></h2>
+<span id="howto-5"></span><h2>6.5. Multi-replica simulations<a class="headerlink" href="#multi-replica-simulations" title="Permalink to this headline">¶</a></h2>
 <p>Several commands in LAMMPS run mutli-replica simulations, meaning
 that multiple instances (replicas) of your simulation are run
 simultaneously, with small amounts of data exchanged between replicas
@@ -521,7 +534,7 @@ physical processors.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="granular-models">
-<span id="howto-6"></span><h2>Granular models<a class="headerlink" href="#granular-models" title="Permalink to this headline">¶</a></h2>
+<span id="howto-6"></span><h2>6.6. Granular models<a class="headerlink" href="#granular-models" title="Permalink to this headline">¶</a></h2>
 <p>Granular system are composed of spherical particles with a diameter,
 as opposed to point particles.  This means they have an angular
 velocity and torque can be imparted to them to cause them to rotate.</p>
@@ -562,7 +575,7 @@ computations between frozen atoms by using this command:</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="tip3p-water-model">
-<span id="howto-7"></span><h2>TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline">¶</a></h2>
+<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline">¶</a></h2>
 <p>The TIP3P water model as implemented in CHARMM
 <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
@@ -614,7 +627,7 @@ details:</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="tip4p-water-model">
-<span id="howto-8"></span><h2>TIP4P water model<a class="headerlink" href="#tip4p-water-model" title="Permalink to this headline">¶</a></h2>
+<span id="howto-8"></span><h2>6.8. TIP4P water model<a class="headerlink" href="#tip4p-water-model" title="Permalink to this headline">¶</a></h2>
 <p>The four-point TIP4P rigid water model extends the traditional
 three-point TIP3P model by adding an additional site, usually
 massless, where the charge associated with the oxygen atom is placed.
@@ -710,7 +723,7 @@ and Coulombic cutoffs are set in the <a class="reference internal" href="pair_lj
 <hr class="docutils" />
 </div>
 <div class="section" id="spc-water-model">
-<span id="howto-9"></span><h2>SPC water model<a class="headerlink" href="#spc-water-model" title="Permalink to this headline">¶</a></h2>
+<span id="howto-9"></span><h2>6.9. SPC water model<a class="headerlink" href="#spc-water-model" title="Permalink to this headline">¶</a></h2>
 <p>The SPC water model specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
@@ -749,7 +762,7 @@ the SPC and SPC/E models.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="coupling-lammps-to-other-codes">
-<span id="howto-10"></span><h2>Coupling LAMMPS to other codes<a class="headerlink" href="#coupling-lammps-to-other-codes" title="Permalink to this headline">¶</a></h2>
+<span id="howto-10"></span><h2>6.10. Coupling LAMMPS to other codes<a class="headerlink" href="#coupling-lammps-to-other-codes" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS is designed to allow it to be coupled to other codes.  For
 example, a quantum mechanics code might compute forces on a subset of
 atoms and pass those forces to LAMMPS.  Or a continuum finite element
@@ -830,7 +843,7 @@ instances of LAMMPS to perform different calculations.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="visualizing-lammps-snapshots">
-<span id="howto-11"></span><h2>Visualizing LAMMPS snapshots<a class="headerlink" href="#visualizing-lammps-snapshots" title="Permalink to this headline">¶</a></h2>
+<span id="howto-11"></span><h2>6.11. Visualizing LAMMPS snapshots<a class="headerlink" href="#visualizing-lammps-snapshots" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS itself does not do visualization, but snapshots from LAMMPS
 simulations can be visualized (and analyzed) in a variety of ways.</p>
 <p>LAMMPS snapshots are created by the <a class="reference internal" href="dump.html"><em>dump</em></a> command which can
@@ -873,7 +886,7 @@ See the <a class="reference internal" href="dump.html"><em>dump</em></a> command
 <hr class="docutils" />
 </div>
 <div class="section" id="triclinic-non-orthogonal-simulation-boxes">
-<span id="howto-12"></span><h2>Triclinic (non-orthogonal) simulation boxes<a class="headerlink" href="#triclinic-non-orthogonal-simulation-boxes" title="Permalink to this headline">¶</a></h2>
+<span id="howto-12"></span><h2>6.12. Triclinic (non-orthogonal) simulation boxes<a class="headerlink" href="#triclinic-non-orthogonal-simulation-boxes" title="Permalink to this headline">¶</a></h2>
 <p>By default, LAMMPS uses an orthogonal simulation box to encompass the
 particles.  The <a class="reference internal" href="boundary.html"><em>boundary</em></a> command sets the boundary
 conditions of the box (periodic, non-periodic, etc).  The orthogonal
@@ -1051,7 +1064,7 @@ on non-equilibrium MD (NEMD) simulations.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="nemd-simulations">
-<span id="howto-13"></span><h2>NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Permalink to this headline">¶</a></h2>
+<span id="howto-13"></span><h2>6.13. NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Permalink to this headline">¶</a></h2>
 <p>Non-equilibrium molecular dynamics or NEMD simulations are typically
 used to measure a fluid&#8217;s rheological properties such as viscosity.
 In LAMMPS, such simulations can be performed by first setting up a
@@ -1081,7 +1094,7 @@ profile consistent with the applied shear strain rate.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="finite-size-spherical-and-aspherical-particles">
-<span id="howto-14"></span><h2>Finite-size spherical and aspherical particles<a class="headerlink" href="#finite-size-spherical-and-aspherical-particles" title="Permalink to this headline">¶</a></h2>
+<span id="howto-14"></span><h2>6.14. Finite-size spherical and aspherical particles<a class="headerlink" href="#finite-size-spherical-and-aspherical-particles" title="Permalink to this headline">¶</a></h2>
 <p>Typical MD models treat atoms or particles as point masses.  Sometimes
 it is desirable to have a model with finite-size particles such as
 spheroids or ellipsoids or generalized aspherical bodies.  The
@@ -1101,7 +1114,7 @@ particles.  The following aspects are discussed in turn:</p>
 colloid, dipole, ellipse, line, peri, pour, and tri directories of the
 <a class="reference internal" href="Section_example.html"><em>examples directory</em></a> in the LAMMPS distribution.</p>
 <div class="section" id="atom-styles">
-<h3>Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h3>
+<h3>6.14.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h3>
 <p>There are several <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that allow for
 definition of finite-size particles: sphere, dipole, ellipsoid, line,
 tri, peri, and body.</p>
@@ -1171,7 +1184,7 @@ object.  When temperature is computed, the correct degrees of freedom
 are used for rotation in a 2d versus 3d system.</p>
 </div>
 <div class="section" id="pair-potentials">
-<h3>Pair potentials<a class="headerlink" href="#pair-potentials" title="Permalink to this headline">¶</a></h3>
+<h3>6.14.2. Pair potentials<a class="headerlink" href="#pair-potentials" title="Permalink to this headline">¶</a></h3>
 <p>When a system with finite-size particles is defined, the particles
 will only rotate and experience torque if the force field computes
 such interactions.  These are the various <a class="reference internal" href="pair_style.html"><em>pair styles</em></a> that generate torque:</p>
@@ -1198,7 +1211,7 @@ The line, tri, and body potentials are used with line segment,
 triangular, and body particles respectively.</p>
 </div>
 <div class="section" id="time-integration">
-<h3>Time integration<a class="headerlink" href="#time-integration" title="Permalink to this headline">¶</a></h3>
+<h3>6.14.3. Time integration<a class="headerlink" href="#time-integration" title="Permalink to this headline">¶</a></h3>
 <p>There are several fixes that perform time integration on finite-size
 spherical particles, meaning the integrators update the rotational
 orientation and angular velocity or angular momentum of the particles:</p>
@@ -1233,7 +1246,7 @@ integration fixes can only be used with <a class="reference internal" href="grou
 contain finite-size particles.</p>
 </div>
 <div class="section" id="computes-thermodynamics-and-dump-output">
-<h3>Computes, thermodynamics, and dump output<a class="headerlink" href="#computes-thermodynamics-and-dump-output" title="Permalink to this headline">¶</a></h3>
+<h3>6.14.4. Computes, thermodynamics, and dump output<a class="headerlink" href="#computes-thermodynamics-and-dump-output" title="Permalink to this headline">¶</a></h3>
 <p>There are several computes that calculate the temperature or
 rotational energy of spherical or ellipsoidal particles:</p>
 <ul class="simple">
@@ -1264,7 +1277,7 @@ corner-point coordinates (for line and tri particles), and
 sub-particle attributes of body particles.</p>
 </div>
 <div class="section" id="rigid-bodies-composed-of-finite-size-particles">
-<h3>Rigid bodies composed of finite-size particles<a class="headerlink" href="#rigid-bodies-composed-of-finite-size-particles" title="Permalink to this headline">¶</a></h3>
+<h3>6.14.5. Rigid bodies composed of finite-size particles<a class="headerlink" href="#rigid-bodies-composed-of-finite-size-particles" title="Permalink to this headline">¶</a></h3>
 <p>The <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command treats a collection of
 particles as a rigid body, computes its inertia tensor, sums the total
 force and torque on the rigid body each timestep due to forces on its
@@ -1293,7 +1306,7 @@ particles are computed via a command like <a class="reference internal" href="pa
 </div>
 </div>
 <div class="section" id="output-from-lammps-thermo-dumps-computes-fixes-variables">
-<span id="howto-15"></span><h2>Output from LAMMPS (thermo, dumps, computes, fixes, variables)<a class="headerlink" href="#output-from-lammps-thermo-dumps-computes-fixes-variables" title="Permalink to this headline">¶</a></h2>
+<span id="howto-15"></span><h2>6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)<a class="headerlink" href="#output-from-lammps-thermo-dumps-computes-fixes-variables" title="Permalink to this headline">¶</a></h2>
 <p>There are four basic kinds of LAMMPS output:</p>
 <ul class="simple">
 <li><a class="reference internal" href="thermo_style.html"><em>Thermodynamic output</em></a>, which is a list
@@ -1330,7 +1343,7 @@ to output and the kind of data they operate on and produce:</p>
 <li><a class="reference internal" href="#table"><span>Summary table of output options and data flow between commands</span></a></li>
 </ul>
 <div class="section" id="global-per-atom-local-data">
-<span id="global"></span><h3>Global/per-atom/local data<a class="headerlink" href="#global-per-atom-local-data" title="Permalink to this headline">¶</a></h3>
+<span id="global"></span><h3>6.15.1. Global/per-atom/local data<a class="headerlink" href="#global-per-atom-local-data" title="Permalink to this headline">¶</a></h3>
 <p>Various output-related commands work with three different styles of
 data: global, per-atom, or local.  A global datum is one or more
 system-wide values, e.g. the temperature of the system.  A per-atom
@@ -1340,7 +1353,7 @@ atoms it owns, but there may be zero or more per atom, e.g. a list of
 bond distances.</p>
 </div>
 <div class="section" id="scalar-vector-array-data">
-<span id="scalar"></span><h3>Scalar/vector/array data<a class="headerlink" href="#scalar-vector-array-data" title="Permalink to this headline">¶</a></h3>
+<span id="scalar"></span><h3>6.15.2. Scalar/vector/array data<a class="headerlink" href="#scalar-vector-array-data" title="Permalink to this headline">¶</a></h3>
 <p>Global, per-atom, and local datums can each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The
 doc page for a &#8220;compute&#8221; or &#8220;fix&#8221; or &#8220;variable&#8221; that generates data
@@ -1374,7 +1387,7 @@ scalar values as input can typically also process elements of a vector
 or array.</p>
 </div>
 <div class="section" id="thermodynamic-output">
-<span id="thermo"></span><h3>Thermodynamic output<a class="headerlink" href="#thermodynamic-output" title="Permalink to this headline">¶</a></h3>
+<span id="thermo"></span><h3>6.15.3. Thermodynamic output<a class="headerlink" href="#thermodynamic-output" title="Permalink to this headline">¶</a></h3>
 <p>The frequency and format of thermodynamic output is set by the
 <a class="reference internal" href="thermo.html"><em>thermo</em></a>, <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>, and
 <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> commands.  The
@@ -1398,7 +1411,7 @@ formula if desired, to make an extensive calculation produce an
 intensive result.</p>
 </div>
 <div class="section" id="dump-file-output">
-<span id="dump"></span><h3>Dump file output<a class="headerlink" href="#dump-file-output" title="Permalink to this headline">¶</a></h3>
+<span id="dump"></span><h3>6.15.4. Dump file output<a class="headerlink" href="#dump-file-output" title="Permalink to this headline">¶</a></h3>
 <p>Dump file output is specified by the <a class="reference internal" href="dump.html"><em>dump</em></a> and
 <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> commands.  There are several
 pre-defined formats (dump atom, dump xtc, etc).</p>
@@ -1419,7 +1432,7 @@ must generate local values for input to the <a class="reference internal" href="
 command.</p>
 </div>
 <div class="section" id="fixes-that-write-output-files">
-<span id="fixoutput"></span><h3>Fixes that write output files<a class="headerlink" href="#fixes-that-write-output-files" title="Permalink to this headline">¶</a></h3>
+<span id="fixoutput"></span><h3>6.15.5. Fixes that write output files<a class="headerlink" href="#fixes-that-write-output-files" title="Permalink to this headline">¶</a></h3>
 <p>Several fixes take various quantities as input and can write output
 files: <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>,
 <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a>, and <a class="reference internal" href="fix_print.html"><em>fix print</em></a>.</p>
@@ -1465,7 +1478,7 @@ command is a means to output a wide variety of quantities separate
 from normal thermodynamic or dump file output.</p>
 </div>
 <div class="section" id="computes-that-process-output-quantities">
-<span id="computeoutput"></span><h3>Computes that process output quantities<a class="headerlink" href="#computes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
+<span id="computeoutput"></span><h3>6.15.6. Computes that process output quantities<a class="headerlink" href="#computes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
 <p>The <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> and <a class="reference internal" href="compute_reduce.html"><em>compute reduce/region</em></a> commands take one or more per-atom
 or local vector quantities as inputs and &#8220;reduce&#8221; them (sum, min, max,
 ave) to scalar quantities.  These are produced as output values which
@@ -1486,7 +1499,7 @@ are produced as output values which can be used as input to other
 output commands.</p>
 </div>
 <div class="section" id="fixes-that-process-output-quantities">
-<span id="id3"></span><h3>Fixes that process output quantities<a class="headerlink" href="#fixes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
+<span id="id3"></span><h3>6.15.7. Fixes that process output quantities<a class="headerlink" href="#fixes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
 <p>The <a class="reference internal" href="fix_vector.html"><em>fix vector</em></a> command can create global vectors as
 output from global scalars as input, accumulating them one element at
 a time.</p>
@@ -1506,7 +1519,7 @@ by a <a class="reference internal" href="fix.html"><em>fix</em></a>, or by an at
 The output of this fix can be used as input to other output commands.</p>
 </div>
 <div class="section" id="computes-that-generate-values-to-output">
-<span id="compute"></span><h3>Computes that generate values to output<a class="headerlink" href="#computes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
+<span id="compute"></span><h3>6.15.8. Computes that generate values to output<a class="headerlink" href="#computes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
 <p>Every <a class="reference internal" href="compute.html"><em>compute</em></a> in LAMMPS produces either global or
 per-atom or local values.  The values can be scalars or vectors or
 arrays of data.  These values can be output using the other commands
@@ -1516,7 +1529,7 @@ values have the word &#8220;atom&#8221; or &#8220;local&#8221; in their style na
 without the word &#8220;atom&#8221; or &#8220;local&#8221; produce global values.</p>
 </div>
 <div class="section" id="fixes-that-generate-values-to-output">
-<span id="fix"></span><h3>Fixes that generate values to output<a class="headerlink" href="#fixes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
+<span id="fix"></span><h3>6.15.9. Fixes that generate values to output<a class="headerlink" href="#fixes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
 <p>Some <a class="reference internal" href="fix.html"><em>fixes</em></a> in LAMMPS produces either global or per-atom or
 local values which can be accessed by other commands.  The values can
 be scalars or vectors or arrays of data.  These values can be output
@@ -1525,7 +1538,7 @@ each fix command tells whether it produces any output quantities and
 describes them.</p>
 </div>
 <div class="section" id="variables-that-generate-values-to-output">
-<span id="variable"></span><h3>Variables that generate values to output<a class="headerlink" href="#variables-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
+<span id="variable"></span><h3>6.15.10. Variables that generate values to output<a class="headerlink" href="#variables-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
 <p>Every <a class="reference internal" href="variable.html"><em>variables</em></a> defined in an input script generates
 either a global scalar value or a per-atom vector (only atom-style
 variables) when it is accessed.  The formulas used to define equal-
@@ -1535,7 +1548,7 @@ and other variables.  The values generated by variables can be output
 using the other commands described in this section.</p>
 </div>
 <div class="section" id="summary-table-of-output-options-and-data-flow-between-commands">
-<span id="table"></span><h3>Summary table of output options and data flow between commands<a class="headerlink" href="#summary-table-of-output-options-and-data-flow-between-commands" title="Permalink to this headline">¶</a></h3>
+<span id="table"></span><h3>6.15.11. Summary table of output options and data flow between commands<a class="headerlink" href="#summary-table-of-output-options-and-data-flow-between-commands" title="Permalink to this headline">¶</a></h3>
 <p>This table summarizes the various commands that can be used for
 generating output from LAMMPS.  Each command produces output data of
 some kind and/or writes data to a file.  Most of the commands can take
@@ -1667,7 +1680,7 @@ vector input could be a column of an array.</p>
 </div>
 </div>
 <div class="section" id="thermostatting-barostatting-and-computing-temperature">
-<span id="howto-16"></span><h2>Thermostatting, barostatting, and computing temperature<a class="headerlink" href="#thermostatting-barostatting-and-computing-temperature" title="Permalink to this headline">¶</a></h2>
+<span id="howto-16"></span><h2>6.16. Thermostatting, barostatting, and computing temperature<a class="headerlink" href="#thermostatting-barostatting-and-computing-temperature" title="Permalink to this headline">¶</a></h2>
 <p>Thermostatting means controlling the temperature of particles in an MD
 simulation.  Barostatting means controlling the pressure.  Since the
 pressure includes a kinetic component due to particle velocities, both
@@ -1803,7 +1816,7 @@ thermodynamic output.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="walls">
-<span id="howto-17"></span><h2>Walls<a class="headerlink" href="#walls" title="Permalink to this headline">¶</a></h2>
+<span id="howto-17"></span><h2>6.17. Walls<a class="headerlink" href="#walls" title="Permalink to this headline">¶</a></h2>
 <p>Walls in an MD simulation are typically used to bound particle motion,
 i.e. to serve as a boundary condition.</p>
 <p>Walls in LAMMPS can be of rough (made of particles) or idealized
@@ -1867,7 +1880,7 @@ frictional walls, as well as triangulated surfaces.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="elastic-constants">
-<span id="howto-18"></span><h2>Elastic constants<a class="headerlink" href="#elastic-constants" title="Permalink to this headline">¶</a></h2>
+<span id="howto-18"></span><h2>6.18. Elastic constants<a class="headerlink" href="#elastic-constants" title="Permalink to this headline">¶</a></h2>
 <p>Elastic constants characterize the stiffness of a material. The formal
 definition is provided by the linear relation that holds between the
 stress and strain tensors in the limit of infinitesimal deformation.
@@ -1899,7 +1912,7 @@ converge and requires careful post-processing <a class="reference internal" href
 <hr class="docutils" />
 </div>
 <div class="section" id="library-interface-to-lammps">
-<span id="howto-19"></span><h2>Library interface to LAMMPS<a class="headerlink" href="#library-interface-to-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="howto-19"></span><h2>6.19. Library interface to LAMMPS<a class="headerlink" href="#library-interface-to-lammps" title="Permalink to this headline">¶</a></h2>
 <p>As described in <a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>, LAMMPS
 can be built as a library, so that it can be called by another code,
 used in a <a class="reference internal" href="#howto-10"><span>coupled manner</span></a> with other
@@ -1974,7 +1987,7 @@ LAMMPS.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="calculating-thermal-conductivity">
-<span id="howto-20"></span><h2>Calculating thermal conductivity<a class="headerlink" href="#calculating-thermal-conductivity" title="Permalink to this headline">¶</a></h2>
+<span id="howto-20"></span><h2>6.20. Calculating thermal conductivity<a class="headerlink" href="#calculating-thermal-conductivity" title="Permalink to this headline">¶</a></h2>
 <p>The thermal conductivity kappa of a material can be measured in at
 least 4 ways using various options in LAMMPS.  See the examples/KAPPA
 directory for scripts that implement the 4 methods discussed here for
@@ -2028,7 +2041,7 @@ formalism.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="calculating-viscosity">
-<span id="howto-21"></span><h2>Calculating viscosity<a class="headerlink" href="#calculating-viscosity" title="Permalink to this headline">¶</a></h2>
+<span id="howto-21"></span><h2>6.21. Calculating viscosity<a class="headerlink" href="#calculating-viscosity" title="Permalink to this headline">¶</a></h2>
 <p>The shear viscosity eta of a fluid can be measured in at least 4 ways
 using various options in LAMMPS.  See the examples/VISCOSITY directory
 for scripts that implement the 4 methods discussed here for a simple
@@ -2149,7 +2162,7 @@ print        &quot;average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3&quot;
 <hr class="docutils" />
 </div>
 <div class="section" id="calculating-a-diffusion-coefficient">
-<span id="howto-22"></span><h2>Calculating a diffusion coefficient<a class="headerlink" href="#calculating-a-diffusion-coefficient" title="Permalink to this headline">¶</a></h2>
+<span id="howto-22"></span><h2>6.22. Calculating a diffusion coefficient<a class="headerlink" href="#calculating-a-diffusion-coefficient" title="Permalink to this headline">¶</a></h2>
 <p>The diffusion coefficient D of a material can be measured in at least
 2 ways using various options in LAMMPS.  See the examples/DIFFUSE
 directory for scripts that implement the 2 methods discussed here for
@@ -2171,7 +2184,7 @@ and thus extract D.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="using-chunks-to-calculate-system-properties">
-<span id="howto-23"></span><h2>Using chunks to calculate system properties<a class="headerlink" href="#using-chunks-to-calculate-system-properties" title="Permalink to this headline">¶</a></h2>
+<span id="howto-23"></span><h2>6.23. Using chunks to calculate system properties<a class="headerlink" href="#using-chunks-to-calculate-system-properties" title="Permalink to this headline">¶</a></h2>
 <p>In LAMMS, &#8220;chunks&#8221; are collections of atoms, as defined by the
 <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns
 each atom to a chunk ID (or to no chunk at all).  The number of chunks
@@ -2188,7 +2201,7 @@ commands, to calculate various properties of a system:</p>
 overviewed.  Then some examples are given of how to compute different
 properties with chunk commands.</p>
 <div class="section" id="compute-chunk-atom-command">
-<h3>Compute chunk/atom command:<a class="headerlink" href="#compute-chunk-atom-command" title="Permalink to this headline">¶</a></h3>
+<h3>6.23.1. Compute chunk/atom command:<a class="headerlink" href="#compute-chunk-atom-command" title="Permalink to this headline">¶</a></h3>
 <p>This compute can assign atoms to chunks of various styles.  Only atoms
 in the specified group and optional specified region are assigned to a
 chunk.  Here are some possible chunk definitions:</p>
@@ -2246,7 +2259,7 @@ the input script that uses a formula to generate a chunk ID for each
 atom.</p>
 </div>
 <div class="section" id="fix-ave-chunk-command">
-<h3>Fix ave/chunk command:<a class="headerlink" href="#fix-ave-chunk-command" title="Permalink to this headline">¶</a></h3>
+<h3>6.23.2. Fix ave/chunk command:<a class="headerlink" href="#fix-ave-chunk-command" title="Permalink to this headline">¶</a></h3>
 <p>This fix takes the ID of a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command as input.  For each chunk,
 it then sums one or more specified per-atom values over the atoms in
 each chunk.  The per-atom values can be any atom property, such as
@@ -2260,7 +2273,7 @@ fix produces a global array as output with one row of values per
 chunk.</p>
 </div>
 <div class="section" id="compute-chunk-commands">
-<h3>Compute <a href="#id68"><span class="problematic" id="id69">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline">¶</a></h3>
+<h3>6.23.3. Compute <a href="#id68"><span class="problematic" id="id69">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline">¶</a></h3>
 <p>Currently the following computes operate on chunks of atoms to produce
 per-chunk values.</p>
 <ul class="simple">
@@ -2297,7 +2310,7 @@ largest cluster or fastest diffusing molecule.</li>
 </ul>
 </div>
 <div class="section" id="example-calculations-with-chunks">
-<h3>Example calculations with chunks<a class="headerlink" href="#example-calculations-with-chunks" title="Permalink to this headline">¶</a></h3>
+<h3>6.23.4. Example calculations with chunks<a class="headerlink" href="#example-calculations-with-chunks" title="Permalink to this headline">¶</a></h3>
 <p>Here are eaxmples using chunk commands to calculate various
 properties:</p>
 <ol class="arabic simple">
@@ -2346,7 +2359,7 @@ fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond igno
 </div>
 </div>
 <div class="section" id="setting-parameters-for-the-kspace-style-pppm-disp-command">
-<span id="howto-24"></span><h2>Setting parameters for the <a class="reference internal" href="kspace_style.html"><em>kspace_style pppm/disp</em></a> command<a class="headerlink" href="#setting-parameters-for-the-kspace-style-pppm-disp-command" title="Permalink to this headline">¶</a></h2>
+<span id="howto-24"></span><h2>6.24. Setting parameters for the <a class="reference internal" href="kspace_style.html"><em>kspace_style pppm/disp</em></a> command<a class="headerlink" href="#setting-parameters-for-the-kspace-style-pppm-disp-command" title="Permalink to this headline">¶</a></h2>
 <p>The PPPM method computes interactions by splitting the pair potential
 into two parts, one of which is computed in a normal pairwise fashion,
 the so-called real-space part, and one of which is computed using the
@@ -2439,7 +2452,7 @@ to specify this command explicitly.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="polarizable-models">
-<span id="howto-25"></span><h2>Polarizable models<a class="headerlink" href="#polarizable-models" title="Permalink to this headline">¶</a></h2>
+<span id="howto-25"></span><h2>6.25. Polarizable models<a class="headerlink" href="#polarizable-models" title="Permalink to this headline">¶</a></h2>
 <p>In polarizable force fields the charge distributions in molecules and
 materials respond to their electrostatic environements. Polarizable
 systems can be simulated in LAMMPS using three methods:</p>
@@ -2509,7 +2522,7 @@ well.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="adiabatic-core-shell-model">
-<span id="howto-26"></span><h2>Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline">¶</a></h2>
+<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline">¶</a></h2>
 <p>The adiabatic core-shell model by <a class="reference internal" href="pair_cs.html#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding
 polarizability to a system.  In order to mimic the electron shell of
 an ion, a satellite particle is attached to it. This way the ions are
@@ -2687,7 +2700,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
 <hr class="docutils" />
 </div>
 <div class="section" id="drude-induced-dipoles">
-<span id="howto-27"></span><h2>Drude induced dipoles<a class="headerlink" href="#drude-induced-dipoles" title="Permalink to this headline">¶</a></h2>
+<span id="howto-27"></span><h2>6.27. Drude induced dipoles<a class="headerlink" href="#drude-induced-dipoles" title="Permalink to this headline">¶</a></h2>
 <p>The thermalized Drude model, similarly to the <a class="reference internal" href="#howto-26"><span>core-shell</span></a>
 model, representes induced dipoles by a pair of charges (the core atom
 and the Drude particle) connected by a harmonic spring. The Drude
@@ -2764,6 +2777,15 @@ Phys, 79, 926 (1983).</p>
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+      
+      
+        <a href="Section_accelerate.html" class="btn btn-neutral" title="5. Accelerating LAMMPS performance" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_intro.html b/doc/Section_intro.html
index 6ed9b5105a..98a0006744 100644
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Introduction &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>1. Introduction &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="2. Getting Started" href="Section_start.html"/>
+        <link rel="prev" title="LAMMPS Documentation" href="Manual.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,31 +73,42 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Introduction</a><ul>
-<li><a class="reference internal" href="#what-is-lammps">What is LAMMPS</a></li>
-<li><a class="reference internal" href="#lammps-features">LAMMPS features</a><ul>
-<li><a class="reference internal" href="#general-features">General features</a></li>
-<li><a class="reference internal" href="#particle-and-model-types">Particle and model types</a></li>
-<li><a class="reference internal" href="#force-fields">Force fields</a></li>
-<li><a class="reference internal" href="#atom-creation">Atom creation</a></li>
-<li><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">Ensembles, constraints, and boundary conditions</a></li>
-<li><a class="reference internal" href="#integrators">Integrators</a></li>
-<li><a class="reference internal" href="#diagnostics">Diagnostics</a></li>
-<li><a class="reference internal" href="#output">Output</a></li>
-<li><a class="reference internal" href="#multi-replica-models">Multi-replica models</a></li>
-<li><a class="reference internal" href="#pre-and-post-processing">Pre- and post-processing</a></li>
-<li><a class="reference internal" href="#specialized-features">Specialized features</a></li>
+              <ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="">1. Introduction</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#lammps-non-features">LAMMPS non-features</a></li>
-<li><a class="reference internal" href="#open-source-distribution">Open source distribution</a></li>
-<li><a class="reference internal" href="#acknowledgments-and-citations">Acknowledgments and citations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -118,7 +131,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Introduction</li>
+    <li>1. Introduction</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -133,7 +146,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="introduction">
-<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
+<h1>1. Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
 <p>This section provides an overview of what LAMMPS can and can&#8217;t do,
 describes what it means for LAMMPS to be an open-source code, and
 acknowledges the funding and people who have contributed to LAMMPS
@@ -147,7 +160,7 @@ over the years.</p>
 <div class="line"><br /></div>
 </div>
 <div class="section" id="what-is-lammps">
-<span id="intro-1"></span><h2>What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="intro-1"></span><h2>1.1. What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS is a classical molecular dynamics code that models an ensemble
 of particles in a liquid, solid, or gaseous state.  It can model
 atomic, polymeric, biological, metallic, granular, and coarse-grained
@@ -198,14 +211,14 @@ LAMMPS are listed in <a class="reference internal" href="#intro-5"><span>this se
 <hr class="docutils" />
 </div>
 <div class="section" id="lammps-features">
-<span id="intro-2"></span><h2>LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline">¶</a></h2>
+<span id="intro-2"></span><h2>1.2. LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline">¶</a></h2>
 <p>This section highlights LAMMPS features, with pointers to specific
 commands which give more details.  If LAMMPS doesn&#8217;t have your
 favorite interatomic potential, boundary condition, or atom type, see
 <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a>, which describes how you can add
 it to LAMMPS.</p>
 <div class="section" id="general-features">
-<h3>General features<a class="headerlink" href="#general-features" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.1. General features<a class="headerlink" href="#general-features" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li>runs on a single processor or in parallel</li>
 <li>distributed-memory message-passing parallelism (MPI)</li>
@@ -224,7 +237,7 @@ it to LAMMPS.</p>
 </ul>
 </div>
 <div class="section" id="particle-and-model-types">
-<h3>Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.2. Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline">¶</a></h3>
 <p>(<a class="reference internal" href="atom_style.html"><em>atom style</em></a> command)</p>
 <ul class="simple">
 <li>atoms</li>
@@ -242,7 +255,7 @@ it to LAMMPS.</p>
 </ul>
 </div>
 <div class="section" id="force-fields">
-<h3>Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.3. Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline">¶</a></h3>
 <p>(<a class="reference internal" href="pair_style.html"><em>pair style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond style</em></a>,
 <a class="reference internal" href="angle_style.html"><em>angle style</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral style</em></a>,
 <a class="reference internal" href="improper_style.html"><em>improper style</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace style</em></a>
@@ -271,7 +284,7 @@ commands)</p>
 </ul>
 </div>
 <div class="section" id="atom-creation">
-<h3>Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.4. Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline">¶</a></h3>
 <p>(<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="lattice.html"><em>lattice</em></a>,
 <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>,
 <a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>, <a class="reference internal" href="replicate.html"><em>replicate</em></a> commands)</p>
@@ -284,7 +297,7 @@ commands)</p>
 </ul>
 </div>
 <div class="section" id="ensembles-constraints-and-boundary-conditions">
-<h3>Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.5. Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline">¶</a></h3>
 <p>(<a class="reference internal" href="fix.html"><em>fix</em></a> command)</p>
 <ul class="simple">
 <li>2d or 3d systems</li>
@@ -304,7 +317,7 @@ commands)</p>
 </ul>
 </div>
 <div class="section" id="integrators">
-<h3>Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.6. Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline">¶</a></h3>
 <p>(<a class="reference internal" href="run.html"><em>run</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>, <a class="reference internal" href="minimize.html"><em>minimize</em></a> commands)</p>
 <ul class="simple">
 <li>velocity-Verlet integrator</li>
@@ -316,13 +329,13 @@ commands)</p>
 </ul>
 </div>
 <div class="section" id="diagnostics">
-<h3>Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.7. Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li>see the various flavors of the <a class="reference internal" href="fix.html"><em>fix</em></a> and <a class="reference internal" href="compute.html"><em>compute</em></a> commands</li>
 </ul>
 </div>
 <div class="section" id="output">
-<h3>Output<a class="headerlink" href="#output" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.8. Output<a class="headerlink" href="#output" title="Permalink to this headline">¶</a></h3>
 <p>(<a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="restart.html"><em>restart</em></a> commands)</p>
 <ul class="simple">
 <li>log file of thermodynamic info</li>
@@ -337,14 +350,14 @@ commands)</p>
 </ul>
 </div>
 <div class="section" id="multi-replica-models">
-<h3>Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.9. Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline">¶</a></h3>
 <p><a class="reference internal" href="neb.html"><em>nudged elastic band</em></a>
 <a class="reference internal" href="prd.html"><em>parallel replica dynamics</em></a>
 <a class="reference internal" href="tad.html"><em>temperature accelerated dynamics</em></a>
 <a class="reference internal" href="temper.html"><em>parallel tempering</em></a></p>
 </div>
 <div class="section" id="pre-and-post-processing">
-<h3>Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.10. Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li>Various pre- and post-processing serial tools are packaged
 with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><em>doc pages</em></a>.</li>
@@ -355,7 +368,7 @@ written in <a class="reference external" href="http://www.python.org">Python</a>
 </ul>
 </div>
 <div class="section" id="specialized-features">
-<h3>Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline">¶</a></h3>
+<h3>1.2.11. Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline">¶</a></h3>
 <p>These are LAMMPS capabilities which you may not think of as typical
 molecular dynamics options:</p>
 <ul class="simple">
@@ -379,7 +392,7 @@ molecular dynamics options:</p>
 </div>
 </div>
 <div class="section" id="lammps-non-features">
-<span id="intro-3"></span><h2>LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline">¶</a></h2>
+<span id="intro-3"></span><h2>1.3. LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS is designed to efficiently compute Newton&#8217;s equations of motion
 for a system of interacting particles.  Many of the tools needed to
 pre- and post-process the data for such simulations are not included
@@ -472,7 +485,7 @@ spatial-decomposition version exist.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="open-source-distribution">
-<span id="intro-4"></span><h2>Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline">¶</a></h2>
+<span id="intro-4"></span><h2>1.4. Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS comes with no warranty of any kind.  As each source file states
 in its header, it is a copyrighted code that is distributed free-of-
 charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL).  This
@@ -534,7 +547,7 @@ encouraged.</li>
 <hr class="docutils" />
 </div>
 <div class="section" id="acknowledgments-and-citations">
-<span id="intro-5"></span><h2>Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline">¶</a></h2>
+<span id="intro-5"></span><h2>1.5. Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
 programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
 <p>Specifically, work on the latest version was funded in part by the US
@@ -603,6 +616,15 @@ version of LAMMPS were the following:</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_start.html" class="btn btn-neutral float-right" title="2. Getting Started" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Manual.html" class="btn btn-neutral" title="LAMMPS Documentation" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_modify.html b/doc/Section_modify.html
index eeeb2c581f..60948b933a 100644
--- a/doc/Section_modify.html
+++ b/doc/Section_modify.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Modifying &amp; extending LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="11. Python interface to LAMMPS" href="Section_python.html"/>
+        <link rel="prev" title="9. Additional tools" href="Section_tools.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,28 +73,39 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Modifying &amp; extending LAMMPS</a><ul>
-<li><a class="reference internal" href="#atom-styles">Atom styles</a></li>
-<li><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">Bond, angle, dihedral, improper potentials</a></li>
-<li><a class="reference internal" href="#compute-styles">Compute styles</a></li>
-<li><a class="reference internal" href="#dump-styles">Dump styles</a></li>
-<li><a class="reference internal" href="#dump-custom-output-options">Dump custom output options</a></li>
-<li><a class="reference internal" href="#fix-styles">Fix styles</a></li>
-<li><a class="reference internal" href="#input-script-commands">Input script commands</a></li>
-<li><a class="reference internal" href="#kspace-computations">Kspace computations</a></li>
-<li><a class="reference internal" href="#minimization-styles">Minimization styles</a></li>
-<li><a class="reference internal" href="#pairwise-potentials">Pairwise potentials</a></li>
-<li><a class="reference internal" href="#region-styles">Region styles</a></li>
-<li><a class="reference internal" href="#body-styles">Body styles</a></li>
-<li><a class="reference internal" href="#thermodynamic-output-options">Thermodynamic output options</a></li>
-<li><a class="reference internal" href="#variable-options">Variable options</a></li>
-<li><a class="reference internal" href="#submitting-new-features-for-inclusion-in-lammps">Submitting new features for inclusion in LAMMPS</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">10. Modifying &amp; extending LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#atom-styles">10.1. Atom styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#compute-styles">10.3. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#dump-styles">10.4. Dump styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#dump-custom-output-options">10.5. Dump custom output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#fix-styles">10.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#input-script-commands">10.7. Input script commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#kspace-computations">10.8. Kspace computations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#minimization-styles">10.9. Minimization styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pairwise-potentials">10.10. Pairwise potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#region-styles">10.11. Region styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#body-styles">10.12. Body styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#variable-options">10.14. Variable options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -115,7 +128,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Modifying &amp; extending LAMMPS</li>
+    <li>10. Modifying &amp; extending LAMMPS</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -130,7 +143,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="modifying-extending-lammps">
-<h1>Modifying &amp; extending LAMMPS<a class="headerlink" href="#modifying-extending-lammps" title="Permalink to this headline">¶</a></h1>
+<h1>10. Modifying &amp; extending LAMMPS<a class="headerlink" href="#modifying-extending-lammps" title="Permalink to this headline">¶</a></h1>
 <p>This section describes how to customize LAMMPS by modifying
 and extending its source code.</p>
 <div class="line-block">
@@ -240,7 +253,7 @@ interested in adding it to the LAMMPS distribution.  See further
 details on this at the bottom of this page.</li>
 </ul>
 <div class="section" id="atom-styles">
-<span id="mod-1"></span><h2>Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-1"></span><h2>10.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h2>
 <p>Classes that define an <a class="reference internal" href="atom_style.html"><em>atom style</em></a> are derived from
 the AtomVec class and managed by the Atom class.  The atom style
 determines what attributes are associated with an atom.  A new atom
@@ -387,7 +400,7 @@ which store the attributes of individual atoms.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="bond-angle-dihedral-improper-potentials">
-<span id="mod-2"></span><h2>Bond, angle, dihedral, improper potentials<a class="headerlink" href="#bond-angle-dihedral-improper-potentials" title="Permalink to this headline">¶</a></h2>
+<span id="mod-2"></span><h2>10.2. Bond, angle, dihedral, improper potentials<a class="headerlink" href="#bond-angle-dihedral-improper-potentials" title="Permalink to this headline">¶</a></h2>
 <p>Classes that compute molecular interactions are derived from the Bond,
 Angle, Dihedral, and Improper classes.  New styles can be created to
 add new potentials to LAMMPS.</p>
@@ -438,7 +451,7 @@ for details and specific additional methods.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="compute-styles">
-<span id="mod-3"></span><h2>Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-3"></span><h2>10.3. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
 <p>Classes that compute scalar and vector quantities like temperature
 and the pressure tensor, as well as classes that compute per-atom
 quantities like kinetic energy and the centro-symmetry parameter
@@ -505,10 +518,10 @@ class.  See compute.h for details.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="dump-styles">
-<span id="mod-4"></span><h2>Dump styles<a class="headerlink" href="#dump-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-4"></span><h2>10.4. Dump styles<a class="headerlink" href="#dump-styles" title="Permalink to this headline">¶</a></h2>
 </div>
 <div class="section" id="dump-custom-output-options">
-<span id="mod-5"></span><h2>Dump custom output options<a class="headerlink" href="#dump-custom-output-options" title="Permalink to this headline">¶</a></h2>
+<span id="mod-5"></span><h2>10.5. Dump custom output options<a class="headerlink" href="#dump-custom-output-options" title="Permalink to this headline">¶</a></h2>
 <p>Classes that dump per-atom info to files are derived from the Dump
 class.  To dump new quantities or in a new format, a new derived dump
 class can be added, but it is typically simpler to modify the
@@ -547,7 +560,7 @@ half-dozen or so locations where code will need to be added.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="fix-styles">
-<span id="mod-6"></span><h2>Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-6"></span><h2>10.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
 <p>In LAMMPS, a &#8220;fix&#8221; is any operation that is computed during
 timestepping that alters some property of the system.  Essentially
 everything that happens during a simulation besides force computation,
@@ -755,7 +768,7 @@ quantities and/or to be summed to the potential energy of the system.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="input-script-commands">
-<span id="mod-7"></span><h2>Input script commands<a class="headerlink" href="#input-script-commands" title="Permalink to this headline">¶</a></h2>
+<span id="mod-7"></span><h2>10.7. Input script commands<a class="headerlink" href="#input-script-commands" title="Permalink to this headline">¶</a></h2>
 <p>New commands can be added to LAMMPS input scripts by adding new
 classes that have a &#8220;command&#8221; method.  For example, the create_atoms,
 read_data, velocity, and run commands are all implemented in this
@@ -781,7 +794,7 @@ needed.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="kspace-computations">
-<span id="mod-8"></span><h2>Kspace computations<a class="headerlink" href="#kspace-computations" title="Permalink to this headline">¶</a></h2>
+<span id="mod-8"></span><h2>10.8. Kspace computations<a class="headerlink" href="#kspace-computations" title="Permalink to this headline">¶</a></h2>
 <p>Classes that compute long-range Coulombic interactions via K-space
 representations (Ewald, PPPM) are derived from the KSpace class.  New
 styles can be created to add new K-space options to LAMMPS.</p>
@@ -811,7 +824,7 @@ class.  See kspace.h for details.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="minimization-styles">
-<span id="mod-9"></span><h2>Minimization styles<a class="headerlink" href="#minimization-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-9"></span><h2>10.9. Minimization styles<a class="headerlink" href="#minimization-styles" title="Permalink to this headline">¶</a></h2>
 <p>Classes that perform energy minimization derived from the Min class.
 New styles can be created to add new minimization algorithms to
 LAMMPS.</p>
@@ -838,7 +851,7 @@ class.  See min.h for details.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="pairwise-potentials">
-<span id="mod-10"></span><h2>Pairwise potentials<a class="headerlink" href="#pairwise-potentials" title="Permalink to this headline">¶</a></h2>
+<span id="mod-10"></span><h2>10.10. Pairwise potentials<a class="headerlink" href="#pairwise-potentials" title="Permalink to this headline">¶</a></h2>
 <p>Classes that compute pairwise interactions are derived from the Pair
 class.  In LAMMPS, pairwise calculation include manybody potentials
 such as EAM or Tersoff where particles interact without a static bond
@@ -886,7 +899,7 @@ includes some optional methods to enable its use with rRESPA.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="region-styles">
-<span id="mod-11"></span><h2>Region styles<a class="headerlink" href="#region-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-11"></span><h2>10.11. Region styles<a class="headerlink" href="#region-styles" title="Permalink to this headline">¶</a></h2>
 <p>Classes that define geometric regions are derived from the Region
 class.  Regions are used elsewhere in LAMMPS to group atoms, delete
 atoms to create a void, insert atoms in a specified region, etc.  New
@@ -908,7 +921,7 @@ class.  See region.h for details.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="body-styles">
-<span id="mod-12"></span><h2>Body styles<a class="headerlink" href="#body-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-12"></span><h2>10.12. Body styles<a class="headerlink" href="#body-styles" title="Permalink to this headline">¶</a></h2>
 <p>Classes that define body particles are derived from the Body class.
 Body particles can represent complex entities, such as surface meshes
 of discrete points, collections of sub-particles, deformable objects,
@@ -956,7 +969,7 @@ class.  See body.h for details.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="thermodynamic-output-options">
-<span id="mod-13"></span><h2>Thermodynamic output options<a class="headerlink" href="#thermodynamic-output-options" title="Permalink to this headline">¶</a></h2>
+<span id="mod-13"></span><h2>10.13. Thermodynamic output options<a class="headerlink" href="#thermodynamic-output-options" title="Permalink to this headline">¶</a></h2>
 <p>There is one class that computes and prints thermodynamic information
 to the screen and log file; see the file thermo.cpp.</p>
 <p>There are two styles defined in thermo.cpp: &#8220;one&#8221; and &#8220;multi&#8221;.  There
@@ -980,7 +993,7 @@ by adding a new keyword to the thermo command.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="variable-options">
-<span id="mod-14"></span><h2>Variable options<a class="headerlink" href="#variable-options" title="Permalink to this headline">¶</a></h2>
+<span id="mod-14"></span><h2>10.14. Variable options<a class="headerlink" href="#variable-options" title="Permalink to this headline">¶</a></h2>
 <p>There is one class that computes and stores <a class="reference internal" href="variable.html"><em>variable</em></a>
 information in LAMMPS; see the file variable.cpp.  The value
 associated with a variable can be periodically printed to the screen
@@ -1014,7 +1027,7 @@ then be accessed by variables) was discussed
 <a class="reference internal" href="Section_howto.html#compute"><span>here</span></a> on this page.</p>
 </div>
 <div class="section" id="submitting-new-features-for-inclusion-in-lammps">
-<span id="mod-15"></span><h2>Submitting new features for inclusion in LAMMPS<a class="headerlink" href="#submitting-new-features-for-inclusion-in-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="mod-15"></span><h2>10.15. Submitting new features for inclusion in LAMMPS<a class="headerlink" href="#submitting-new-features-for-inclusion-in-lammps" title="Permalink to this headline">¶</a></h2>
 <p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  If they are broadly useful we may add them as core files to
@@ -1152,6 +1165,15 @@ feature.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_python.html" class="btn btn-neutral float-right" title="11. Python interface to LAMMPS" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_tools.html" class="btn btn-neutral" title="9. Additional tools" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index 6d903eb0b3..e87a45ca53 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Packages &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>4. Packages &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
+        <link rel="prev" title="3. Commands" href="Section_commands.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,34 +73,45 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Packages</a><ul>
-<li><a class="reference internal" href="#standard-packages">Standard packages</a></li>
-<li><a class="reference internal" href="#user-packages">User packages</a></li>
-<li><a class="reference internal" href="#user-atc-package">USER-ATC package</a></li>
-<li><a class="reference internal" href="#user-awpmd-package">USER-AWPMD package</a></li>
-<li><a class="reference internal" href="#user-cg-cmm-package">USER-CG-CMM package</a></li>
-<li><a class="reference internal" href="#user-colvars-package">USER-COLVARS package</a></li>
-<li><a class="reference internal" href="#user-cuda-package">USER-CUDA package</a></li>
-<li><a class="reference internal" href="#user-diffraction-package">USER-DIFFRACTION package</a></li>
-<li><a class="reference internal" href="#user-drude-package">USER-DRUDE package</a></li>
-<li><a class="reference internal" href="#user-eff-package">USER-EFF package</a></li>
-<li><a class="reference internal" href="#user-fep-package">USER-FEP package</a></li>
-<li><a class="reference internal" href="#user-intel-package">USER-INTEL package</a></li>
-<li><a class="reference internal" href="#user-lb-package">USER-LB package</a></li>
-<li><a class="reference internal" href="#user-misc-package">USER-MISC package</a></li>
-<li><a class="reference internal" href="#user-molfile-package">USER-MOLFILE package</a></li>
-<li><a class="reference internal" href="#user-omp-package">USER-OMP package</a></li>
-<li><a class="reference internal" href="#user-phonon-package">USER-PHONON package</a></li>
-<li><a class="reference internal" href="#user-qmmm-package">USER-QMMM package</a></li>
-<li><a class="reference internal" href="#user-qtb-package">USER-QTB package</a></li>
-<li><a class="reference internal" href="#user-reaxc-package">USER-REAXC package</a></li>
-<li><a class="reference internal" href="#user-sph-package">USER-SPH package</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">4. Packages</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.3. USER-ATC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.4. USER-AWPMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.6. USER-COLVARS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.7. USER-CUDA package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.9. USER-DRUDE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.10. USER-EFF package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.11. USER-FEP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.12. USER-INTEL package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.13. USER-LB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.14. USER-MISC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.15. USER-MOLFILE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.16. USER-OMP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.17. USER-PHONON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.18. USER-QMMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.19. USER-QTB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.20. USER-REAXC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.21. USER-SPH package</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -121,7 +134,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Packages</li>
+    <li>4. Packages</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -136,7 +149,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="packages">
-<h1>Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
+<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
 <p>This section gives a quick overview of the add-on packages that extend
 LAMMPS functionality.</p>
 <div class="line-block">
@@ -157,7 +170,7 @@ between standard packages and user packages in LAMMPS.</p>
 standard packages, just a one-line description is given.  For user
 packages, more details are provided.</p>
 <div class="section" id="standard-packages">
-<span id="pkg-1"></span><h2>Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-1"></span><h2>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
 <p>The current list of standard packages is as follows:</p>
 <table border="1" class="docutils">
 <colgroup>
@@ -539,7 +552,7 @@ info on where to download the library.  <a class="reference internal" href="Sect
 on how to build LAMMPS with both kinds of auxiliary libraries.</p>
 </div>
 <div class="section" id="user-packages">
-<span id="pkg-2"></span><h2>User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-2"></span><h2>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
 <p>The current list of user-contributed packages is as follows:</p>
 <table border="1" class="docutils">
 <colgroup>
@@ -863,7 +876,7 @@ below.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-atc-package">
-<h2>USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.3. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
 <p>This package implements a &#8220;fix atc&#8221; command which can be used in a
 LAMMPS input script.  This fix can be employed to either do concurrent
 coupling of MD with FE-based physics surrogates or on-the-fly
@@ -883,7 +896,7 @@ you have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-awpmd-package">
-<h2>USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.4. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains a LAMMPS implementation of the Antisymmetrized
 Wave Packet Molecular Dynamics (AWPMD) method.</p>
 <p>See the doc page for the pair_style awpmd/cut command to get started.</p>
@@ -898,7 +911,7 @@ have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-cg-cmm-package">
-<h2>USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.5. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
 <p>This package implements 3 commands which can be used in a LAMMPS input
 script:</p>
 <ul class="simple">
@@ -933,7 +946,7 @@ simulation systems.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-colvars-package">
-<h2>USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.6. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
 <p>This package implements the &#8220;fix colvars&#8221; command which can be
 used in a LAMMPS input script.</p>
 <p>This fix allows to use &#8220;collective variables&#8221; to implement
@@ -962,7 +975,7 @@ beta quality.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-cuda-package">
-<h2>USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.7. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
 <p>This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
 GPUs.</p>
@@ -980,7 +993,7 @@ tu-ilmenau.de).  Contact him directly if you have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-diffraction-package">
-<h2>USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.8. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains the commands neeed to calculate x-ray and
 electron diffraction intensities based on kinematic diffraction
 theory.</p>
@@ -996,7 +1009,7 @@ Arkansas.  Contact him directly if you have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-drude-package">
-<h2>USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.9. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
 <p>This package implements methods for simulating polarizable systems
 in LAMMPS using thermalized Drude oscillators.</p>
 <p>See these doc pages and their related commands to get started:</p>
@@ -1016,7 +1029,7 @@ Agilio Padua.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-eff-package">
-<h2>USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.10. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains a LAMMPS implementation of the electron Force
 Field (eFF) currently under development at Caltech, as described in
 A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@@ -1050,7 +1063,7 @@ have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-fep-package">
-<h2>USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.11. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
 <p>This package provides methods for performing free energy perturbation
 simulations with soft-core pair potentials in LAMMPS.</p>
 <p>See these doc pages and their related commands to get started:</p>
@@ -1065,7 +1078,7 @@ Contact him directly if you have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-intel-package">
-<h2>USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
 <p>This package provides options for performing neighbor list and
 non-bonded force calculations in single, mixed, or double precision
 and also a capability for accelerating calculations with an
@@ -1077,7 +1090,7 @@ Intel(R) Xeon Phi(TM) coprocessor.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-lb-package">
-<h2>USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.13. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains a LAMMPS implementation of a background
 Lattice-Boltzmann fluid, which can be used to model MD particles
 influenced by hydrodynamic forces.</p>
@@ -1089,7 +1102,7 @@ Western Ontario.  Contact them directly if you have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-misc-package">
-<h2>USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.14. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
 <p>The files in this package are a potpourri of (mostly) unrelated
 features contributed to LAMMPS by users.  Each feature is a single
 pair of files (<a href="#id3"><span class="problematic" id="id4">*</span></a>.cpp and <a href="#id5"><span class="problematic" id="id6">*</span></a>.h).</p>
@@ -1106,7 +1119,7 @@ about the feature or its coding.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-molfile-package">
-<h2>USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.15. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
 <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
@@ -1125,7 +1138,7 @@ application itself.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-omp-package">
-<h2>USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.16. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
 <p>This package provides OpenMP multi-threading support and
 other optimizations of various LAMMPS pair styles, dihedral
 styles, and fix styles.</p>
@@ -1136,7 +1149,7 @@ styles, and fix styles.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-phonon-package">
-<h2>USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.17. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains a fix phonon command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.</p>
@@ -1148,7 +1161,7 @@ if you have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-qmmm-package">
-<h2>USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.18. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
 <p>This package provides a fix qmmm command which allows LAMMPS to be
 used in a QM/MM simulation, currently only in combination with pw.x
 code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
@@ -1165,7 +1178,7 @@ without changes to LAMMPS itself.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-qtb-package">
-<h2>USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.19. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
 <p>This package provides a self-consistent quantum treatment of the
 vibrational modes in a classical molecular dynamics simulation.  By
 coupling the MD simulation to a colored thermostat, it introduces zero
@@ -1187,7 +1200,7 @@ have questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-reaxc-package">
-<h2>USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.20. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
 <p>This package contains a implementation for LAMMPS of the ReaxFF force
 field.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
@@ -1215,7 +1228,7 @@ questions.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="user-sph-package">
-<h2>USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.21. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
 <p>This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:</p>
 <ul class="simple">
@@ -1242,6 +1255,15 @@ you have questions.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_accelerate.html" class="btn btn-neutral float-right" title="5. Accelerating LAMMPS performance" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_commands.html" class="btn btn-neutral" title="3. Commands" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_perf.html b/doc/Section_perf.html
index e656585da6..7ca825c2d8 100644
--- a/doc/Section_perf.html
+++ b/doc/Section_perf.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Performance &amp; scalability &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>8. Performance &amp; scalability &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="9. Additional tools" href="Section_tools.html"/>
+        <link rel="prev" title="7. Example problems" href="Section_example.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,11 +73,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Performance &amp; scalability</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -98,7 +111,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Performance &amp; scalability</li>
+    <li>8. Performance &amp; scalability</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -113,7 +126,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="performance-scalability">
-<h1>Performance &amp; scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline">¶</a></h1>
+<h1>8. Performance &amp; scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline">¶</a></h1>
 <p>LAMMPS performance on several prototypical benchmarks and machines is
 discussed on the Benchmarks page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where
 CPU timings and parallel efficiencies are listed.  Here, the
@@ -212,6 +225,15 @@ on 1500 processors that ran at 85% parallel efficiency.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_tools.html" class="btn btn-neutral float-right" title="9. Additional tools" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_example.html" class="btn btn-neutral" title="7. Example problems" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_python.html b/doc/Section_python.html
index ed550b5565..ae99204158 100644
--- a/doc/Section_python.html
+++ b/doc/Section_python.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Python interface to LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>11. Python interface to LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="12. Errors" href="Section_errors.html"/>
+        <link rel="prev" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,26 +73,37 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Python interface to LAMMPS</a><ul>
-<li><a class="reference internal" href="#overview-of-running-lammps-from-python">Overview of running LAMMPS from Python</a></li>
-<li><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">Overview of using Python from a LAMMPS script</a></li>
-<li><a class="reference internal" href="#building-lammps-as-a-shared-library">Building LAMMPS as a shared library</a></li>
-<li><a class="reference internal" href="#installing-the-python-wrapper-into-python">Installing the Python wrapper into Python</a></li>
-<li><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">Extending Python with MPI to run in parallel</a></li>
-<li><a class="reference internal" href="#testing-the-python-lammps-interface">Testing the Python-LAMMPS interface</a><ul>
-<li><a class="reference internal" href="#test-lammps-and-python-in-serial"><strong>Test LAMMPS and Python in serial:</strong></a></li>
-<li><a class="reference internal" href="#test-lammps-and-python-in-parallel"><strong>Test LAMMPS and Python in parallel:</strong></a></li>
-<li><a class="reference internal" href="#running-python-scripts"><strong>Running Python scripts:</strong></a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">11. Python interface to LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-serial">11.6.1. <strong>Test LAMMPS and Python in serial:</strong></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-parallel">11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#running-python-scripts">11.6.3. <strong>Running Python scripts:</strong></a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#using-lammps-from-python">Using LAMMPS from Python</a></li>
-<li><a class="reference internal" href="#example-python-scripts-that-use-lammps">Example Python scripts that use LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -113,7 +126,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Python interface to LAMMPS</li>
+    <li>11. Python interface to LAMMPS</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -128,7 +141,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="python-interface-to-lammps">
-<h1>Python interface to LAMMPS<a class="headerlink" href="#python-interface-to-lammps" title="Permalink to this headline">¶</a></h1>
+<h1>11. Python interface to LAMMPS<a class="headerlink" href="#python-interface-to-lammps" title="Permalink to this headline">¶</a></h1>
 <p>LAMMPS can work together with Python in two ways.  First, Python can
 wrap LAMMPS through the <a class="reference internal" href="Section_howto.html#howto-19"><span>LAMMPS library interface</span></a>, so that a Python script can
 create one or more instances of LAMMPS and launch one or more
@@ -174,7 +187,7 @@ interesting Python functions that can be called from a LAMMPS input
 script, that you think would be useful to other users, please <a class="reference external" href="http://lammps.sandia.gov/authors.html">email them to the developers</a>.  We can
 include them in the LAMMPS distribution.</p>
 <div class="section" id="overview-of-running-lammps-from-python">
-<span id="py-1"></span><h2>Overview of running LAMMPS from Python<a class="headerlink" href="#overview-of-running-lammps-from-python" title="Permalink to this headline">¶</a></h2>
+<span id="py-1"></span><h2>11.1. Overview of running LAMMPS from Python<a class="headerlink" href="#overview-of-running-lammps-from-python" title="Permalink to this headline">¶</a></h2>
 <p>The LAMMPS distribution includes a python directory with all you need
 to run LAMMPS from Python.  The python/lammps.py file wraps the LAMMPS
 library interface, with one wrapper function per LAMMPS library
@@ -214,7 +227,7 @@ check which version of Python you have installed, by simply typing
 <hr class="docutils" />
 </div>
 <div class="section" id="overview-of-using-python-from-a-lammps-script">
-<span id="py-2"></span><h2>Overview of using Python from a LAMMPS script<a class="headerlink" href="#overview-of-using-python-from-a-lammps-script" title="Permalink to this headline">¶</a></h2>
+<span id="py-2"></span><h2>11.2. Overview of using Python from a LAMMPS script<a class="headerlink" href="#overview-of-using-python-from-a-lammps-script" title="Permalink to this headline">¶</a></h2>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">It is not currently possible to use the
@@ -275,7 +288,7 @@ file and the shared library.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="building-lammps-as-a-shared-library">
-<span id="py-3"></span><h2>Building LAMMPS as a shared library<a class="headerlink" href="#building-lammps-as-a-shared-library" title="Permalink to this headline">¶</a></h2>
+<span id="py-3"></span><h2>11.3. Building LAMMPS as a shared library<a class="headerlink" href="#building-lammps-as-a-shared-library" title="Permalink to this headline">¶</a></h2>
 <p>Instructions on how to build LAMMPS as a shared library are given in
 <a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>.  A shared library is one
 that is dynamically loadable, which is what Python requires to wrap
@@ -297,7 +310,7 @@ system.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="installing-the-python-wrapper-into-python">
-<span id="py-4"></span><h2>Installing the Python wrapper into Python<a class="headerlink" href="#installing-the-python-wrapper-into-python" title="Permalink to this headline">¶</a></h2>
+<span id="py-4"></span><h2>11.4. Installing the Python wrapper into Python<a class="headerlink" href="#installing-the-python-wrapper-into-python" title="Permalink to this headline">¶</a></h2>
 <p>For Python to invoke LAMMPS, there are 2 files it needs to know about:</p>
 <ul class="simple">
 <li>python/lammps.py</li>
@@ -359,7 +372,7 @@ environment variable as described above.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="extending-python-with-mpi-to-run-in-parallel">
-<span id="py-5"></span><h2>Extending Python with MPI to run in parallel<a class="headerlink" href="#extending-python-with-mpi-to-run-in-parallel" title="Permalink to this headline">¶</a></h2>
+<span id="py-5"></span><h2>11.5. Extending Python with MPI to run in parallel<a class="headerlink" href="#extending-python-with-mpi-to-run-in-parallel" title="Permalink to this headline">¶</a></h2>
 <p>If you wish to run LAMMPS in parallel from Python, you need to extend
 your Python with an interface to MPI.  This also allows you to
 make MPI calls directly from Python in your script, if you desire.</p>
@@ -445,7 +458,7 @@ the right one.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="testing-the-python-lammps-interface">
-<span id="py-6"></span><h2>Testing the Python-LAMMPS interface<a class="headerlink" href="#testing-the-python-lammps-interface" title="Permalink to this headline">¶</a></h2>
+<span id="py-6"></span><h2>11.6. Testing the Python-LAMMPS interface<a class="headerlink" href="#testing-the-python-lammps-interface" title="Permalink to this headline">¶</a></h2>
 <p>To test if LAMMPS is callable from Python, launch Python interactively
 and type:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
@@ -472,7 +485,7 @@ first importing from the lammps.py file:</p>
 library and about insuring Python can find the necessary two files
 it needs.</p>
 <div class="section" id="test-lammps-and-python-in-serial">
-<h3><strong>Test LAMMPS and Python in serial:</strong><a class="headerlink" href="#test-lammps-and-python-in-serial" title="Permalink to this headline">¶</a></h3>
+<h3>11.6.1. <strong>Test LAMMPS and Python in serial:</strong><a class="headerlink" href="#test-lammps-and-python-in-serial" title="Permalink to this headline">¶</a></h3>
 <p>To run a LAMMPS test in serial, type these lines into Python
 interactively from the bench directory:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
@@ -492,7 +505,7 @@ typed something like:</p>
 </div>
 </div>
 <div class="section" id="test-lammps-and-python-in-parallel">
-<h3><strong>Test LAMMPS and Python in parallel:</strong><a class="headerlink" href="#test-lammps-and-python-in-parallel" title="Permalink to this headline">¶</a></h3>
+<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong><a class="headerlink" href="#test-lammps-and-python-in-parallel" title="Permalink to this headline">¶</a></h3>
 <p>To run LAMMPS in parallel, assuming you have installed the
 <a class="reference external" href="http://datamining.anu.edu.au/~ole/pypar">Pypar</a> package as discussed
 above, create a test.py file containing these lines:</p>
@@ -526,7 +539,7 @@ script should be pypar.finalize(), to insure MPI is shut down
 correctly.</p>
 </div>
 <div class="section" id="running-python-scripts">
-<h3><strong>Running Python scripts:</strong><a class="headerlink" href="#running-python-scripts" title="Permalink to this headline">¶</a></h3>
+<h3>11.6.3. <strong>Running Python scripts:</strong><a class="headerlink" href="#running-python-scripts" title="Permalink to this headline">¶</a></h3>
 <p>Note that any Python script (not just for LAMMPS) can be invoked in
 one of several ways:</p>
 <div class="highlight-python"><div class="highlight"><pre>% python foo.script
@@ -553,7 +566,7 @@ Python on a single processor, not in parallel.</p>
 </div>
 </div>
 <div class="section" id="using-lammps-from-python">
-<span id="py-7"></span><h2>Using LAMMPS from Python<a class="headerlink" href="#using-lammps-from-python" title="Permalink to this headline">¶</a></h2>
+<span id="py-7"></span><h2>11.7. Using LAMMPS from Python<a class="headerlink" href="#using-lammps-from-python" title="Permalink to this headline">¶</a></h2>
 <p>As described above, the Python interface to LAMMPS consists of a
 Python &#8220;lammps&#8221; module, the source code for which is in
 python/lammps.py, which creates a &#8220;lammps&#8221; object, with a set of
@@ -770,7 +783,7 @@ Python script.  Isn&#8217;t ctypes amazing?</li>
 </ul>
 </div>
 <div class="section" id="example-python-scripts-that-use-lammps">
-<span id="py-8"></span><h2>Example Python scripts that use LAMMPS<a class="headerlink" href="#example-python-scripts-that-use-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="py-8"></span><h2>11.8. Example Python scripts that use LAMMPS<a class="headerlink" href="#example-python-scripts-that-use-lammps" title="Permalink to this headline">¶</a></h2>
 <p>These are the Python scripts included as demos in the python/examples
 directory of the LAMMPS distribution, to illustrate the kinds of
 things that are possible when Python wraps LAMMPS.  If you create your
@@ -837,7 +850,7 @@ variables that have to match the VMD installation on your system.</p>
 source code for individual scripts for comments about what they do.</p>
 <p>Here are screenshots of the vizplotgui_tool.py script in action for
 different visualization package options.  Click to see larger images:</p>
-<a data-lightbox="group-18a49424-552b-4e40-84e6-3c68f302c35c"
+<a data-lightbox="group-abad215d-0434-41e2-bc11-9f41aac64349"
                    href="_images/screenshot_gl.jpg"
                    class=""
                    title=""
@@ -847,7 +860,7 @@ different visualization package options.  Click to see larger images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-2b79ab21-07b7-47a3-81c3-94a3021a26e0"
+                    </a><a data-lightbox="group-0060607e-2e72-4d15-a243-c7e743159460"
                    href="_images/screenshot_atomeye.jpg"
                    class=""
                    title=""
@@ -857,7 +870,7 @@ different visualization package options.  Click to see larger images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-f4ded497-3be9-4ca3-99ca-0b3b2731bb5b"
+                    </a><a data-lightbox="group-678e5623-6cd3-4bcb-8ec4-1ca57392d6d8"
                    href="_images/screenshot_pymol.jpg"
                    class=""
                    title=""
@@ -867,7 +880,7 @@ different visualization package options.  Click to see larger images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-0c7ab672-9c97-4a40-b3ac-1a55870e2905"
+                    </a><a data-lightbox="group-ca92cc6f-e5c3-492e-a2da-af16743cbf57"
                    href="_images/screenshot_vmd.jpg"
                    class=""
                    title=""
@@ -885,6 +898,15 @@ different visualization package options.  Click to see larger images:</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_errors.html" class="btn btn-neutral float-right" title="12. Errors" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_modify.html" class="btn btn-neutral" title="10. Modifying &amp; extending LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/Section_start.html b/doc/Section_start.html
index a369d55cec..165165f7df 100644
--- a/doc/Section_start.html
+++ b/doc/Section_start.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Getting Started &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>2. Getting Started &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="3. Commands" href="Section_commands.html"/>
+        <link rel="prev" title="1. Introduction" href="Section_intro.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,28 +73,39 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Getting Started</a><ul>
-<li><a class="reference internal" href="#what-s-in-the-lammps-distribution">What&#8217;s in the LAMMPS distribution</a></li>
-<li><a class="reference internal" href="#making-lammps">Making LAMMPS</a></li>
-<li><a class="reference internal" href="#making-lammps-with-optional-packages">Making LAMMPS with optional packages</a></li>
-<li><a class="reference internal" href="#building-lammps-via-the-make-py-script">Building LAMMPS via the Make.py script</a></li>
-<li><a class="reference internal" href="#building-lammps-as-a-library">Building LAMMPS as a library</a><ul>
-<li><a class="reference internal" href="#static-library"><strong>Static library:</strong></a></li>
-<li><a class="reference internal" href="#shared-library"><strong>Shared library:</strong></a></li>
-<li><a class="reference internal" href="#additional-requirement-for-using-a-shared-library"><strong>Additional requirement for using a shared library:</strong></a></li>
-<li><a class="reference internal" href="#calling-the-lammps-library"><strong>Calling the LAMMPS library:</strong></a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">2. Getting Started</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#making-lammps">2.2. Making LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#static-library">2.5.1. <strong>Static library:</strong></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#shared-library">2.5.2. <strong>Shared library:</strong></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#additional-requirement-for-using-a-shared-library">2.5.3. <strong>Additional requirement for using a shared library:</strong></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#calling-the-lammps-library">2.5.4. <strong>Calling the LAMMPS library:</strong></a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#running-lammps">Running LAMMPS</a></li>
-<li><a class="reference internal" href="#command-line-options">Command-line options</a></li>
-<li><a class="reference internal" href="#lammps-screen-output">LAMMPS screen output</a></li>
-<li><a class="reference internal" href="#tips-for-users-of-previous-lammps-versions">Tips for users of previous LAMMPS versions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#running-lammps">2.6. Running LAMMPS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#command-line-options">2.7. Command-line options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lammps-screen-output">2.8. LAMMPS screen output</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -115,7 +128,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Getting Started</li>
+    <li>2. Getting Started</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -130,7 +143,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="getting-started">
-<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
+<h1>2. Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
 <p>This section describes how to build and run LAMMPS, for both new and
 experienced users.</p>
 <div class="line-block">
@@ -146,7 +159,7 @@ experienced users.</p>
 <div class="line"><br /></div>
 </div>
 <div class="section" id="what-s-in-the-lammps-distribution">
-<span id="start-1"></span><h2>What&#8217;s in the LAMMPS distribution<a class="headerlink" href="#what-s-in-the-lammps-distribution" title="Permalink to this headline">¶</a></h2>
+<span id="start-1"></span><h2>2.1. What&#8217;s in the LAMMPS distribution<a class="headerlink" href="#what-s-in-the-lammps-distribution" title="Permalink to this headline">¶</a></h2>
 <p>When you download a LAMMPS tarball you will need to unzip and untar
 the downloaded file with the following commands, after placing the
 tarball in an appropriate directory.</p>
@@ -204,7 +217,7 @@ launch a LAMMPS Windows executable on a Windows box.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="making-lammps">
-<span id="start-2"></span><h2>Making LAMMPS<a class="headerlink" href="#making-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="start-2"></span><h2>2.2. Making LAMMPS<a class="headerlink" href="#making-lammps" title="Permalink to this headline">¶</a></h2>
 <p>This section has the following sub-sections:</p>
 <ul class="simple">
 <li><a class="reference internal" href="#start-2-1"><span>Read this first</span></a></li>
@@ -667,7 +680,7 @@ on both a basic build and a customized build with pacakges you select.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="making-lammps-with-optional-packages">
-<span id="start-3"></span><h2>Making LAMMPS with optional packages<a class="headerlink" href="#making-lammps-with-optional-packages" title="Permalink to this headline">¶</a></h2>
+<span id="start-3"></span><h2>2.3. Making LAMMPS with optional packages<a class="headerlink" href="#making-lammps-with-optional-packages" title="Permalink to this headline">¶</a></h2>
 <p>This section has the following sub-sections:</p>
 <ul class="simple">
 <li><a class="reference internal" href="#start-3-1"><span>Package basics</span></a></li>
@@ -931,7 +944,7 @@ settings for CCFLAGS.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="building-lammps-via-the-make-py-script">
-<span id="start-4"></span><h2>Building LAMMPS via the Make.py script<a class="headerlink" href="#building-lammps-via-the-make-py-script" title="Permalink to this headline">¶</a></h2>
+<span id="start-4"></span><h2>2.4. Building LAMMPS via the Make.py script<a class="headerlink" href="#building-lammps-via-the-make-py-script" title="Permalink to this headline">¶</a></h2>
 <p>The src directory includes a Make.py script, written in Python, which
 can be used to automate various steps of the build process.  It is
 particularly useful for working with the accelerator packages, as well
@@ -1062,14 +1075,14 @@ and MPI options to use, via the &#8220;-cc&#8221; and &#8220;-mpi&#8221; switche
 <hr class="docutils" />
 </div>
 <div class="section" id="building-lammps-as-a-library">
-<span id="start-5"></span><h2>Building LAMMPS as a library<a class="headerlink" href="#building-lammps-as-a-library" title="Permalink to this headline">¶</a></h2>
+<span id="start-5"></span><h2>2.5. Building LAMMPS as a library<a class="headerlink" href="#building-lammps-as-a-library" title="Permalink to this headline">¶</a></h2>
 <p>LAMMPS can be built as either a static or shared library, which can
 then be called from another application or a scripting language.  See
 <a class="reference internal" href="Section_howto.html#howto-10"><span>this section</span></a> for more info on coupling
 LAMMPS to other codes.  See <a class="reference internal" href="Section_python.html"><em>this section</em></a> for
 more info on wrapping and running LAMMPS from Python.</p>
 <div class="section" id="static-library">
-<h3><strong>Static library:</strong><a class="headerlink" href="#static-library" title="Permalink to this headline">¶</a></h3>
+<h3>2.5.1. <strong>Static library:</strong><a class="headerlink" href="#static-library" title="Permalink to this headline">¶</a></h3>
 <p>To build LAMMPS as a static library (<a href="#id7"><span class="problematic" id="id8">*</span></a>.a file on Linux), type</p>
 <div class="highlight-python"><div class="highlight"><pre>make foo mode=lib
 </pre></div>
@@ -1083,7 +1096,7 @@ link to.  It will also create a soft link liblammps.a, which will
 point to the most recently built static library.</p>
 </div>
 <div class="section" id="shared-library">
-<h3><strong>Shared library:</strong><a class="headerlink" href="#shared-library" title="Permalink to this headline">¶</a></h3>
+<h3>2.5.2. <strong>Shared library:</strong><a class="headerlink" href="#shared-library" title="Permalink to this headline">¶</a></h3>
 <p>To build LAMMPS as a shared library (<a href="#id9"><span class="problematic" id="id10">*</span></a>.so file on Linux), which can be
 dynamically loaded, e.g. from Python, type</p>
 <div class="highlight-python"><div class="highlight"><pre>make foo mode=shlib
@@ -1136,7 +1149,7 @@ you do not have write privileges for /usr/local/lib.  The end result
 should be the file /usr/local/lib/libmpich.so.</p>
 </div>
 <div class="section" id="additional-requirement-for-using-a-shared-library">
-<h3><strong>Additional requirement for using a shared library:</strong><a class="headerlink" href="#additional-requirement-for-using-a-shared-library" title="Permalink to this headline">¶</a></h3>
+<h3>2.5.3. <strong>Additional requirement for using a shared library:</strong><a class="headerlink" href="#additional-requirement-for-using-a-shared-library" title="Permalink to this headline">¶</a></h3>
 <p>The operating system finds shared libraries to load at run-time using
 the environment variable LD_LIBRARY_PATH.  So you may wish to copy the
 file src/liblammps.so or src/liblammps_g++.so (for example) to a place
@@ -1151,7 +1164,7 @@ that use it.</p>
 </div>
 </div>
 <div class="section" id="calling-the-lammps-library">
-<h3><strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline">¶</a></h3>
+<h3>2.5.4. <strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline">¶</a></h3>
 <p>Either flavor of library (static or shared0 allows one or more LAMMPS
 objects to be instantiated from the calling program.</p>
 <p>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
@@ -1174,7 +1187,7 @@ interface and how to extend it for your needs.</p>
 </div>
 </div>
 <div class="section" id="running-lammps">
-<span id="start-6"></span><h2>Running LAMMPS<a class="headerlink" href="#running-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="start-6"></span><h2>2.6. Running LAMMPS<a class="headerlink" href="#running-lammps" title="Permalink to this headline">¶</a></h2>
 <p>By default, LAMMPS runs by reading commands from standard input.  Thus
 if you run the LAMMPS executable by itself, e.g.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">lmp_linux</span>
@@ -1276,7 +1289,7 @@ more processors or setup a smaller problem.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="command-line-options">
-<span id="start-7"></span><h2>Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline">¶</a></h2>
+<span id="start-7"></span><h2>2.7. Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline">¶</a></h2>
 <p>At run time, LAMMPS recognizes several optional command-line switches
 which may be used in any order.  Either the full word or a one-or-two
 letter abbreviation can be used:</p>
@@ -1688,7 +1701,7 @@ negative numeric value.  It is OK if the first value1 starts with a
 <hr class="docutils" />
 </div>
 <div class="section" id="lammps-screen-output">
-<span id="start-8"></span><h2>LAMMPS screen output<a class="headerlink" href="#lammps-screen-output" title="Permalink to this headline">¶</a></h2>
+<span id="start-8"></span><h2>2.8. LAMMPS screen output<a class="headerlink" href="#lammps-screen-output" title="Permalink to this headline">¶</a></h2>
 <p>As LAMMPS reads an input script, it prints information to both the
 screen and a log file about significant actions it takes to setup a
 simulation.  When the simulation is ready to begin, LAMMPS performs
@@ -1784,7 +1797,7 @@ communication, roughly 75% in the example above.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="tips-for-users-of-previous-lammps-versions">
-<span id="start-9"></span><h2>Tips for users of previous LAMMPS versions<a class="headerlink" href="#tips-for-users-of-previous-lammps-versions" title="Permalink to this headline">¶</a></h2>
+<span id="start-9"></span><h2>2.9. Tips for users of previous LAMMPS versions<a class="headerlink" href="#tips-for-users-of-previous-lammps-versions" title="Permalink to this headline">¶</a></h2>
 <p>The current C++ began with a complete rewrite of LAMMPS 2001, which
 was written in F90.  Features of earlier versions of LAMMPS are listed
 in <a class="reference internal" href="Section_history.html"><em>Section_history</em></a>.  The F90 and F77 versions
@@ -1821,6 +1834,15 @@ close if you have setup the problem for both codes the same.</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_commands.html" class="btn btn-neutral float-right" title="3. Commands" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_intro.html" class="btn btn-neutral" title="1. Introduction" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
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diff --git a/doc/Section_tools.html b/doc/Section_tools.html
index ced60ae735..8a28d0bf48 100644
--- a/doc/Section_tools.html
+++ b/doc/Section_tools.html
@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Additional tools &mdash; LAMMPS 15 May 2015 version documentation</title>
+  <title>9. Additional tools &mdash; LAMMPS 15 May 2015 version documentation</title>
   
 
   
@@ -32,7 +32,9 @@
   
 
   
-    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> 
+    <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+        <link rel="next" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
+        <link rel="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -71,44 +73,55 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Additional tools</a><ul>
-<li><a class="reference internal" href="#amber2lmp-tool">amber2lmp tool</a></li>
-<li><a class="reference internal" href="#binary2txt-tool">binary2txt tool</a></li>
-<li><a class="reference internal" href="#ch2lmp-tool">ch2lmp tool</a></li>
-<li><a class="reference internal" href="#chain-tool">chain tool</a></li>
-<li><a class="reference internal" href="#colvars-tools">colvars tools</a></li>
-<li><a class="reference internal" href="#createatoms-tool">createatoms tool</a></li>
-<li><a class="reference internal" href="#data2xmovie-tool">data2xmovie tool</a></li>
-<li><a class="reference internal" href="#eam-database-tool">eam database tool</a></li>
-<li><a class="reference internal" href="#eam-generate-tool">eam generate tool</a></li>
-<li><a class="reference internal" href="#eff-tool">eff tool</a></li>
-<li><a class="reference internal" href="#emacs-tool">emacs tool</a></li>
-<li><a class="reference internal" href="#fep-tool">fep tool</a></li>
-<li><a class="reference internal" href="#i-pi-tool">i-pi tool</a></li>
-<li><a class="reference internal" href="#ipp-tool">ipp tool</a></li>
-<li><a class="reference internal" href="#kate-tool">kate tool</a></li>
-<li><a class="reference internal" href="#lmp2arc-tool">lmp2arc tool</a></li>
-<li><a class="reference internal" href="#lmp2cfg-tool">lmp2cfg tool</a></li>
-<li><a class="reference internal" href="#lmp2vmd-tool">lmp2vmd tool</a></li>
-<li><a class="reference internal" href="#matlab-tool">matlab tool</a></li>
-<li><a class="reference internal" href="#micelle2d-tool">micelle2d tool</a></li>
-<li><a class="reference internal" href="#moltemplate-tool">moltemplate tool</a></li>
-<li><a class="reference internal" href="#msi2lmp-tool">msi2lmp tool</a></li>
-<li><a class="reference internal" href="#phonon-tool">phonon tool</a></li>
-<li><a class="reference internal" href="#polymer-bonding-tool">polymer bonding tool</a></li>
-<li><a class="reference internal" href="#pymol-asphere-tool">pymol_asphere tool</a></li>
-<li><a class="reference internal" href="#python-tool">python tool</a></li>
-<li><a class="reference internal" href="#reax-tool">reax tool</a></li>
-<li><a class="reference internal" href="#restart2data-tool">restart2data tool</a></li>
-<li><a class="reference internal" href="#vim-tool">vim tool</a></li>
-<li><a class="reference internal" href="#xmgrace-tool">xmgrace tool</a></li>
-<li><a class="reference internal" href="#xmovie-tool">xmovie tool</a></li>
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">9. Additional tools</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
@@ -131,7 +144,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-    <li>Additional tools</li>
+    <li>9. Additional tools</li>
       <li class="wy-breadcrumbs-aside">
         
           
@@ -146,7 +159,7 @@
            <div itemprop="articleBody">
             
   <div class="section" id="additional-tools">
-<h1>Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline">¶</a></h1>
+<h1>9. Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline">¶</a></h1>
 <p>LAMMPS is designed to be a computational kernel for performing
 molecular dynamics computations.  Additional pre- and post-processing
 steps are often necessary to setup and analyze a simulation.  A few
@@ -203,7 +216,7 @@ own sub-directories with their own Makefiles.</p>
 </ul>
 <hr class="docutils" />
 <div class="section" id="amber2lmp-tool">
-<span id="amber"></span><h2>amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="amber"></span><h2>9.1. amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline">¶</a></h2>
 <p>The amber2lmp sub-directory contains two Python scripts for converting
 files back-and-forth between the AMBER MD code and LAMMPS.  See the
 README file in amber2lmp for more information.</p>
@@ -216,7 +229,7 @@ necessary modifications yourself.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="binary2txt-tool">
-<span id="binary"></span><h2>binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline">¶</a></h2>
+<span id="binary"></span><h2>9.2. binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline">¶</a></h2>
 <p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
 into ASCII text files.  The syntax for running the tool is</p>
 <div class="highlight-python"><div class="highlight"><pre>binary2txt file1 file2 ...
@@ -228,7 +241,7 @@ since binary files are not compatible across all platforms.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="ch2lmp-tool">
-<span id="charmm"></span><h2>ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="charmm"></span><h2>9.3. ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline">¶</a></h2>
 <p>The ch2lmp sub-directory contains tools for converting files
 back-and-forth between the CHARMM MD code and LAMMPS.</p>
 <p>They are intended to make it easy to use CHARMM as a builder and as a
@@ -241,7 +254,7 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="chain-tool">
-<span id="chain"></span><h2>chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline">¶</a></h2>
+<span id="chain"></span><h2>9.4. chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline">¶</a></h2>
 <p>The file chain.f creates a LAMMPS data file containing bead-spring
 polymer chains and/or monomer solvent atoms.  It uses a text file
 containing chain definition parameters as an input.  The created
@@ -257,7 +270,7 @@ system for the <a class="reference internal" href="Section_perf.html"><em>chain
 <hr class="docutils" />
 </div>
 <div class="section" id="colvars-tools">
-<span id="colvars"></span><h2>colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline">¶</a></h2>
+<span id="colvars"></span><h2>9.5. colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline">¶</a></h2>
 <p>The colvars directory contains a collection of tools for postprocessing
 data produced by the colvars collective variable library.
 To compile the tools, edit the makefile for your system and run &#8220;make&#8221;.</p>
@@ -275,7 +288,7 @@ gmail.com) at ICTP, Italy.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="createatoms-tool">
-<span id="create"></span><h2>createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline">¶</a></h2>
+<span id="create"></span><h2>9.6. createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/createatoms directory contains a Fortran program called
 createAtoms.f which can generate a variety of interesting crystal
 structures and geometries and output the resulting list of atom
@@ -285,7 +298,7 @@ coordinates in LAMMPS or other formats.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="data2xmovie-tool">
-<span id="data"></span><h2>data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline">¶</a></h2>
+<span id="data"></span><h2>9.7. data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline">¶</a></h2>
 <p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
 suitable for visualizing with the <a class="reference internal" href="#xmovie"><span>xmovie</span></a> tool, as if it had
 been output with a dump command from LAMMPS itself.  The syntax for
@@ -297,7 +310,7 @@ running the tool is</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="eam-database-tool">
-<span id="eamdb"></span><h2>eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline">¶</a></h2>
+<span id="eamdb"></span><h2>9.8. eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/eam_database directory contains a Fortran program that will
 generate EAM alloy setfl potential files for any combination of 16
 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
@@ -309,7 +322,7 @@ and is based on his paper:</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="eam-generate-tool">
-<span id="eamgn"></span><h2>eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline">¶</a></h2>
+<span id="eamgn"></span><h2>9.9. eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/eam_generate directory contains several one-file C programs
 that convert an analytic formula into a tabulated <a class="reference internal" href="pair_eam.html"><em>embedded atom method (EAM)</em></a> setfl potential file.  The potentials they
 produce are in the potentials directory, and can be used with the
@@ -319,7 +332,7 @@ produce are in the potentials directory, and can be used with the
 <hr class="docutils" />
 </div>
 <div class="section" id="eff-tool">
-<span id="eff"></span><h2>eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline">¶</a></h2>
+<span id="eff"></span><h2>9.10. eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/eff directory contains various scripts for generating
 structures and post-processing output for simulations using the
 electron force field (eFF).</p>
@@ -328,7 +341,7 @@ electron force field (eFF).</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="emacs-tool">
-<span id="emacs"></span><h2>emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline">¶</a></h2>
+<span id="emacs"></span><h2>9.11. emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/emacs directory contains a Lips add-on file for Emacs that
 enables a lammps-mode for editing of input scripts when using Emacs,
 with various highlighting options setup.</p>
@@ -337,7 +350,7 @@ with various highlighting options setup.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="fep-tool">
-<span id="fep"></span><h2>fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline">¶</a></h2>
+<span id="fep"></span><h2>9.12. fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
 simulations using the USER-FEP package.</p>
@@ -347,7 +360,7 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="i-pi-tool">
-<span id="ipi"></span><h2>i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline">¶</a></h2>
+<span id="ipi"></span><h2>9.13. i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/i-pi directory contains a version of the i-PI package, with
 all the LAMMPS-unrelated files removed.  It is provided so that it can
 be used with the <a class="reference internal" href="fix_ipi.html"><em>fix ipi</em></a> command to perform
@@ -361,7 +374,7 @@ calculations with LAMMPS.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="ipp-tool">
-<span id="ipp"></span><h2>ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="ipp"></span><h2>9.14. ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline">¶</a></h2>
 <p>The tools/ipp directory contains a Perl script ipp which can be used
 to facilitate the creation of a complicated file (say, a lammps input
 script or tools/createatoms input file) using a template file.</p>
@@ -372,7 +385,7 @@ tools/createatoms tool&#8217;s input file.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="kate-tool">
-<span id="kate"></span><h2>kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline">¶</a></h2>
+<span id="kate"></span><h2>9.15. kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline">¶</a></h2>
 <p>The file in the tools/kate directory is an add-on to the Kate editor
 in the KDE suite that allow syntax highlighting of LAMMPS input
 scripts.  See the README.txt file for details.</p>
@@ -381,7 +394,7 @@ scripts.  See the README.txt file for details.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="lmp2arc-tool">
-<span id="arc"></span><h2>lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline">¶</a></h2>
+<span id="arc"></span><h2>9.16. lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline">¶</a></h2>
 <p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
 files to the format for Accelrys&#8217; Insight MD code (formerly
 MSI/Biosym and its Discover MD code).  See the README file for more
@@ -394,7 +407,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="lmp2cfg-tool">
-<span id="cfg"></span><h2>lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline">¶</a></h2>
+<span id="cfg"></span><h2>9.17. lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline">¶</a></h2>
 <p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
 files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
 <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer.  See
@@ -403,7 +416,7 @@ the README file for more information.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="lmp2vmd-tool">
-<span id="vmd"></span><h2>lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline">¶</a></h2>
+<span id="vmd"></span><h2>9.18. lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline">¶</a></h2>
 <p>The lmp2vmd sub-directory contains a README.txt file that describes
 details of scripts and plugin support within the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
 dump files.</p>
@@ -412,7 +425,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="matlab-tool">
-<span id="matlab"></span><h2>matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline">¶</a></h2>
+<span id="matlab"></span><h2>9.19. matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline">¶</a></h2>
 <p>The matlab sub-directory contains several <span class="xref std std-ref">MATLAB</span> scripts for
 post-processing LAMMPS output.  The scripts include readers for log
 and dump files, a reader for EAM potential files, and a converter that
@@ -425,7 +438,7 @@ visualizer.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="micelle2d-tool">
-<span id="micelle"></span><h2>micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline">¶</a></h2>
+<span id="micelle"></span><h2>9.20. micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline">¶</a></h2>
 <p>The file micelle2d.f creates a LAMMPS data file containing short lipid
 chains in a monomer solution.  It uses a text file containing lipid
 definition parameters as an input.  The created molecules and solvent
@@ -441,7 +454,7 @@ definition file.  This tool was used to create the system for the
 <hr class="docutils" />
 </div>
 <div class="section" id="moltemplate-tool">
-<span id="moltemplate"></span><h2>moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline">¶</a></h2>
+<span id="moltemplate"></span><h2>9.21. moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline">¶</a></h2>
 <p>The moltemplate sub-directory contains a Python-based tool for
 building molecular systems based on a text-file description, and
 creating LAMMPS data files that encode their molecular topology as
@@ -453,7 +466,7 @@ supports it.  It has its own WWW page at
 <hr class="docutils" />
 </div>
 <div class="section" id="msi2lmp-tool">
-<span id="msi"></span><h2>msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="msi"></span><h2>9.22. msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline">¶</a></h2>
 <p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
 data files from Accelrys&#8217; Insight MD code (formerly MSI/Biosym and
 its Discover MD code).  See the README file for more information.</p>
@@ -466,7 +479,7 @@ experiment with it yourself.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="phonon-tool">
-<span id="phonon"></span><h2>phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline">¶</a></h2>
+<span id="phonon"></span><h2>9.23. phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline">¶</a></h2>
 <p>The phonon sub-directory contains a post-processing tool useful for
 analyzing the output of the <a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a> command in
 the USER-PHONON package.</p>
@@ -478,7 +491,7 @@ University.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="polymer-bonding-tool">
-<span id="polybond"></span><h2>polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline">¶</a></h2>
+<span id="polybond"></span><h2>9.24. polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline">¶</a></h2>
 <p>The polybond sub-directory contains a Python-based tool useful for
 performing &#8220;programmable polymer bonding&#8221;.  The Python file
 lmpsdata.py provides a &#8220;Lmpsdata&#8221; class with various methods which can
@@ -489,7 +502,7 @@ complex bonding topologies.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="pymol-asphere-tool">
-<span id="pymol"></span><h2>pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline">¶</a></h2>
+<span id="pymol"></span><h2>9.25. pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline">¶</a></h2>
 <p>The pymol_asphere sub-directory contains a tool for converting a
 LAMMPS dump file that contains orientation info for ellipsoidal
 particles into an input file for the <span class="xref std std-ref">PyMol visualization package</span>.</p>
@@ -500,7 +513,7 @@ examples directory within pymol_asphere for more information.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="python-tool">
-<span id="pythontools"></span><h2>python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline">¶</a></h2>
+<span id="pythontools"></span><h2>9.26. python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline">¶</a></h2>
 <p>The python sub-directory contains several Python scripts
 that perform common LAMMPS post-processing tasks, such as:</p>
 <ul class="simple">
@@ -515,7 +528,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="reax-tool">
-<span id="reax"></span><h2>reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline">¶</a></h2>
+<span id="reax"></span><h2>9.27. reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline">¶</a></h2>
 <p>The reax sub-directory contains stand-alond codes that can
 post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><em>fix reax/bonds</em></a>
 command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><em>ReaxFF</em></a>.  See
@@ -524,7 +537,7 @@ the README.txt file for more info.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="restart2data-tool">
-<span id="restart"></span><h2>restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline">¶</a></h2>
+<span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline">¶</a></h2>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">This tool is now obsolete and is not included in the
@@ -563,7 +576,7 @@ of files are written by LAMMPS, and how the files are named.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="vim-tool">
-<span id="vim"></span><h2>vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline">¶</a></h2>
+<span id="vim"></span><h2>9.29. vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline">¶</a></h2>
 <p>The files in the tools/vim directory are add-ons to the VIM editor
 that allow easier editing of LAMMPS input scripts.  See the README.txt
 file for details.</p>
@@ -572,7 +585,7 @@ ziegenhain.com)</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="xmgrace-tool">
-<span id="xmgrace"></span><h2>xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline">¶</a></h2>
+<span id="xmgrace"></span><h2>9.30. xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline">¶</a></h2>
 <p>The files in the tools/xmgrace directory can be used to plot the
 thermodynamic data in LAMMPS log files via the xmgrace plotting
 package.  There are several tools in the directory that can be used in
@@ -584,7 +597,7 @@ simulation.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="xmovie-tool">
-<span id="xmovie"></span><h2>xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline">¶</a></h2>
+<span id="xmovie"></span><h2>9.31. xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline">¶</a></h2>
 <p>The xmovie tool is an X-based visualization package that can read
 LAMMPS dump files and animate them.  It is in its own sub-directory
 with the tools directory.  You may need to modify its Makefile so that
@@ -615,6 +628,15 @@ distributing his great tool!</p>
           </div>
           <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="Section_modify.html" class="btn btn-neutral float-right" title="10. Modifying &amp; extending LAMMPS" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="Section_perf.html" class="btn btn-neutral" title="8. Performance &amp; scalability" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
 
   <hr/>
 
diff --git a/doc/_sources/Manual.txt b/doc/_sources/Manual.txt
index 46d881b3c3..2020b2c494 100644
--- a/doc/_sources/Manual.txt
+++ b/doc/_sources/Manual.txt
@@ -71,7 +71,7 @@ it gives quick access to documentation for all LAMMPS commands.
 
 .. toctree::
    :maxdepth: 2
-   :numbered: // comment
+   :numbered:
    
    Section_intro
    Section_start
@@ -91,8 +91,8 @@ it gives quick access to documentation for all LAMMPS commands.
 Indices and tables
 ==================
 
-* :ref:`genindex` // comment
-* :ref:`search` // comment
+* :ref:`genindex`
+* :ref:`search`
    
 .. raw:: html
 
diff --git a/doc/accelerate_cuda.html b/doc/accelerate_cuda.html
index c07d20d512..9d72bb76f5 100644
--- a/doc/accelerate_cuda.html
+++ b/doc/accelerate_cuda.html
@@ -71,14 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">5.USER-CUDA package</a><ul>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/accelerate_gpu.html b/doc/accelerate_gpu.html
index 17c71584a3..e10f0da364 100644
--- a/doc/accelerate_gpu.html
+++ b/doc/accelerate_gpu.html
@@ -71,14 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">5.GPU package</a><ul>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/accelerate_intel.html b/doc/accelerate_intel.html
index 9409a80b45..79a19f26da 100644
--- a/doc/accelerate_intel.html
+++ b/doc/accelerate_intel.html
@@ -71,14 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">5.USER-INTEL package</a><ul>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/accelerate_kokkos.html b/doc/accelerate_kokkos.html
index b5dbc00d35..d358157912 100644
--- a/doc/accelerate_kokkos.html
+++ b/doc/accelerate_kokkos.html
@@ -71,14 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">5.KOKKOS package</a><ul>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/accelerate_omp.html b/doc/accelerate_omp.html
index 5655e31065..ff6c8702a0 100644
--- a/doc/accelerate_omp.html
+++ b/doc/accelerate_omp.html
@@ -71,14 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">5.USER-OMP package</a><ul>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/accelerate_opt.html b/doc/accelerate_opt.html
index d85dd2f50b..d79d441d62 100644
--- a/doc/accelerate_opt.html
+++ b/doc/accelerate_opt.html
@@ -71,14 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">5.OPT package</a><ul>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_charmm.html b/doc/angle_charmm.html
index fcfb578950..f7291a37ca 100644
--- a/doc/angle_charmm.html
+++ b/doc/angle_charmm.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style charmm command</a></li>
-<li><a class="reference internal" href="#angle-style-charmm-kk-command">angle_style charmm/kk command</a></li>
-<li><a class="reference internal" href="#angle-style-charmm-omp-command">angle_style charmm/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_class2.html b/doc/angle_class2.html
index 6531840361..b8d6d3c871 100644
--- a/doc/angle_class2.html
+++ b/doc/angle_class2.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style class2 command</a></li>
-<li><a class="reference internal" href="#angle-style-class2-omp-command">angle_style class2/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_coeff.html b/doc/angle_coeff.html
index 858c047547..b0e5ca7147 100644
--- a/doc/angle_coeff.html
+++ b/doc/angle_coeff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_coeff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_cosine.html b/doc/angle_cosine.html
index 33fcd0d788..ea68ca3d78 100644
--- a/doc/angle_cosine.html
+++ b/doc/angle_cosine.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style cosine command</a></li>
-<li><a class="reference internal" href="#angle-style-cosine-omp-command">angle_style cosine/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_cosine_delta.html b/doc/angle_cosine_delta.html
index ca4a9d8ac0..7920c8ab9a 100644
--- a/doc/angle_cosine_delta.html
+++ b/doc/angle_cosine_delta.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style cosine/delta command</a></li>
-<li><a class="reference internal" href="#angle-style-cosine-delta-omp-command">angle_style cosine/delta/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_cosine_periodic.html b/doc/angle_cosine_periodic.html
index 4e5138bbff..945db4de6f 100644
--- a/doc/angle_cosine_periodic.html
+++ b/doc/angle_cosine_periodic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style cosine/periodic command</a></li>
-<li><a class="reference internal" href="#angle-style-cosine-periodic-omp-command">angle_style cosine/periodic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_cosine_shift.html b/doc/angle_cosine_shift.html
index a50e43105b..dc38712069 100644
--- a/doc/angle_cosine_shift.html
+++ b/doc/angle_cosine_shift.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style cosine/shift command</a></li>
-<li><a class="reference internal" href="#angle-style-cosine-shift-omp-command">angle_style cosine/shift/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_cosine_shift_exp.html b/doc/angle_cosine_shift_exp.html
index 2a7d3b6065..ff3b1cb40c 100644
--- a/doc/angle_cosine_shift_exp.html
+++ b/doc/angle_cosine_shift_exp.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style cosine/shift/exp command</a></li>
-<li><a class="reference internal" href="#angle-style-cosine-shift-exp-omp-command">angle_style cosine/shift/exp/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_cosine_squared.html b/doc/angle_cosine_squared.html
index c626e36f00..18e8651503 100644
--- a/doc/angle_cosine_squared.html
+++ b/doc/angle_cosine_squared.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style cosine/squared command</a></li>
-<li><a class="reference internal" href="#angle-style-cosine-squared-omp-command">angle_style cosine/squared/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_dipole.html b/doc/angle_dipole.html
index d6a1632274..eec7ff2234 100644
--- a/doc/angle_dipole.html
+++ b/doc/angle_dipole.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style dipole command</a></li>
-<li><a class="reference internal" href="#angle-style-dipole-omp-command">angle_style dipole/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_fourier.html b/doc/angle_fourier.html
index e16f48c73a..80cfb68c06 100644
--- a/doc/angle_fourier.html
+++ b/doc/angle_fourier.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style fourier command</a></li>
-<li><a class="reference internal" href="#angle-style-fourier-omp-command">angle_style fourier/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_fourier_simple.html b/doc/angle_fourier_simple.html
index 04075def30..ef9392db3d 100644
--- a/doc/angle_fourier_simple.html
+++ b/doc/angle_fourier_simple.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style fourier/simple command</a></li>
-<li><a class="reference internal" href="#angle-style-fourier-simple-omp-command">angle_style fourier/simple/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_harmonic.html b/doc/angle_harmonic.html
index 211adab4fa..49d9fe4d9a 100644
--- a/doc/angle_harmonic.html
+++ b/doc/angle_harmonic.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style harmonic command</a></li>
-<li><a class="reference internal" href="#angle-style-harmonic-kk-command">angle_style harmonic/kk command</a></li>
-<li><a class="reference internal" href="#angle-style-harmonic-omp-command">angle_style harmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_hybrid.html b/doc/angle_hybrid.html
index f857bd4662..ebe07c66dc 100644
--- a/doc/angle_hybrid.html
+++ b/doc/angle_hybrid.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style hybrid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_none.html b/doc/angle_none.html
index 95bd494d24..323e900983 100644
--- a/doc/angle_none.html
+++ b/doc/angle_none.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style none command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_quartic.html b/doc/angle_quartic.html
index 418829561d..e6031bd250 100644
--- a/doc/angle_quartic.html
+++ b/doc/angle_quartic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style quartic command</a></li>
-<li><a class="reference internal" href="#angle-style-quartic-omp-command">angle_style quartic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_sdk.html b/doc/angle_sdk.html
index 5b3ae13a2b..ef6f739f51 100644
--- a/doc/angle_sdk.html
+++ b/doc/angle_sdk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style sdk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_style.html b/doc/angle_style.html
index a03fb3042b..5fa54ae6ba 100644
--- a/doc/angle_style.html
+++ b/doc/angle_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/angle_table.html b/doc/angle_table.html
index 433b9e3459..06a5947c77 100644
--- a/doc/angle_table.html
+++ b/doc/angle_table.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">angle_style table command</a></li>
-<li><a class="reference internal" href="#angle-style-table-omp-command">angle_style table/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/atom_modify.html b/doc/atom_modify.html
index 328f6f15bd..f22a02dc8b 100644
--- a/doc/atom_modify.html
+++ b/doc/atom_modify.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">atom_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/atom_style.html b/doc/atom_style.html
index a3372600c2..833e034cdf 100644
--- a/doc/atom_style.html
+++ b/doc/atom_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">atom_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/balance.html b/doc/balance.html
index 96ff0e4496..51e6294845 100644
--- a/doc/balance.html
+++ b/doc/balance.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">balance command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -260,7 +264,7 @@ the processor that owns them.  The leftmost diagram is the default
 partitioning of the simulation box across processors (one sub-box for
 each of 16 processors); the middle diagram is after a &#8220;grid&#8221; method
 has been applied.</p>
-<a data-lightbox="group-022505f1-dc20-4757-8079-1c46a98561c1"
+<a data-lightbox="group-be41eda3-1235-46a9-a40b-77e8fd6ad5ad"
                    href="_images/balance_uniform.jpg"
                    class=""
                    title=""
@@ -270,7 +274,7 @@ has been applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-33c706ca-ec21-410d-8dea-549388d6ccd9"
+                    </a><a data-lightbox="group-7a12768d-cd54-48b6-9995-f7cf94f0625f"
                    href="_images/balance_nonuniform.jpg"
                    class=""
                    title=""
@@ -280,7 +284,7 @@ has been applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-eb041c99-4215-4b9b-8dbd-437cfbda53dd"
+                    </a><a data-lightbox="group-430fe552-2b09-44ab-b73a-959b24d83be3"
                    href="_images/balance_rcb.jpg"
                    class=""
                    title=""
diff --git a/doc/body.html b/doc/body.html
index 269c59c903..395f9c2b57 100644
--- a/doc/body.html
+++ b/doc/body.html
@@ -71,11 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Body particles</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_class2.html b/doc/bond_class2.html
index 51660727fd..5a38be9089 100644
--- a/doc/bond_class2.html
+++ b/doc/bond_class2.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style class2 command</a></li>
-<li><a class="reference internal" href="#bond-style-class2-omp-command">bond_style class2/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_coeff.html b/doc/bond_coeff.html
index 03f8ce3cea..62049c831c 100644
--- a/doc/bond_coeff.html
+++ b/doc/bond_coeff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_coeff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_fene.html b/doc/bond_fene.html
index 181a7b095f..b3f5b7dae2 100644
--- a/doc/bond_fene.html
+++ b/doc/bond_fene.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style fene command</a></li>
-<li><a class="reference internal" href="#bond-style-fene-kk-command">bond_style fene/kk command</a></li>
-<li><a class="reference internal" href="#bond-style-fene-omp-command">bond_style fene/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html
index 4eaded2c23..1c6ef1391a 100644
--- a/doc/bond_fene_expand.html
+++ b/doc/bond_fene_expand.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style fene/expand command</a></li>
-<li><a class="reference internal" href="#bond-style-fene-expand-omp-command">bond_style fene/expand/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_harmonic.html b/doc/bond_harmonic.html
index 432cbdabbf..5a7945443c 100644
--- a/doc/bond_harmonic.html
+++ b/doc/bond_harmonic.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style harmonic command</a></li>
-<li><a class="reference internal" href="#bond-style-harmonic-kk-command">bond_style harmonic/kk command</a></li>
-<li><a class="reference internal" href="#bond-style-harmonic-omp-command">bond_style harmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_harmonic_shift.html b/doc/bond_harmonic_shift.html
index b02b2aefcd..71dbec85df 100644
--- a/doc/bond_harmonic_shift.html
+++ b/doc/bond_harmonic_shift.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style harmonic/shift command</a></li>
-<li><a class="reference internal" href="#bond-style-harmonic-shift-omp-command">bond_style harmonic/shift/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_harmonic_shift_cut.html b/doc/bond_harmonic_shift_cut.html
index 9429d4b58d..c5fdac49a0 100644
--- a/doc/bond_harmonic_shift_cut.html
+++ b/doc/bond_harmonic_shift_cut.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style harmonic/shift/cut command</a></li>
-<li><a class="reference internal" href="#bond-style-harmonic-shift-cut-omp-command">bond_style harmonic/shift/cut/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_hybrid.html b/doc/bond_hybrid.html
index 700465ebb5..facb59d7cd 100644
--- a/doc/bond_hybrid.html
+++ b/doc/bond_hybrid.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style hybrid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_morse.html b/doc/bond_morse.html
index 1f2b6a5544..c61d28fe84 100644
--- a/doc/bond_morse.html
+++ b/doc/bond_morse.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style morse command</a></li>
-<li><a class="reference internal" href="#bond-style-morse-omp-command">bond_style morse/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_none.html b/doc/bond_none.html
index 27331d64b8..99cf94369b 100644
--- a/doc/bond_none.html
+++ b/doc/bond_none.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style none command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_nonlinear.html b/doc/bond_nonlinear.html
index d9b922e483..511a7a7a89 100644
--- a/doc/bond_nonlinear.html
+++ b/doc/bond_nonlinear.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style nonlinear command</a></li>
-<li><a class="reference internal" href="#bond-style-nonlinear-omp-command">bond_style nonlinear/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_quartic.html b/doc/bond_quartic.html
index 3176b87c56..8500798131 100644
--- a/doc/bond_quartic.html
+++ b/doc/bond_quartic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style quartic command</a></li>
-<li><a class="reference internal" href="#bond-style-quartic-omp-command">bond_style quartic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_style.html b/doc/bond_style.html
index 992bd282a9..58589a58e5 100644
--- a/doc/bond_style.html
+++ b/doc/bond_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/bond_table.html b/doc/bond_table.html
index ed22cb9375..c82d39abd0 100644
--- a/doc/bond_table.html
+++ b/doc/bond_table.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">bond_style table command</a></li>
-<li><a class="reference internal" href="#bond-style-table-omp-command">bond_style table/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/boundary.html b/doc/boundary.html
index 12e642395d..d30e58f10d 100644
--- a/doc/boundary.html
+++ b/doc/boundary.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">boundary command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/box.html b/doc/box.html
index 716dad40de..5d3ff9a4bf 100644
--- a/doc/box.html
+++ b/doc/box.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">box command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/change_box.html b/doc/change_box.html
index c4c00f7ac7..84f5fe73ec 100644
--- a/doc/change_box.html
+++ b/doc/change_box.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">change_box command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/clear.html b/doc/clear.html
index 2c05911421..c5f62772b3 100644
--- a/doc/clear.html
+++ b/doc/clear.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">clear command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/comm_modify.html b/doc/comm_modify.html
index fad4c8f635..90da72d542 100644
--- a/doc/comm_modify.html
+++ b/doc/comm_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">comm_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/comm_style.html b/doc/comm_style.html
index 5c2e096211..5994c404fb 100644
--- a/doc/comm_style.html
+++ b/doc/comm_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">comm_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute.html b/doc/compute.html
index 7bc5bf2f41..430b76aaa7 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ackland_atom.html b/doc/compute_ackland_atom.html
index 1587e21024..6eced7e3da 100644
--- a/doc/compute_ackland_atom.html
+++ b/doc/compute_ackland_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ackland/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_angle_local.html b/doc/compute_angle_local.html
index 9b04c55089..2ef282ffd7 100644
--- a/doc/compute_angle_local.html
+++ b/doc/compute_angle_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute angle/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_angmom_chunk.html b/doc/compute_angmom_chunk.html
index cfb9e6f2f5..c47e774cf3 100644
--- a/doc/compute_angmom_chunk.html
+++ b/doc/compute_angmom_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute angmom/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_basal_atom.html b/doc/compute_basal_atom.html
index 1f10e810e9..ede5677efa 100644
--- a/doc/compute_basal_atom.html
+++ b/doc/compute_basal_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute basal/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_body_local.html b/doc/compute_body_local.html
index c57240c136..d2c467e515 100644
--- a/doc/compute_body_local.html
+++ b/doc/compute_body_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute body/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_bond_local.html b/doc/compute_bond_local.html
index 14af46f93d..84dd7084a3 100644
--- a/doc/compute_bond_local.html
+++ b/doc/compute_bond_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute bond/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html
index e31bb9de0f..4e1c3340cd 100644
--- a/doc/compute_centro_atom.html
+++ b/doc/compute_centro_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute centro/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_chunk_atom.html b/doc/compute_chunk_atom.html
index ba3f6447b1..306d9d769f 100644
--- a/doc/compute_chunk_atom.html
+++ b/doc/compute_chunk_atom.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute chunk/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_cluster_atom.html b/doc/compute_cluster_atom.html
index e7e238483e..fbaa84dc51 100644
--- a/doc/compute_cluster_atom.html
+++ b/doc/compute_cluster_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute cluster/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_cna_atom.html b/doc/compute_cna_atom.html
index 9944202382..c4e638d901 100644
--- a/doc/compute_cna_atom.html
+++ b/doc/compute_cna_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute cna/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_com.html b/doc/compute_com.html
index ad41c7659a..fcc0e2e1de 100644
--- a/doc/compute_com.html
+++ b/doc/compute_com.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute com command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_com_chunk.html b/doc/compute_com_chunk.html
index b1c5c7b543..198884804c 100644
--- a/doc/compute_com_chunk.html
+++ b/doc/compute_com_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute com/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_contact_atom.html b/doc/compute_contact_atom.html
index 0ce40913bb..73acc85d9c 100644
--- a/doc/compute_contact_atom.html
+++ b/doc/compute_contact_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute contact/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html
index 44bcb8f80a..ead3130fec 100644
--- a/doc/compute_coord_atom.html
+++ b/doc/compute_coord_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute coord/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html
index 03f8033590..3e3603d5e8 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_damage_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute damage/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_dihedral_local.html b/doc/compute_dihedral_local.html
index 1b571cb892..ec76231f1b 100644
--- a/doc/compute_dihedral_local.html
+++ b/doc/compute_dihedral_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute dihedral/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_dilatation_atom.html b/doc/compute_dilatation_atom.html
index 960cd4a562..879ca93ad9 100644
--- a/doc/compute_dilatation_atom.html
+++ b/doc/compute_dilatation_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute dilatation/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html
index 6584752de6..ba9ab618d7 100644
--- a/doc/compute_displace_atom.html
+++ b/doc/compute_displace_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute displace/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_erotate_asphere.html b/doc/compute_erotate_asphere.html
index 5438b97004..189819cd22 100644
--- a/doc/compute_erotate_asphere.html
+++ b/doc/compute_erotate_asphere.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute erotate/asphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_erotate_rigid.html b/doc/compute_erotate_rigid.html
index f3a4ae3b51..fe9eb3d09d 100644
--- a/doc/compute_erotate_rigid.html
+++ b/doc/compute_erotate_rigid.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute erotate/rigid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_erotate_sphere.html b/doc/compute_erotate_sphere.html
index 0c6c9abf52..71f70a6a51 100644
--- a/doc/compute_erotate_sphere.html
+++ b/doc/compute_erotate_sphere.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute erotate/sphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_erotate_sphere_atom.html b/doc/compute_erotate_sphere_atom.html
index 86bf51bf4f..ba93f416d3 100644
--- a/doc/compute_erotate_sphere_atom.html
+++ b/doc/compute_erotate_sphere_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute erotate/sphere/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_event_displace.html b/doc/compute_event_displace.html
index db6245b63f..87e4d4a52f 100644
--- a/doc/compute_event_displace.html
+++ b/doc/compute_event_displace.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute event/displace command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_fep.html b/doc/compute_fep.html
index a79535300a..acf5cf2520 100644
--- a/doc/compute_fep.html
+++ b/doc/compute_fep.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute fep command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_group_group.html b/doc/compute_group_group.html
index ef35584864..c1cb90f792 100644
--- a/doc/compute_group_group.html
+++ b/doc/compute_group_group.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute group/group command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html
index 8856f90e88..9a7e19aac8 100644
--- a/doc/compute_gyration.html
+++ b/doc/compute_gyration.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute gyration command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_gyration_chunk.html b/doc/compute_gyration_chunk.html
index 6b015885c4..d1bbdabf5e 100644
--- a/doc/compute_gyration_chunk.html
+++ b/doc/compute_gyration_chunk.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute gyration/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_heat_flux.html b/doc/compute_heat_flux.html
index 76c0c746d3..a6c3acdec0 100644
--- a/doc/compute_heat_flux.html
+++ b/doc/compute_heat_flux.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute heat/flux command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_improper_local.html b/doc/compute_improper_local.html
index e020e1b297..e4ffac2c17 100644
--- a/doc/compute_improper_local.html
+++ b/doc/compute_improper_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute improper/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_inertia_chunk.html b/doc/compute_inertia_chunk.html
index 077e68b64b..c63b67ae66 100644
--- a/doc/compute_inertia_chunk.html
+++ b/doc/compute_inertia_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute inertia/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ke.html b/doc/compute_ke.html
index 832a5ab7a8..9323b997e3 100644
--- a/doc/compute_ke.html
+++ b/doc/compute_ke.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ke command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html
index 1cbf62db73..96efdf209c 100644
--- a/doc/compute_ke_atom.html
+++ b/doc/compute_ke_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ke/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ke_atom_eff.html b/doc/compute_ke_atom_eff.html
index 601b5d9736..7e6f39a027 100644
--- a/doc/compute_ke_atom_eff.html
+++ b/doc/compute_ke_atom_eff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ke/atom/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ke_eff.html b/doc/compute_ke_eff.html
index 6fd3b7680d..573492f1c7 100644
--- a/doc/compute_ke_eff.html
+++ b/doc/compute_ke_eff.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ke/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ke_rigid.html b/doc/compute_ke_rigid.html
index 0894bae607..c4bb398c36 100644
--- a/doc/compute_ke_rigid.html
+++ b/doc/compute_ke_rigid.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ke/rigid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_meso_e_atom.html b/doc/compute_meso_e_atom.html
index f9f625139e..42799e289f 100644
--- a/doc/compute_meso_e_atom.html
+++ b/doc/compute_meso_e_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute meso_e/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_meso_rho_atom.html b/doc/compute_meso_rho_atom.html
index f0363e50be..1fae15b8e1 100644
--- a/doc/compute_meso_rho_atom.html
+++ b/doc/compute_meso_rho_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute meso_rho/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_meso_t_atom.html b/doc/compute_meso_t_atom.html
index baf808673b..307cc822ec 100644
--- a/doc/compute_meso_t_atom.html
+++ b/doc/compute_meso_t_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute meso_t/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_modify.html b/doc/compute_modify.html
index 895445b575..5cf714eb0b 100644
--- a/doc/compute_modify.html
+++ b/doc/compute_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_msd.html b/doc/compute_msd.html
index b71ab21a12..2a02e6d65a 100644
--- a/doc/compute_msd.html
+++ b/doc/compute_msd.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute msd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_msd_chunk.html b/doc/compute_msd_chunk.html
index 08a9004740..9bf4c15773 100644
--- a/doc/compute_msd_chunk.html
+++ b/doc/compute_msd_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute msd/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_msd_nongauss.html b/doc/compute_msd_nongauss.html
index 7a5274cf58..904989ad86 100644
--- a/doc/compute_msd_nongauss.html
+++ b/doc/compute_msd_nongauss.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute msd/nongauss command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_omega_chunk.html b/doc/compute_omega_chunk.html
index a81984fc93..a5fcd48ac5 100644
--- a/doc/compute_omega_chunk.html
+++ b/doc/compute_omega_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute omega/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_pair.html b/doc/compute_pair.html
index b9947db510..4ea8a47ad6 100644
--- a/doc/compute_pair.html
+++ b/doc/compute_pair.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute pair command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_pair_local.html b/doc/compute_pair_local.html
index a6779f209e..cde85f05c2 100644
--- a/doc/compute_pair_local.html
+++ b/doc/compute_pair_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute pair/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_pe.html b/doc/compute_pe.html
index 5ab475a436..5dfc8fae63 100644
--- a/doc/compute_pe.html
+++ b/doc/compute_pe.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute pe command</a></li>
-<li><a class="reference internal" href="#compute-pe-cuda-command">compute pe/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html
index 99c6e1fe49..0863dbd97a 100644
--- a/doc/compute_pe_atom.html
+++ b/doc/compute_pe_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute pe/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_plasticity_atom.html b/doc/compute_plasticity_atom.html
index f8aec584d4..1017942544 100644
--- a/doc/compute_plasticity_atom.html
+++ b/doc/compute_plasticity_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute plasticity/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html
index 3c3b3ea4bd..6280852964 100644
--- a/doc/compute_pressure.html
+++ b/doc/compute_pressure.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute pressure command</a></li>
-<li><a class="reference internal" href="#compute-pressure-cuda-command">compute pressure/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html
index 7daf52a51f..8bbe9473d7 100644
--- a/doc/compute_property_atom.html
+++ b/doc/compute_property_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute property/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_property_chunk.html b/doc/compute_property_chunk.html
index 726bb05328..24bef3366f 100644
--- a/doc/compute_property_chunk.html
+++ b/doc/compute_property_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute property/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html
index 391b82e376..e0b55f073a 100644
--- a/doc/compute_property_local.html
+++ b/doc/compute_property_local.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute property/local command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html
index df69c9d25e..3ff1eeb003 100644
--- a/doc/compute_rdf.html
+++ b/doc/compute_rdf.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute rdf command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html
index 3fa16b7b69..32bf5be8f6 100644
--- a/doc/compute_reduce.html
+++ b/doc/compute_reduce.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute reduce command</a></li>
-<li><a class="reference internal" href="#compute-reduce-region-command">compute reduce/region command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_saed.html b/doc/compute_saed.html
index 4202696454..58cdbd610a 100644
--- a/doc/compute_saed.html
+++ b/doc/compute_saed.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute saed command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -178,7 +181,7 @@ position of each atom, fj are atomic scattering factors.</p>
 reciprocal lattice nodes. The mesh spacing is defined either (a)  by
 the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.</p>
-<a data-lightbox="group-e8932333-9eca-4cdc-8b3f-74fb5ad39868"
+<a data-lightbox="group-59ebfa1f-2682-4e85-8723-aaad71f16549"
                    href="_images/saed_mesh.jpg"
                    class=""
                    title=""
@@ -215,7 +218,7 @@ intersecting Ewald sphere.  Diffraction intensities will only be
 computed at the intersection of the reciprocal lattice mesh and a
 <em>dR_Ewald</em> thick surface of the Ewald sphere.  See the example 3D
 intestiety data and the intersection of a [010] zone axis in the below image.</p>
-<a data-lightbox="group-0164466b-c5e5-48d4-ba75-5dfe407cce93"
+<a data-lightbox="group-02bf6c2f-3186-4f52-82eb-5a24fa516cfd"
                    href="_images/saed_ewald_intersect.jpg"
                    class=""
                    title=""
diff --git a/doc/compute_slice.html b/doc/compute_slice.html
index a6dee96c55..c964ae8231 100644
--- a/doc/compute_slice.html
+++ b/doc/compute_slice.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute slice command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_sna_atom.html b/doc/compute_sna_atom.html
index 4650a20cfc..d4a721a5d0 100644
--- a/doc/compute_sna_atom.html
+++ b/doc/compute_sna_atom.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute sna/atom command</a></li>
-<li><a class="reference internal" href="#compute-snad-atom-command">compute snad/atom command</a></li>
-<li><a class="reference internal" href="#compute-snav-atom-command">compute snav/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html
index ca9484156c..8b1e101e9c 100644
--- a/doc/compute_stress_atom.html
+++ b/doc/compute_stress_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute stress/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp.html b/doc/compute_temp.html
index dc25b06f0f..2199ee2a10 100644
--- a/doc/compute_temp.html
+++ b/doc/compute_temp.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp command</a></li>
-<li><a class="reference internal" href="#compute-temp-cuda-command">compute temp/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html
index 994c552bea..a3ed191f2e 100644
--- a/doc/compute_temp_asphere.html
+++ b/doc/compute_temp_asphere.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/asphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_chunk.html b/doc/compute_temp_chunk.html
index 96030b5cd6..519a3f66b5 100644
--- a/doc/compute_temp_chunk.html
+++ b/doc/compute_temp_chunk.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_com.html b/doc/compute_temp_com.html
index 1c03b323da..16268a6ff7 100644
--- a/doc/compute_temp_com.html
+++ b/doc/compute_temp_com.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/com command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_cs.html b/doc/compute_temp_cs.html
index 0e6a03a54f..b06cb449ba 100644
--- a/doc/compute_temp_cs.html
+++ b/doc/compute_temp_cs.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/cs command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html
index eb9e456de9..6b1a5cb33a 100644
--- a/doc/compute_temp_deform.html
+++ b/doc/compute_temp_deform.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/deform command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_deform_eff.html b/doc/compute_temp_deform_eff.html
index a89f2e0105..293ee7fea2 100644
--- a/doc/compute_temp_deform_eff.html
+++ b/doc/compute_temp_deform_eff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/deform/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_drude.html b/doc/compute_temp_drude.html
index 0cfff19d60..35b8702094 100644
--- a/doc/compute_temp_drude.html
+++ b/doc/compute_temp_drude.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/drude command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_eff.html b/doc/compute_temp_eff.html
index 6e12a248e9..126d0efc50 100644
--- a/doc/compute_temp_eff.html
+++ b/doc/compute_temp_eff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html
index f368d76c6a..5cefaf325b 100644
--- a/doc/compute_temp_partial.html
+++ b/doc/compute_temp_partial.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/partial command</a></li>
-<li><a class="reference internal" href="#compute-temp-partial-cuda-command">compute temp/partial/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_profile.html b/doc/compute_temp_profile.html
index b6fa80df26..2a980d335b 100644
--- a/doc/compute_temp_profile.html
+++ b/doc/compute_temp_profile.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/profile command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html
index b6cf5454bf..bbed00c8de 100644
--- a/doc/compute_temp_ramp.html
+++ b/doc/compute_temp_ramp.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/ramp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html
index 892b1ad4b7..f5509e1c53 100644
--- a/doc/compute_temp_region.html
+++ b/doc/compute_temp_region.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/region command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_region_eff.html b/doc/compute_temp_region_eff.html
index 0dfca69f19..74882a3657 100644
--- a/doc/compute_temp_region_eff.html
+++ b/doc/compute_temp_region_eff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/region/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_rotate.html b/doc/compute_temp_rotate.html
index b8b7887f03..7be51832f6 100644
--- a/doc/compute_temp_rotate.html
+++ b/doc/compute_temp_rotate.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/rotate command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html
index 6a14e3f490..e83c04d618 100644
--- a/doc/compute_temp_sphere.html
+++ b/doc/compute_temp_sphere.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute temp/sphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_ti.html b/doc/compute_ti.html
index b962ca3f8d..4fba0a348a 100644
--- a/doc/compute_ti.html
+++ b/doc/compute_ti.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute ti command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_torque_chunk.html b/doc/compute_torque_chunk.html
index f9e36d3656..b7e9d65336 100644
--- a/doc/compute_torque_chunk.html
+++ b/doc/compute_torque_chunk.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute torque/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_vacf.html b/doc/compute_vacf.html
index ee08d2dbb8..b577f73f6d 100644
--- a/doc/compute_vacf.html
+++ b/doc/compute_vacf.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute vacf command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_vcm_chunk.html b/doc/compute_vcm_chunk.html
index 444c6c3bd7..ab6e9d93ca 100644
--- a/doc/compute_vcm_chunk.html
+++ b/doc/compute_vcm_chunk.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute vcm/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_voronoi_atom.html b/doc/compute_voronoi_atom.html
index ad4540a6bd..11c04d290a 100644
--- a/doc/compute_voronoi_atom.html
+++ b/doc/compute_voronoi_atom.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute voronoi/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html
index 57d3a5c64c..0e66816125 100644
--- a/doc/compute_xrd.html
+++ b/doc/compute_xrd.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">compute xrd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -181,7 +184,7 @@ the optional <em>LP</em> keyword.</p>
 reciprocal lattice nodes. The mesh spacing is defined either (a)
 by the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.</p>
-<a data-lightbox="group-4cb07d20-1b72-4b88-b799-aadc6e950f2e"
+<a data-lightbox="group-b594ec59-db88-4076-b9a2-0026d73658c4"
                    href="_images/xrd_mesh.jpg"
                    class=""
                    title=""
diff --git a/doc/create_atoms.html b/doc/create_atoms.html
index f7980c3ea9..d92dcff003 100644
--- a/doc/create_atoms.html
+++ b/doc/create_atoms.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">create_atoms command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -337,7 +340,7 @@ variable        v equal &quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) +
 create_atoms 1 box var v set x xx set y yy
 </pre></div>
 </div>
-<a data-lightbox="group-dc1611ed-f44e-47c4-a61a-d8696c9be612"
+<a data-lightbox="group-33c0efcb-d94d-4219-a127-595ee2853510"
                    href="_images/sinusoid.jpg"
                    class=""
                    title=""
diff --git a/doc/create_bonds.html b/doc/create_bonds.html
index c97c753984..da36a89501 100644
--- a/doc/create_bonds.html
+++ b/doc/create_bonds.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">create_bonds command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/create_box.html b/doc/create_box.html
index 979d32ecc7..6fbb043ede 100644
--- a/doc/create_box.html
+++ b/doc/create_box.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">create_box command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/delete_atoms.html b/doc/delete_atoms.html
index 535d25512a..bac8d33e0c 100644
--- a/doc/delete_atoms.html
+++ b/doc/delete_atoms.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">delete_atoms command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/delete_bonds.html b/doc/delete_bonds.html
index 8ff3d9050a..4e22467846 100644
--- a/doc/delete_bonds.html
+++ b/doc/delete_bonds.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">delete_bonds command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dielectric.html b/doc/dielectric.html
index cec1a103c0..33c97b563c 100644
--- a/doc/dielectric.html
+++ b/doc/dielectric.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dielectric command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html
index 1a977c4f03..bd4dc58785 100644
--- a/doc/dihedral_charmm.html
+++ b/doc/dihedral_charmm.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style charmm command</a></li>
-<li><a class="reference internal" href="#dihedral-style-charmm-kk-command">dihedral_style charmm/kk command</a></li>
-<li><a class="reference internal" href="#dihedral-style-charmm-omp-command">dihedral_style charmm/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_class2.html b/doc/dihedral_class2.html
index 83834885ac..43fca11ef6 100644
--- a/doc/dihedral_class2.html
+++ b/doc/dihedral_class2.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style class2 command</a></li>
-<li><a class="reference internal" href="#dihedral-style-class2-omp-command">dihedral_style class2/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_coeff.html b/doc/dihedral_coeff.html
index 7ed367dd2f..6253f33f06 100644
--- a/doc/dihedral_coeff.html
+++ b/doc/dihedral_coeff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_coeff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_cosine_shift_exp.html b/doc/dihedral_cosine_shift_exp.html
index 5e5e8776cf..cf8d36d05c 100644
--- a/doc/dihedral_cosine_shift_exp.html
+++ b/doc/dihedral_cosine_shift_exp.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style cosine/shift/exp command</a></li>
-<li><a class="reference internal" href="#dihedral-style-cosine-shift-exp-omp-command">dihedral_style cosine/shift/exp/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_fourier.html b/doc/dihedral_fourier.html
index d28cdd8e88..3c47399ae1 100644
--- a/doc/dihedral_fourier.html
+++ b/doc/dihedral_fourier.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style fourier command</a></li>
-<li><a class="reference internal" href="#dihedral-style-fourier-omp-command">dihedral_style fourier/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_harmonic.html b/doc/dihedral_harmonic.html
index 08d26f8882..1fdeadcd01 100644
--- a/doc/dihedral_harmonic.html
+++ b/doc/dihedral_harmonic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style harmonic command</a></li>
-<li><a class="reference internal" href="#dihedral-style-harmonic-omp-command">dihedral_style harmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_helix.html b/doc/dihedral_helix.html
index a732939bb7..36379e2718 100644
--- a/doc/dihedral_helix.html
+++ b/doc/dihedral_helix.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style helix command</a></li>
-<li><a class="reference internal" href="#dihedral-style-helix-omp-command">dihedral_style helix/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_hybrid.html b/doc/dihedral_hybrid.html
index 56a0ccb1fb..d2baa444fc 100644
--- a/doc/dihedral_hybrid.html
+++ b/doc/dihedral_hybrid.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style hybrid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_multi_harmonic.html b/doc/dihedral_multi_harmonic.html
index 06db32302c..029e8c0f2f 100644
--- a/doc/dihedral_multi_harmonic.html
+++ b/doc/dihedral_multi_harmonic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style multi/harmonic command</a></li>
-<li><a class="reference internal" href="#dihedral-style-multi-harmonic-omp-command">dihedral_style multi/harmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_nharmonic.html b/doc/dihedral_nharmonic.html
index 9d8d03b577..8ed2f36a04 100644
--- a/doc/dihedral_nharmonic.html
+++ b/doc/dihedral_nharmonic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style nharmonic command</a></li>
-<li><a class="reference internal" href="#dihedral-style-nharmonic-omp-command">dihedral_style nharmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_none.html b/doc/dihedral_none.html
index 4121a004c5..d92ce03276 100644
--- a/doc/dihedral_none.html
+++ b/doc/dihedral_none.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style none command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_opls.html b/doc/dihedral_opls.html
index 5b06a43feb..aef5464d1b 100644
--- a/doc/dihedral_opls.html
+++ b/doc/dihedral_opls.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style opls command</a></li>
-<li><a class="reference internal" href="#dihedral-style-opls-kk-command">dihedral_style opls/kk command</a></li>
-<li><a class="reference internal" href="#dihedral-style-opls-omp-command">dihedral_style opls/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_quadratic.html b/doc/dihedral_quadratic.html
index a0aa1983f1..cf50d5f171 100644
--- a/doc/dihedral_quadratic.html
+++ b/doc/dihedral_quadratic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style quadratic command</a></li>
-<li><a class="reference internal" href="#dihedral-style-quadratic-omp-command">dihedral_style quadratic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_style.html b/doc/dihedral_style.html
index ccebd79021..ecdf7c1b8c 100644
--- a/doc/dihedral_style.html
+++ b/doc/dihedral_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dihedral_table.html b/doc/dihedral_table.html
index 60b76ce3e6..28c64e89cc 100644
--- a/doc/dihedral_table.html
+++ b/doc/dihedral_table.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dihedral_style table command</a></li>
-<li><a class="reference internal" href="#dihedral-style-table-omp-command">dihedral_style table/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dimension.html b/doc/dimension.html
index d3328a6b11..f497085664 100644
--- a/doc/dimension.html
+++ b/doc/dimension.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dimension command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html
index 771ff84f39..c004fe2e73 100644
--- a/doc/displace_atoms.html
+++ b/doc/displace_atoms.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">displace_atoms command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dump.html b/doc/dump.html
index c1129a588d..2dc2037487 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dump command</a></li>
-<li><a class="reference internal" href="#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
-<li><a class="reference internal" href="#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
-<li><a class="reference internal" href="#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dump_image.html b/doc/dump_image.html
index 650449bb5e..2fef87e97f 100644
--- a/doc/dump_image.html
+++ b/doc/dump_image.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dump image command</a></li>
-<li><a class="reference internal" href="#dump-movie-command">dump movie command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -217,7 +219,7 @@ from an existing dump file, and using these dump commands in the rerun
 script to generate the images/movie.</p>
 <p>Here are two sample images, rendered as 1024x1024 JPEG files.  Click
 to see the full-size images:</p>
-<DIV ALIGN=center><a data-lightbox="group-e192ca54-87f4-4dc9-beb3-6c451b74e02e"
+<DIV ALIGN=center><a data-lightbox="group-a8d1ce4b-2f8a-471c-84fd-5e80856b9d57"
                    href="_images/dump1.jpg"
                    class=""
                    title=""
@@ -227,7 +229,7 @@ to see the full-size images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-11e5599d-f653-4fdc-b86a-e4354aea5ceb"
+                    </a><a data-lightbox="group-0e6fb646-7cf3-4c1b-9ebb-e93f758d7891"
                    href="_images/dump2.jpg"
                    class=""
                    title=""
diff --git a/doc/dump_modify.html b/doc/dump_modify.html
index f54640f0f0..bcb61e559c 100644
--- a/doc/dump_modify.html
+++ b/doc/dump_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dump_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/dump_molfile.html b/doc/dump_molfile.html
index 4d18f8d208..c8eb0e1a1f 100644
--- a/doc/dump_molfile.html
+++ b/doc/dump_molfile.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">dump molfile command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/echo.html b/doc/echo.html
index 2e2d8c0b1c..091c391294 100644
--- a/doc/echo.html
+++ b/doc/echo.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">echo command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix.html b/doc/fix.html
index 3c2e83b594..a2b593ff26 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html
index 4ae37520dd..455eb8966f 100644
--- a/doc/fix_adapt.html
+++ b/doc/fix_adapt.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix adapt command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_adapt_fep.html b/doc/fix_adapt_fep.html
index f4abbda506..94587dba4e 100644
--- a/doc/fix_adapt_fep.html
+++ b/doc/fix_adapt_fep.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix adapt/fep command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html
index dbf5fc8899..3f4c2078d5 100644
--- a/doc/fix_addforce.html
+++ b/doc/fix_addforce.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix addforce command</a></li>
-<li><a class="reference internal" href="#fix-addforce-cuda-command">fix addforce/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_addtorque.html b/doc/fix_addtorque.html
index 5c1803aea1..1dc50b1742 100644
--- a/doc/fix_addtorque.html
+++ b/doc/fix_addtorque.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix addtorque command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_append_atoms.html b/doc/fix_append_atoms.html
index badfbfc571..64aaafa6ac 100644
--- a/doc/fix_append_atoms.html
+++ b/doc/fix_append_atoms.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix append/atoms command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_atc.html b/doc/fix_atc.html
index c5085c13ef..d9df172ce3 100644
--- a/doc/fix_atc.html
+++ b/doc/fix_atc.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix atc command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_atom_swap.html b/doc/fix_atom_swap.html
index 0999c92a54..981bb3ff25 100644
--- a/doc/fix_atom_swap.html
+++ b/doc/fix_atom_swap.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix atom/swap command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html
index 73f3d55ffd..dc23784380 100644
--- a/doc/fix_ave_atom.html
+++ b/doc/fix_ave_atom.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_chunk.html b/doc/fix_ave_chunk.html
index 0088d85a89..5e9cfbaa20 100644
--- a/doc/fix_ave_chunk.html
+++ b/doc/fix_ave_chunk.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/chunk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_correlate.html b/doc/fix_ave_correlate.html
index 50ad652a5e..19cce7b1d6 100644
--- a/doc/fix_ave_correlate.html
+++ b/doc/fix_ave_correlate.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/correlate command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html
index 73446ec01b..27b334822d 100644
--- a/doc/fix_ave_histo.html
+++ b/doc/fix_ave_histo.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/histo command</a></li>
-<li><a class="reference internal" href="#fix-ave-histo-weight-command">fix ave/histo/weight command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html
index 23cbd4178f..acabe52d8b 100644
--- a/doc/fix_ave_spatial.html
+++ b/doc/fix_ave_spatial.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/spatial command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_spatial_sphere.html b/doc/fix_ave_spatial_sphere.html
index 827005c306..f855aad247 100644
--- a/doc/fix_ave_spatial_sphere.html
+++ b/doc/fix_ave_spatial_sphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/spatial/sphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index 46d6b9d01a..4aaea3d336 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ave/time command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html
index a708c22662..e094f9f96c 100644
--- a/doc/fix_aveforce.html
+++ b/doc/fix_aveforce.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix aveforce command</a></li>
-<li><a class="reference internal" href="#fix-aveforce-cuda-command">fix aveforce/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_balance.html b/doc/fix_balance.html
index 75c7302c89..b567d192cf 100644
--- a/doc/fix_balance.html
+++ b/doc/fix_balance.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix balance command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -233,7 +236,7 @@ that owns them.  The leftmost diagram is the default partitioning of
 the simulation box across processors (one sub-box for each of 16
 processors); the middle diagram is after a &#8220;grid&#8221; method has been
 applied.</p>
-<a data-lightbox="group-81a0acf3-2704-4e8c-999d-f210ed19b6fb"
+<a data-lightbox="group-3c3a3ca4-30c8-41c7-aeb3-4f9488855663"
                    href="_images/balance_uniform.jpg"
                    class=""
                    title=""
@@ -243,7 +246,7 @@ applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-179f972b-1283-4638-9dc8-06f905f8ec46"
+                    </a><a data-lightbox="group-9caab12f-e8e4-4609-a2ff-f142dd4226d3"
                    href="_images/balance_nonuniform.jpg"
                    class=""
                    title=""
@@ -253,7 +256,7 @@ applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-7ab5baf9-d2bb-4e63-91dc-357beed9ae5b"
+                    </a><a data-lightbox="group-30de4a9e-ee03-4752-8522-d6699eb5af54"
                    href="_images/balance_rcb.jpg"
                    class=""
                    title=""
diff --git a/doc/fix_bond_break.html b/doc/fix_bond_break.html
index a48bc3a9a4..314eb761ad 100644
--- a/doc/fix_bond_break.html
+++ b/doc/fix_bond_break.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix bond/break command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_bond_create.html b/doc/fix_bond_create.html
index 0538bf43db..786cf08d21 100644
--- a/doc/fix_bond_create.html
+++ b/doc/fix_bond_create.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix bond/create command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_bond_swap.html b/doc/fix_bond_swap.html
index c6e6bd7d7a..06647f5c77 100644
--- a/doc/fix_bond_swap.html
+++ b/doc/fix_bond_swap.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix bond/swap command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_box_relax.html b/doc/fix_box_relax.html
index 30888ac8ce..f710e80148 100644
--- a/doc/fix_box_relax.html
+++ b/doc/fix_box_relax.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix box/relax command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_colvars.html b/doc/fix_colvars.html
index e04a5788f7..333d36ccdd 100644
--- a/doc/fix_colvars.html
+++ b/doc/fix_colvars.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix colvars command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_deform.html b/doc/fix_deform.html
index 5035955d0b..2818c948f5 100644
--- a/doc/fix_deform.html
+++ b/doc/fix_deform.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix deform command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html
index 08b4f68377..b8af4f375f 100644
--- a/doc/fix_deposit.html
+++ b/doc/fix_deposit.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix deposit command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_drag.html b/doc/fix_drag.html
index c055bab1d9..57890192f0 100644
--- a/doc/fix_drag.html
+++ b/doc/fix_drag.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix drag command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_drude.html b/doc/fix_drude.html
index ee7b8527e8..3abf31119a 100644
--- a/doc/fix_drude.html
+++ b/doc/fix_drude.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix drude command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_drude_transform.html b/doc/fix_drude_transform.html
index 139279042a..6ada4fbd1d 100644
--- a/doc/fix_drude_transform.html
+++ b/doc/fix_drude_transform.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix drude/transform/direct command</a></li>
-<li><a class="reference internal" href="#fix-drude-transform-inverse-command">fix drude/transform/inverse command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_dt_reset.html b/doc/fix_dt_reset.html
index 7af002d0c5..10201fb1d5 100644
--- a/doc/fix_dt_reset.html
+++ b/doc/fix_dt_reset.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix dt/reset command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_efield.html b/doc/fix_efield.html
index 072d0dcec7..c6ad4d3ece 100644
--- a/doc/fix_efield.html
+++ b/doc/fix_efield.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix efield command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html
index ac8118a8e8..d9fb418975 100644
--- a/doc/fix_enforce2d.html
+++ b/doc/fix_enforce2d.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix enforce2d command</a></li>
-<li><a class="reference internal" href="#fix-enforce2d-cuda-command">fix enforce2d/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_evaporate.html b/doc/fix_evaporate.html
index e29b74d215..766c3a4458 100644
--- a/doc/fix_evaporate.html
+++ b/doc/fix_evaporate.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix evaporate command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_external.html b/doc/fix_external.html
index 4c978321d8..6f14b23520 100644
--- a/doc/fix_external.html
+++ b/doc/fix_external.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix external command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html
index b28e8d4d05..9455f68342 100644
--- a/doc/fix_freeze.html
+++ b/doc/fix_freeze.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix freeze command</a></li>
-<li><a class="reference internal" href="#fix-freeze-cuda-command">fix freeze/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html
index a170165449..90944af00b 100644
--- a/doc/fix_gcmc.html
+++ b/doc/fix_gcmc.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix gcmc command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_gld.html b/doc/fix_gld.html
index b8b53209fd..190643368f 100644
--- a/doc/fix_gld.html
+++ b/doc/fix_gld.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix gld command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_gle.html b/doc/fix_gle.html
index 8e2e3e0caa..667b3433fe 100644
--- a/doc/fix_gle.html
+++ b/doc/fix_gle.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix gle command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html
index e3e19daa9d..5f35105357 100644
--- a/doc/fix_gravity.html
+++ b/doc/fix_gravity.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix gravity command</a></li>
-<li><a class="reference internal" href="#fix-gravity-cuda-command">fix gravity/cuda command</a></li>
-<li><a class="reference internal" href="#fix-gravity-omp-command">fix gravity/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_heat.html b/doc/fix_heat.html
index 80c07c39f0..33f26a5213 100644
--- a/doc/fix_heat.html
+++ b/doc/fix_heat.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix heat command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_imd.html b/doc/fix_imd.html
index a3abc0f02c..4e8fd268f9 100644
--- a/doc/fix_imd.html
+++ b/doc/fix_imd.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix imd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_indent.html b/doc/fix_indent.html
index c4c9e1ef64..8da6806d32 100644
--- a/doc/fix_indent.html
+++ b/doc/fix_indent.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix indent command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ipi.html b/doc/fix_ipi.html
index 2c03c2bdbf..5047039156 100644
--- a/doc/fix_ipi.html
+++ b/doc/fix_ipi.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ipi command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index 062f755382..649bbe7994 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix langevin command</a></li>
-<li><a class="reference internal" href="#fix-langevin-kk-command">fix langevin/kk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_langevin_drude.html b/doc/fix_langevin_drude.html
index 723c909894..104474e7b0 100644
--- a/doc/fix_langevin_drude.html
+++ b/doc/fix_langevin_drude.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix langevin/drude command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_langevin_eff.html b/doc/fix_langevin_eff.html
index 918bfaee80..5cb16c4208 100644
--- a/doc/fix_langevin_eff.html
+++ b/doc/fix_langevin_eff.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix langevin/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_lb_fluid.html b/doc/fix_lb_fluid.html
index f21ec76d22..b6fcbe1ab5 100644
--- a/doc/fix_lb_fluid.html
+++ b/doc/fix_lb_fluid.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix lb/fluid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_lb_momentum.html b/doc/fix_lb_momentum.html
index e39c69f3dc..699c068b1d 100644
--- a/doc/fix_lb_momentum.html
+++ b/doc/fix_lb_momentum.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix lb/momentum command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_lb_pc.html b/doc/fix_lb_pc.html
index c4f3526750..e90c0181ff 100644
--- a/doc/fix_lb_pc.html
+++ b/doc/fix_lb_pc.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix lb/pc command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_lb_rigid_pc_sphere.html b/doc/fix_lb_rigid_pc_sphere.html
index 0cae51b22b..2cbc0e2b2c 100644
--- a/doc/fix_lb_rigid_pc_sphere.html
+++ b/doc/fix_lb_rigid_pc_sphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix lb/rigid/pc/sphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_lb_viscous.html b/doc/fix_lb_viscous.html
index af33ffedc8..7d519090b0 100644
--- a/doc/fix_lb_viscous.html
+++ b/doc/fix_lb_viscous.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix lb/viscous command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_lineforce.html b/doc/fix_lineforce.html
index a8d043e227..4c539d3243 100644
--- a/doc/fix_lineforce.html
+++ b/doc/fix_lineforce.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix lineforce command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_meso.html b/doc/fix_meso.html
index 90c82b8ad5..bd437891f5 100644
--- a/doc/fix_meso.html
+++ b/doc/fix_meso.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix meso command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_meso_stationary.html b/doc/fix_meso_stationary.html
index 9e7384ebdf..7c3e201a99 100644
--- a/doc/fix_meso_stationary.html
+++ b/doc/fix_meso_stationary.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix meso/stationary command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_modify.html b/doc/fix_modify.html
index adedf9ee4c..f82a24493b 100644
--- a/doc/fix_modify.html
+++ b/doc/fix_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html
index 2f6b853c6d..da69360c46 100644
--- a/doc/fix_momentum.html
+++ b/doc/fix_momentum.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix momentum command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_move.html b/doc/fix_move.html
index 7954158a9a..773f8cbfa4 100644
--- a/doc/fix_move.html
+++ b/doc/fix_move.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix move command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_msst.html b/doc/fix_msst.html
index 42adfa4382..781c59c57e 100644
--- a/doc/fix_msst.html
+++ b/doc/fix_msst.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix msst command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_neb.html b/doc/fix_neb.html
index f436b56b8f..efdc5e5477 100644
--- a/doc/fix_neb.html
+++ b/doc/fix_neb.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix neb command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nh.html b/doc/fix_nh.html
index ff70899481..34a7b0c506 100644
--- a/doc/fix_nh.html
+++ b/doc/fix_nh.html
@@ -71,27 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nvt command</a></li>
-<li><a class="reference internal" href="#fix-nvt-cuda-command">fix nvt/cuda command</a></li>
-<li><a class="reference internal" href="#fix-nvt-omp-command">fix nvt/omp command</a></li>
-<li><a class="reference internal" href="#fix-npt-command">fix npt command</a></li>
-<li><a class="reference internal" href="#fix-npt-cuda-command">fix npt/cuda command</a></li>
-<li><a class="reference internal" href="#fix-npt-omp-command">fix npt/omp command</a></li>
-<li><a class="reference internal" href="#fix-nph-command">fix nph command</a></li>
-<li><a class="reference internal" href="#fix-nph-omp-command">fix nph/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nh_eff.html b/doc/fix_nh_eff.html
index 7d7fa2a030..b96f76f360 100644
--- a/doc/fix_nh_eff.html
+++ b/doc/fix_nh_eff.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nvt/eff command</a></li>
-<li><a class="reference internal" href="#fix-npt-eff-command">fix npt/eff command</a></li>
-<li><a class="reference internal" href="#fix-nph-eff-command">fix nph/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nph_asphere.html b/doc/fix_nph_asphere.html
index 606de61836..b39c1b8ecf 100644
--- a/doc/fix_nph_asphere.html
+++ b/doc/fix_nph_asphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nph/asphere command</a></li>
-<li><a class="reference internal" href="#fix-nph-asphere-omp-command">fix nph/asphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nph_sphere.html b/doc/fix_nph_sphere.html
index 12ff1372c6..0a03a408c5 100644
--- a/doc/fix_nph_sphere.html
+++ b/doc/fix_nph_sphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nph/sphere command</a></li>
-<li><a class="reference internal" href="#fix-nph-sphere-omp-command">fix nph/sphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nphug.html b/doc/fix_nphug.html
index 231824aee2..c61bfeba96 100644
--- a/doc/fix_nphug.html
+++ b/doc/fix_nphug.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nphug command</a></li>
-<li><a class="reference internal" href="#fix-nphug-omp-command">fix nphug/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index e263467b6f..43af050032 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix npt/asphere command</a></li>
-<li><a class="reference internal" href="#fix-npt-asphere-omp-command">fix npt/asphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_npt_sphere.html b/doc/fix_npt_sphere.html
index cf2758cf6b..6aef8fd8e5 100644
--- a/doc/fix_npt_sphere.html
+++ b/doc/fix_npt_sphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix npt/sphere command</a></li>
-<li><a class="reference internal" href="#fix-npt-sphere-omp-command">fix npt/sphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve.html b/doc/fix_nve.html
index aef04fef0c..bee2229964 100644
--- a/doc/fix_nve.html
+++ b/doc/fix_nve.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve command</a></li>
-<li><a class="reference internal" href="#fix-nve-cuda-command">fix nve/cuda command</a></li>
-<li><a class="reference internal" href="#fix-nve-kk-command">fix nve/kk command</a></li>
-<li><a class="reference internal" href="#fix-nve-omp-command">fix nve/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html
index d817e0db56..756ead116e 100644
--- a/doc/fix_nve_asphere.html
+++ b/doc/fix_nve_asphere.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/asphere command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_asphere_noforce.html b/doc/fix_nve_asphere_noforce.html
index fe905ae567..adb934dd16 100644
--- a/doc/fix_nve_asphere_noforce.html
+++ b/doc/fix_nve_asphere_noforce.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/asphere/noforce command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_body.html b/doc/fix_nve_body.html
index d6ca4f13dd..00641b9448 100644
--- a/doc/fix_nve_body.html
+++ b/doc/fix_nve_body.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/body command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_eff.html b/doc/fix_nve_eff.html
index 5dc8819a52..02b5e7e85c 100644
--- a/doc/fix_nve_eff.html
+++ b/doc/fix_nve_eff.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_limit.html b/doc/fix_nve_limit.html
index fcd3ca44a3..a3e6a64d84 100644
--- a/doc/fix_nve_limit.html
+++ b/doc/fix_nve_limit.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/limit command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_line.html b/doc/fix_nve_line.html
index 3168d8095b..870cbfab9c 100644
--- a/doc/fix_nve_line.html
+++ b/doc/fix_nve_line.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/line command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_noforce.html b/doc/fix_nve_noforce.html
index d1105db138..b2c89494e6 100644
--- a/doc/fix_nve_noforce.html
+++ b/doc/fix_nve_noforce.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/noforce command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html
index e18ad03e56..8683040c84 100644
--- a/doc/fix_nve_sphere.html
+++ b/doc/fix_nve_sphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/sphere command</a></li>
-<li><a class="reference internal" href="#fix-nve-sphere-omp-command">fix nve/sphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nve_tri.html b/doc/fix_nve_tri.html
index bc7c44a397..2d5adc789c 100644
--- a/doc/fix_nve_tri.html
+++ b/doc/fix_nve_tri.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nve/tri command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html
index a1d7a3e675..922d4e85d9 100644
--- a/doc/fix_nvt_asphere.html
+++ b/doc/fix_nvt_asphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nvt/asphere command</a></li>
-<li><a class="reference internal" href="#fix-nvt-asphere-omp-command">fix nvt/asphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html
index 425fee3a86..50dd7bfec9 100644
--- a/doc/fix_nvt_sllod.html
+++ b/doc/fix_nvt_sllod.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nvt/sllod command</a></li>
-<li><a class="reference internal" href="#fix-nvt-sllod-omp-command">fix nvt/sllod/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nvt_sllod_eff.html b/doc/fix_nvt_sllod_eff.html
index fe5e07030a..84f036f16f 100644
--- a/doc/fix_nvt_sllod_eff.html
+++ b/doc/fix_nvt_sllod_eff.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nvt/sllod/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_nvt_sphere.html b/doc/fix_nvt_sphere.html
index 9196213935..9d5fc29112 100644
--- a/doc/fix_nvt_sphere.html
+++ b/doc/fix_nvt_sphere.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix nvt/sphere command</a></li>
-<li><a class="reference internal" href="#fix-nvt-sphere-omp-command">fix nvt/sphere/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_oneway.html b/doc/fix_oneway.html
index 4232bf7c6d..e175849311 100644
--- a/doc/fix_oneway.html
+++ b/doc/fix_oneway.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix oneway command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html
index a4a8d3db7d..514be39ac2 100644
--- a/doc/fix_orient_fcc.html
+++ b/doc/fix_orient_fcc.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix orient/fcc command</a><ul>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_phonon.html b/doc/fix_phonon.html
index 0c58f0b28d..1a03183d54 100644
--- a/doc/fix_phonon.html
+++ b/doc/fix_phonon.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix phonon command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_pimd.html b/doc/fix_pimd.html
index 7bd63c3598..47d76b5f7d 100644
--- a/doc/fix_pimd.html
+++ b/doc/fix_pimd.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix pimd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_planeforce.html b/doc/fix_planeforce.html
index 21c2d771a1..d4b8163baa 100644
--- a/doc/fix_planeforce.html
+++ b/doc/fix_planeforce.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix planeforce command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_poems.html b/doc/fix_poems.html
index 5141e7f72d..cd55db7b62 100644
--- a/doc/fix_poems.html
+++ b/doc/fix_poems.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix poems</a><ul>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_pour.html b/doc/fix_pour.html
index 48ea78d403..d6871e48f3 100644
--- a/doc/fix_pour.html
+++ b/doc/fix_pour.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix pour command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_press_berendsen.html b/doc/fix_press_berendsen.html
index 9c1565bef3..3e8a7db809 100644
--- a/doc/fix_press_berendsen.html
+++ b/doc/fix_press_berendsen.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix press/berendsen command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_print.html b/doc/fix_print.html
index 35bc9990b5..252f42dc9d 100644
--- a/doc/fix_print.html
+++ b/doc/fix_print.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix print command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_property_atom.html b/doc/fix_property_atom.html
index 6e372bbd64..5d3cd62f7b 100644
--- a/doc/fix_property_atom.html
+++ b/doc/fix_property_atom.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix property/atom command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_qbmsst.html b/doc/fix_qbmsst.html
index 2c16c028a7..73ac2ccc12 100644
--- a/doc/fix_qbmsst.html
+++ b/doc/fix_qbmsst.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix qbmsst command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_qeq.html b/doc/fix_qeq.html
index 582f75075a..1f792863e9 100644
--- a/doc/fix_qeq.html
+++ b/doc/fix_qeq.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix qeq/point command</a></li>
-<li><a class="reference internal" href="#fix-qeq-shielded-command">fix qeq/shielded command</a></li>
-<li><a class="reference internal" href="#fix-qeq-slater-command">fix qeq/slater command</a></li>
-<li><a class="reference internal" href="#fix-qeq-dynamic-command">fix qeq/dynamic command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_qeq_comb.html b/doc/fix_qeq_comb.html
index 4f425269b5..ecd61640a2 100644
--- a/doc/fix_qeq_comb.html
+++ b/doc/fix_qeq_comb.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix qeq/comb command</a></li>
-<li><a class="reference internal" href="#fix-qeq-comb-omp-command">fix qeq/comb/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_qeq_reax.html b/doc/fix_qeq_reax.html
index 17b17950d2..ecb5eebb51 100644
--- a/doc/fix_qeq_reax.html
+++ b/doc/fix_qeq_reax.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix qeq/reax command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_qmmm.html b/doc/fix_qmmm.html
index 9bd2e070f3..3d09f9e145 100644
--- a/doc/fix_qmmm.html
+++ b/doc/fix_qmmm.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix qmmm command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_qtb.html b/doc/fix_qtb.html
index 45e751e2b0..28f5312012 100644
--- a/doc/fix_qtb.html
+++ b/doc/fix_qtb.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix qtb command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_reax_bonds.html b/doc/fix_reax_bonds.html
index 696887119f..247de5a64b 100644
--- a/doc/fix_reax_bonds.html
+++ b/doc/fix_reax_bonds.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix reax/bonds command</a></li>
-<li><a class="reference internal" href="#fix-reax-c-bonds-command">fix reax/c/bonds command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_reaxc_species.html b/doc/fix_reaxc_species.html
index 8441aa98b5..12c4b5bcea 100644
--- a/doc/fix_reaxc_species.html
+++ b/doc/fix_reaxc_species.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix reax/c/species command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html
index 755e24148f..dddacbefb5 100644
--- a/doc/fix_recenter.html
+++ b/doc/fix_recenter.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix recenter command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_restrain.html b/doc/fix_restrain.html
index 2f00a08663..98bac49737 100644
--- a/doc/fix_restrain.html
+++ b/doc/fix_restrain.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix restrain command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html
index 26e567f43c..9976d3ceed 100644
--- a/doc/fix_rigid.html
+++ b/doc/fix_rigid.html
@@ -71,29 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix rigid command</a></li>
-<li><a class="reference internal" href="#fix-rigid-nve-command">fix rigid/nve command</a></li>
-<li><a class="reference internal" href="#fix-rigid-nvt-command">fix rigid/nvt command</a></li>
-<li><a class="reference internal" href="#fix-rigid-npt-command">fix rigid/npt command</a></li>
-<li><a class="reference internal" href="#fix-rigid-nph-command">fix rigid/nph command</a></li>
-<li><a class="reference internal" href="#fix-rigid-small-command">fix rigid/small command</a></li>
-<li><a class="reference internal" href="#fix-rigid-nve-small-command">fix rigid/nve/small command</a></li>
-<li><a class="reference internal" href="#fix-rigid-nvt-small-command">fix rigid/nvt/small command</a></li>
-<li><a class="reference internal" href="#fix-rigid-npt-small-command">fix rigid/npt/small command</a></li>
-<li><a class="reference internal" href="#fix-rigid-nph-small-command">fix rigid/nph/small command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_saed_vtk.html b/doc/fix_saed_vtk.html
index 6a78fb0be3..f9e3cfb3fe 100644
--- a/doc/fix_saed_vtk.html
+++ b/doc/fix_saed_vtk.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix saed/vtk command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html
index 032b9f3e25..1ef8711068 100644
--- a/doc/fix_setforce.html
+++ b/doc/fix_setforce.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix setforce command</a></li>
-<li><a class="reference internal" href="#fix-setforce-cuda-command">fix setforce/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_shake.html b/doc/fix_shake.html
index 01069fd272..026f47cfb3 100644
--- a/doc/fix_shake.html
+++ b/doc/fix_shake.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix shake command</a></li>
-<li><a class="reference internal" href="#fix-shake-cuda-command">fix shake/cuda command</a></li>
-<li><a class="reference internal" href="#fix-rattle-command">fix rattle command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_smd.html b/doc/fix_smd.html
index fd4fe5cc0f..57519d8fd6 100644
--- a/doc/fix_smd.html
+++ b/doc/fix_smd.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix smd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_spring.html b/doc/fix_spring.html
index 5100e6c983..20dc15928a 100644
--- a/doc/fix_spring.html
+++ b/doc/fix_spring.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix spring command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_spring_rg.html b/doc/fix_spring_rg.html
index a008ff5baa..bad950f2ac 100644
--- a/doc/fix_spring_rg.html
+++ b/doc/fix_spring_rg.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix spring/rg command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_spring_self.html b/doc/fix_spring_self.html
index 1bd8cb17e9..07eac84645 100644
--- a/doc/fix_spring_self.html
+++ b/doc/fix_spring_self.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix spring/self command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_srd.html b/doc/fix_srd.html
index f9a5819795..84c53b465b 100644
--- a/doc/fix_srd.html
+++ b/doc/fix_srd.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix srd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_store_force.html b/doc/fix_store_force.html
index 8ed6c890cf..d80f67e8fe 100644
--- a/doc/fix_store_force.html
+++ b/doc/fix_store_force.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix store/force command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html
index 8c0a3ec969..9f2a78fb80 100644
--- a/doc/fix_store_state.html
+++ b/doc/fix_store_state.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix store/state command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html
index 1e06f6c948..cdd52561e0 100644
--- a/doc/fix_temp_berendsen.html
+++ b/doc/fix_temp_berendsen.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix temp/berendsen command</a></li>
-<li><a class="reference internal" href="#fix-temp-berendsen-cuda-command">fix temp/berendsen/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_temp_csvr.html b/doc/fix_temp_csvr.html
index 700b0159f4..2d37d3d7aa 100644
--- a/doc/fix_temp_csvr.html
+++ b/doc/fix_temp_csvr.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix temp/csvr command</a></li>
-<li><a class="reference internal" href="#fix-temp-csld-command">fix temp/csld command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html
index 2d1d3d10c9..259276c30b 100644
--- a/doc/fix_temp_rescale.html
+++ b/doc/fix_temp_rescale.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix temp/rescale command</a></li>
-<li><a class="reference internal" href="#fix-temp-rescale-cuda-command">fix temp/rescale/cuda command</a></li>
-<li><a class="reference internal" href="#fix-temp-rescale-limit-cuda-command">fix temp/rescale/limit/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_temp_rescale_eff.html b/doc/fix_temp_rescale_eff.html
index c230e0b8e8..0281509542 100644
--- a/doc/fix_temp_rescale_eff.html
+++ b/doc/fix_temp_rescale_eff.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix temp/rescale/eff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_tfmc.html b/doc/fix_tfmc.html
index 7eee4def77..86f223316e 100644
--- a/doc/fix_tfmc.html
+++ b/doc/fix_tfmc.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix tfmc command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_thermal_conductivity.html b/doc/fix_thermal_conductivity.html
index 0fcd4c28cc..636bb82b7e 100644
--- a/doc/fix_thermal_conductivity.html
+++ b/doc/fix_thermal_conductivity.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix thermal/conductivity command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ti_rs.html b/doc/fix_ti_rs.html
index b409b19369..ae47a6362e 100644
--- a/doc/fix_ti_rs.html
+++ b/doc/fix_ti_rs.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ti/rs command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ti_spring.html b/doc/fix_ti_spring.html
index 5945f56a2a..885226889e 100644
--- a/doc/fix_ti_spring.html
+++ b/doc/fix_ti_spring.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ti/spring command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_tmd.html b/doc/fix_tmd.html
index eb43e52bf7..935f3d8ab5 100644
--- a/doc/fix_tmd.html
+++ b/doc/fix_tmd.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix tmd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_ttm.html b/doc/fix_ttm.html
index 09d3cf7eb1..dd1a33b591 100644
--- a/doc/fix_ttm.html
+++ b/doc/fix_ttm.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix ttm command</a></li>
-<li><a class="reference internal" href="#fix-ttm-mod-command">fix ttm/mod command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_tune_kspace.html b/doc/fix_tune_kspace.html
index a26614ffa0..945fd9164a 100644
--- a/doc/fix_tune_kspace.html
+++ b/doc/fix_tune_kspace.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix tune/kspace command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_vector.html b/doc/fix_vector.html
index e68be69a94..32fe399caf 100644
--- a/doc/fix_vector.html
+++ b/doc/fix_vector.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix vector command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html
index 742e2ef2e0..3abae3157c 100644
--- a/doc/fix_viscosity.html
+++ b/doc/fix_viscosity.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix viscosity command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html
index 7efa77dffc..9c6326ceba 100644
--- a/doc/fix_viscous.html
+++ b/doc/fix_viscous.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix viscous command</a></li>
-<li><a class="reference internal" href="#fix-viscous-cuda-command">fix viscous/cuda command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_wall.html b/doc/fix_wall.html
index 5e2aaafba6..16d107b93f 100644
--- a/doc/fix_wall.html
+++ b/doc/fix_wall.html
@@ -71,24 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix wall/lj93 command</a></li>
-<li><a class="reference internal" href="#fix-wall-lj126-command">fix wall/lj126 command</a></li>
-<li><a class="reference internal" href="#fix-wall-lj1043-command">fix wall/lj1043 command</a></li>
-<li><a class="reference internal" href="#fix-wall-colloid-command">fix wall/colloid command</a></li>
-<li><a class="reference internal" href="#fix-wall-harmonic-command">fix wall/harmonic command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html
index 2005aa324c..d140f8fce3 100644
--- a/doc/fix_wall_gran.html
+++ b/doc/fix_wall_gran.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix wall/gran command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_wall_piston.html b/doc/fix_wall_piston.html
index 92687bc77e..5e8bba762c 100644
--- a/doc/fix_wall_piston.html
+++ b/doc/fix_wall_piston.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix wall/piston command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html
index b0ca51c1b4..b8d30e3a1b 100644
--- a/doc/fix_wall_reflect.html
+++ b/doc/fix_wall_reflect.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix wall/reflect command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_wall_region.html b/doc/fix_wall_region.html
index d1b3c73094..93d445d60d 100644
--- a/doc/fix_wall_region.html
+++ b/doc/fix_wall_region.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix wall/region command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/fix_wall_srd.html b/doc/fix_wall_srd.html
index 15005bd163..01439852e1 100644
--- a/doc/fix_wall_srd.html
+++ b/doc/fix_wall_srd.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">fix wall/srd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/genindex.html b/doc/genindex.html
index 66d31544a9..b92abe245c 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -72,8 +72,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"></div>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+
           
         
       </div>
diff --git a/doc/group.html b/doc/group.html
index d11f350104..0f8e3a730d 100644
--- a/doc/group.html
+++ b/doc/group.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">group command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/group2ndx.html b/doc/group2ndx.html
index 95036af6df..c8a69575db 100644
--- a/doc/group2ndx.html
+++ b/doc/group2ndx.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">group2ndx command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/if.html b/doc/if.html
index 0d8ddeb3e0..10c5bff656 100644
--- a/doc/if.html
+++ b/doc/if.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">if command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_class2.html b/doc/improper_class2.html
index 4c56f1d40d..7dcb39292e 100644
--- a/doc/improper_class2.html
+++ b/doc/improper_class2.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style class2 command</a></li>
-<li><a class="reference internal" href="#improper-style-class2-omp-command">improper_style class2/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_coeff.html b/doc/improper_coeff.html
index c195e35b88..8cd6103e7b 100644
--- a/doc/improper_coeff.html
+++ b/doc/improper_coeff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_coeff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_cossq.html b/doc/improper_cossq.html
index 8cd3a326e1..44fe889238 100644
--- a/doc/improper_cossq.html
+++ b/doc/improper_cossq.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style cossq command</a></li>
-<li><a class="reference internal" href="#improper-style-cossq-omp-command">improper_style cossq/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_cvff.html b/doc/improper_cvff.html
index fadcf3dc6f..bdf769fbb6 100644
--- a/doc/improper_cvff.html
+++ b/doc/improper_cvff.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style cvff command</a></li>
-<li><a class="reference internal" href="#improper-style-cvff-omp-command">improper_style cvff/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_fourier.html b/doc/improper_fourier.html
index 8a6f5f72cb..42d8d3a57a 100644
--- a/doc/improper_fourier.html
+++ b/doc/improper_fourier.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style fourier command</a></li>
-<li><a class="reference internal" href="#improper-style-fourier-omp-command">improper_style fourier/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_harmonic.html b/doc/improper_harmonic.html
index 5c22c5115d..34f6158b3b 100644
--- a/doc/improper_harmonic.html
+++ b/doc/improper_harmonic.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style harmonic command</a></li>
-<li><a class="reference internal" href="#improper-style-harmonic-kk-command">improper_style harmonic/kk command</a></li>
-<li><a class="reference internal" href="#improper-style-harmonic-omp-command">improper_style harmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_hybrid.html b/doc/improper_hybrid.html
index b0d84d8c5e..0c82ac2dda 100644
--- a/doc/improper_hybrid.html
+++ b/doc/improper_hybrid.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style hybrid command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_none.html b/doc/improper_none.html
index 8a53edf311..f213204ce7 100644
--- a/doc/improper_none.html
+++ b/doc/improper_none.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style none command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_ring.html b/doc/improper_ring.html
index 5f05d7d1e4..243f2a5357 100644
--- a/doc/improper_ring.html
+++ b/doc/improper_ring.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style ring command</a></li>
-<li><a class="reference internal" href="#improper-style-ring-omp-command">improper_style ring/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_style.html b/doc/improper_style.html
index 1731bd46f6..dff01c8080 100644
--- a/doc/improper_style.html
+++ b/doc/improper_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/improper_umbrella.html b/doc/improper_umbrella.html
index 84d5549173..f13730c84c 100644
--- a/doc/improper_umbrella.html
+++ b/doc/improper_umbrella.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">improper_style umbrella command</a></li>
-<li><a class="reference internal" href="#improper-style-umbrella-omp-command">improper_style umbrella/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/include.html b/doc/include.html
index 13809a6f32..756f8b539c 100644
--- a/doc/include.html
+++ b/doc/include.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">include command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/info.html b/doc/info.html
index 3ddf5d38cb..85700766f8 100644
--- a/doc/info.html
+++ b/doc/info.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">info command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/jump.html b/doc/jump.html
index 3800d62554..7e0e4fe2ef 100644
--- a/doc/jump.html
+++ b/doc/jump.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">jump command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/kspace_modify.html b/doc/kspace_modify.html
index 48ea59182b..4b754da8e2 100644
--- a/doc/kspace_modify.html
+++ b/doc/kspace_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">kspace_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/kspace_style.html b/doc/kspace_style.html
index 7eb9617dcd..273b2812db 100644
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">kspace_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/label.html b/doc/label.html
index 4ef27abcbb..b1160fe291 100644
--- a/doc/label.html
+++ b/doc/label.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">label command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/lattice.html b/doc/lattice.html
index 077f51e00a..1a123ad21e 100644
--- a/doc/lattice.html
+++ b/doc/lattice.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">lattice command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/log.html b/doc/log.html
index 074b94723a..7e016aa565 100644
--- a/doc/log.html
+++ b/doc/log.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">log command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/mass.html b/doc/mass.html
index 49ada99059..570f7ae2aa 100644
--- a/doc/mass.html
+++ b/doc/mass.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">mass command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/min_modify.html b/doc/min_modify.html
index e99379bfa8..740389337b 100644
--- a/doc/min_modify.html
+++ b/doc/min_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">min_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/min_style.html b/doc/min_style.html
index 6aed250304..beb1b978ea 100644
--- a/doc/min_style.html
+++ b/doc/min_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">min_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/minimize.html b/doc/minimize.html
index 9470436061..13d95d3a70 100644
--- a/doc/minimize.html
+++ b/doc/minimize.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">minimize command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/molecule.html b/doc/molecule.html
index e8f733b9ee..0dd45bf085 100644
--- a/doc/molecule.html
+++ b/doc/molecule.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">molecule command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/neb.html b/doc/neb.html
index 2f2e54f01b..8bcc80203b 100644
--- a/doc/neb.html
+++ b/doc/neb.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">neb command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
@@ -474,7 +478,7 @@ barrier.</p>
 neb_combine.py script run on the dump files produced by the two
 example input scripts in examples/neb.  Click on them to see a larger
 image.</p>
-<a data-lightbox="group-6deb607f-8ab1-40f5-b335-d0d60b4fa35e"
+<a data-lightbox="group-f5c1df75-20d4-4a80-810c-e8bb668cdbe1"
                    href="_images/hop1.jpg"
                    class=""
                    title=""
@@ -484,7 +488,7 @@ image.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-686d4075-8a0d-469a-a341-c26360cd0b3a"
+                    </a><a data-lightbox="group-445d89a5-1eb9-4204-8d86-136f90dc78ca"
                    href="_images/hop2.jpg"
                    class=""
                    title=""
diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html
index 53dd717ad1..f141cd370e 100644
--- a/doc/neigh_modify.html
+++ b/doc/neigh_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">neigh_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/neighbor.html b/doc/neighbor.html
index 9c3770268a..40617b49cb 100644
--- a/doc/neighbor.html
+++ b/doc/neighbor.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">neighbor command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/newton.html b/doc/newton.html
index cad2e8520b..d6ee4e1721 100644
--- a/doc/newton.html
+++ b/doc/newton.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">newton command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/next.html b/doc/next.html
index 94ebe59363..ffa07feb2e 100644
--- a/doc/next.html
+++ b/doc/next.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">next command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/package.html b/doc/package.html
index 28396de5f8..9b17496865 100644
--- a/doc/package.html
+++ b/doc/package.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">package command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_adp.html b/doc/pair_adp.html
index 89dd053a33..2fb4753bbc 100644
--- a/doc/pair_adp.html
+++ b/doc/pair_adp.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style adp command</a></li>
-<li><a class="reference internal" href="#pair-style-adp-omp-command">pair_style adp/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html
index 61db7e7945..b5d916ecee 100644
--- a/doc/pair_airebo.html
+++ b/doc/pair_airebo.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style airebo command</a></li>
-<li><a class="reference internal" href="#pair-style-airebo-omp-command">pair_style airebo/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-rebo-command">pair_style rebo command</a></li>
-<li><a class="reference internal" href="#pair-style-rebo-omp-command">pair_style rebo/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_awpmd.html b/doc/pair_awpmd.html
index 45165c798c..b8d9a01223 100644
--- a/doc/pair_awpmd.html
+++ b/doc/pair_awpmd.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style awpmd/cut command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_beck.html b/doc/pair_beck.html
index 15ea861919..2d9660fdc3 100644
--- a/doc/pair_beck.html
+++ b/doc/pair_beck.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style beck command</a></li>
-<li><a class="reference internal" href="#pair-style-beck-gpu-command">pair_style beck/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-beck-omp-command">pair_style beck/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_body.html b/doc/pair_body.html
index 2fbcd28892..7da16a7be5 100644
--- a/doc/pair_body.html
+++ b/doc/pair_body.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style body command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_bop.html b/doc/pair_bop.html
index 934d7be4cf..97e3db4e7b 100644
--- a/doc/pair_bop.html
+++ b/doc/pair_bop.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style bop command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_born.html b/doc/pair_born.html
index 83f0214fe5..1eff56e6ad 100644
--- a/doc/pair_born.html
+++ b/doc/pair_born.html
@@ -71,30 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style born command</a></li>
-<li><a class="reference internal" href="#pair-style-born-omp-command">pair_style born/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-born-gpu-command">pair_style born/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-long-command">pair_style born/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-long-cs-command">pair_style born/coul/long/cs command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-long-cuda-command">pair_style born/coul/long/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-long-gpu-command">pair_style born/coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-long-omp-command">pair_style born/coul/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-msm-command">pair_style born/coul/msm command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-msm-omp-command">pair_style born/coul/msm/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-wolf-command">pair_style born/coul/wolf command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-wolf-gpu-command">pair_style born/coul/wolf/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-born-coul-wolf-omp-command">pair_style born/coul/wolf/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_brownian.html b/doc/pair_brownian.html
index 748071730f..9fde4e0c95 100644
--- a/doc/pair_brownian.html
+++ b/doc/pair_brownian.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style brownian command</a></li>
-<li><a class="reference internal" href="#pair-style-brownian-omp-command">pair_style brownian/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-brownian-poly-command">pair_style brownian/poly command</a></li>
-<li><a class="reference internal" href="#pair-style-brownian-poly-omp-command">pair_style brownian/poly/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_buck.html b/doc/pair_buck.html
index 0132678735..760b1a7790 100644
--- a/doc/pair_buck.html
+++ b/doc/pair_buck.html
@@ -71,35 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style buck command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-cuda-command">pair_style buck/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-gpu-command">pair_style buck/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-kk-command">pair_style buck/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-omp-command">pair_style buck/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-cut-command">pair_style buck/coul/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-cut-cuda-command">pair_style buck/coul/cut/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-cut-gpu-command">pair_style buck/coul/cut/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-cut-kk-command">pair_style buck/coul/cut/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-cut-omp-command">pair_style buck/coul/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-command">pair_style buck/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-cs-command">pair_style buck/coul/long/cs command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-cuda-command">pair_style buck/coul/long/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-gpu-command">pair_style buck/coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-kk-command">pair_style buck/coul/long/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-omp-command">pair_style buck/coul/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-msm-command">pair_style buck/coul/msm command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-msm-omp-command">pair_style buck/coul/msm/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_buck_long.html b/doc/pair_buck_long.html
index 83ee3f3efb..1eef4b69c5 100644
--- a/doc/pair_buck_long.html
+++ b/doc/pair_buck_long.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style buck/long/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-long-coul-long-omp-command">pair_style buck/long/coul/long/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html
index d99951405b..21d43c4e2d 100644
--- a/doc/pair_charmm.html
+++ b/doc/pair_charmm.html
@@ -71,31 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/charmm/coul/charmm command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-charmm-cuda-command">pair_style lj/charmm/coul/charmm/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-charmm-omp-command">pair_style lj/charmm/coul/charmm/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-charmm-implicit-command">pair_style lj/charmm/coul/charmm/implicit command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-charmm-implicit-cuda-command">pair_style lj/charmm/coul/charmm/implicit/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-charmm-implicit-omp-command">pair_style lj/charmm/coul/charmm/implicit/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-command">pair_style lj/charmm/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-cuda-command">pair_style lj/charmm/coul/long/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-gpu-command">pair_style lj/charmm/coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-intel-command">pair_style lj/charmm/coul/long/intel command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-opt-command">pair_style lj/charmm/coul/long/opt command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-omp-command">pair_style lj/charmm/coul/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-msm-command">pair_style lj/charmm/coul/msm command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-msm-omp-command">pair_style lj/charmm/coul/msm/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_class2.html b/doc/pair_class2.html
index c99769c09b..5651d3dce4 100644
--- a/doc/pair_class2.html
+++ b/doc/pair_class2.html
@@ -71,31 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/class2 command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-cuda-command">pair_style lj/class2/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-gpu-command">pair_style lj/class2/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-kk-command">pair_style lj/class2/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-omp-command">pair_style lj/class2/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-cut-command">pair_style lj/class2/coul/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-cut-cuda-command">pair_style lj/class2/coul/cut/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-cut-kk-command">pair_style lj/class2/coul/cut/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-cut-omp-command">pair_style lj/class2/coul/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-long-command">pair_style lj/class2/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-long-cuda-command">pair_style lj/class2/coul/long/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-long-gpu-command">pair_style lj/class2/coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-long-kk-command">pair_style lj/class2/coul/long/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-class2-coul-long-omp-command">pair_style lj/class2/coul/long/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index a1bc88e6bb..660fa3859f 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_coeff command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_colloid.html b/doc/pair_colloid.html
index 52b3345e2b..e2b7d4fe03 100644
--- a/doc/pair_colloid.html
+++ b/doc/pair_colloid.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style colloid command</a></li>
-<li><a class="reference internal" href="#pair-style-colloid-gpu-command">pair_style colloid/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-colloid-omp-command">pair_style colloid/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_comb.html b/doc/pair_comb.html
index 5ca071eb4e..327773f672 100644
--- a/doc/pair_comb.html
+++ b/doc/pair_comb.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style comb command</a></li>
-<li><a class="reference internal" href="#pair-style-comb-omp-command">pair_style comb/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-comb3-command">pair_style comb3 command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_coul.html b/doc/pair_coul.html
index 50f38dcc0f..d84ac4ac20 100644
--- a/doc/pair_coul.html
+++ b/doc/pair_coul.html
@@ -71,44 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style coul/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-cut-gpu-command">pair_style coul/cut/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-cut-kk-command">pair_style coul/cut/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-cut-omp-command">pair_style coul/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-debye-command">pair_style coul/debye command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-debye-gpu-command">pair_style coul/debye/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-debye-kk-command">pair_style coul/debye/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-debye-omp-command">pair_style coul/debye/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-dsf-command">pair_style coul/dsf command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-dsf-gpu-command">pair_style coul/dsf/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-dsf-kk-command">pair_style coul/dsf/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-dsf-omp-command">pair_style coul/dsf/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-command">pair_style coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-cs-command">pair_style coul/long/cs command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-omp-command">pair_style coul/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-gpu-command">pair_style coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-kk-command">pair_style coul/long/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-msm-command">pair_style coul/msm command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-msm-omp-command">pair_style coul/msm/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-streitz-command">pair_style coul/streitz command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-wolf-command">pair_style coul/wolf command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-wolf-kk-command">pair_style coul/wolf/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-wolf-omp-command">pair_style coul/wolf/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-tip4p-cut-command">pair_style tip4p/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-tip4p-long-command">pair_style tip4p/long command</a></li>
-<li><a class="reference internal" href="#pair-style-tip4p-cut-omp-command">pair_style tip4p/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-tip4p-long-omp-command">pair_style tip4p/long/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_coul_diel.html b/doc/pair_coul_diel.html
index 1056ce88fb..95ae37441b 100644
--- a/doc/pair_coul_diel.html
+++ b/doc/pair_coul_diel.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style coul/diel command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-diel-omp-command">pair_style coul/diel/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_cs.html b/doc/pair_cs.html
index 2cd161ddcc..f9ab8b530a 100644
--- a/doc/pair_cs.html
+++ b/doc/pair_cs.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style born/coul/long/cs command</a></li>
-<li><a class="reference internal" href="#pair-style-buck-coul-long-cs-command">pair_style buck/coul/long/cs command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_dipole.html b/doc/pair_dipole.html
index 2f267a7fc8..81d40aa417 100644
--- a/doc/pair_dipole.html
+++ b/doc/pair_dipole.html
@@ -71,25 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/cut/dipole/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-dipole-cut-gpu-command">pair_style lj/cut/dipole/cut/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-dipole-cut-omp-command">pair_style lj/cut/dipole/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sf-dipole-sf-command">pair_style lj/sf/dipole/sf command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sf-dipole-sf-gpu-command">pair_style lj/sf/dipole/sf/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sf-dipole-sf-omp-command">pair_style lj/sf/dipole/sf/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-dipole-long-command">pair_style lj/cut/dipole/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-long-dipole-long-command">pair_style lj/long/dipole/long command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html
index 2a97844586..ac9ae019df 100644
--- a/doc/pair_dpd.html
+++ b/doc/pair_dpd.html
@@ -71,23 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style dpd command</a></li>
-<li><a class="reference internal" href="#pair-style-dpd-gpu-command">pair_style dpd/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-dpd-omp-command">pair_style dpd/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-dpd-tstat-command">pair_style dpd/tstat command</a></li>
-<li><a class="reference internal" href="#pair-style-dpd-tstat-gpu-command">pair_style dpd/tstat/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-dpd-tstat-omp-command">pair_style dpd/tstat/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_dsmc.html b/doc/pair_dsmc.html
index 943afbc259..054f1c86ca 100644
--- a/doc/pair_dsmc.html
+++ b/doc/pair_dsmc.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style dsmc command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_eam.html b/doc/pair_eam.html
index 99be5bc173..6fe4011970 100644
--- a/doc/pair_eam.html
+++ b/doc/pair_eam.html
@@ -71,37 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style eam command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-cuda-command">pair_style eam/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-gpu-command">pair_style eam/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-kk-command">pair_style eam/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-omp-command">pair_style eam/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-opt-command">pair_style eam/opt command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-alloy-command">pair_style eam/alloy command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-alloy-cuda-command">pair_style eam/alloy/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-alloy-gpu-command">pair_style eam/alloy/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-alloy-kk-command">pair_style eam/alloy/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-alloy-omp-command">pair_style eam/alloy/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-alloy-opt-command">pair_style eam/alloy/opt command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-cd-command">pair_style eam/cd command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-cd-omp-command">pair_style eam/cd/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-fs-command">pair_style eam/fs command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-fs-cuda-command">pair_style eam/fs/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-fs-gpu-command">pair_style eam/fs/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-fs-kk-command">pair_style eam/fs/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-fs-omp-command">pair_style eam/fs/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-eam-fs-opt-command">pair_style eam/fs/opt command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_edip.html b/doc/pair_edip.html
index 750f878dd7..10bec3af94 100644
--- a/doc/pair_edip.html
+++ b/doc/pair_edip.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style edip command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_eff.html b/doc/pair_eff.html
index 9616fa5cc1..ef0b423f1b 100644
--- a/doc/pair_eff.html
+++ b/doc/pair_eff.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style eff/cut command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_eim.html b/doc/pair_eim.html
index 0527a786ac..158e274552 100644
--- a/doc/pair_eim.html
+++ b/doc/pair_eim.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style eim command</a></li>
-<li><a class="reference internal" href="#pair-style-eim-omp-command">pair_style eim/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_gauss.html b/doc/pair_gauss.html
index 132a256ad6..edca55e392 100644
--- a/doc/pair_gauss.html
+++ b/doc/pair_gauss.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style gauss command</a></li>
-<li><a class="reference internal" href="#pair-style-gauss-gpu-command">pair_style gauss/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-gauss-omp-command">pair_style gauss/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-gauss-cut-command">pair_style gauss/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-gauss-cut-omp-command">pair_style gauss/cut/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html
index 7c7b6e963d..b96b2cbaba 100644
--- a/doc/pair_gayberne.html
+++ b/doc/pair_gayberne.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style gayberne command</a></li>
-<li><a class="reference internal" href="#pair-style-gayberne-gpu-command">pair_style gayberne/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-gayberne-intel-command">pair_style gayberne/intel command</a></li>
-<li><a class="reference internal" href="#pair-style-gayberne-omp-command">pair_style gayberne/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_gran.html b/doc/pair_gran.html
index 249c5cb447..35367583ab 100644
--- a/doc/pair_gran.html
+++ b/doc/pair_gran.html
@@ -71,24 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style gran/hooke command</a></li>
-<li><a class="reference internal" href="#pair-style-gran-cuda-command">pair_style gran/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-gran-omp-command">pair_style gran/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-gran-hooke-history-command">pair_style gran/hooke/history command</a></li>
-<li><a class="reference internal" href="#pair-style-gran-hooke-history-omp-command">pair_style gran/hooke/history/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-gran-hertz-history-command">pair_style gran/hertz/history command</a></li>
-<li><a class="reference internal" href="#pair-style-gran-hertz-history-omp-command">pair_style gran/hertz/history/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_gromacs.html b/doc/pair_gromacs.html
index 8fb4eaee58..cbb11c1e97 100644
--- a/doc/pair_gromacs.html
+++ b/doc/pair_gromacs.html
@@ -71,24 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/gromacs command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-gromacs-cuda-command">pair_style lj/gromacs/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-gromacs-gpu-command">pair_style lj/gromacs/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-gromacs-omp-command">pair_style lj/gromacs/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-gromacs-coul-gromacs-command">pair_style lj/gromacs/coul/gromacs command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-gromacs-coul-gromacs-cuda-command">pair_style lj/gromacs/coul/gromacs/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-gromacs-coul-gromacs-omp-command">pair_style lj/gromacs/coul/gromacs/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_hbond_dreiding.html b/doc/pair_hbond_dreiding.html
index e392e5dd91..8f074322f9 100644
--- a/doc/pair_hbond_dreiding.html
+++ b/doc/pair_hbond_dreiding.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style hbond/dreiding/lj command</a></li>
-<li><a class="reference internal" href="#pair-style-hbond-dreiding-lj-omp-command">pair_style hbond/dreiding/lj/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-hbond-dreiding-morse-command">pair_style hbond/dreiding/morse command</a></li>
-<li><a class="reference internal" href="#pair-style-hbond-dreiding-morse-omp-command">pair_style hbond/dreiding/morse/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html
index b2fe5ad2bd..80e56b555c 100644
--- a/doc/pair_hybrid.html
+++ b/doc/pair_hybrid.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style hybrid command</a></li>
-<li><a class="reference internal" href="#pair-style-hybrid-omp-command">pair_style hybrid/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-hybrid-overlay-command">pair_style hybrid/overlay command</a></li>
-<li><a class="reference internal" href="#pair-style-hybrid-overlay-omp-command">pair_style hybrid/overlay/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_kim.html b/doc/pair_kim.html
index 461a4ce0af..febaadd865 100644
--- a/doc/pair_kim.html
+++ b/doc/pair_kim.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style kim command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lcbop.html b/doc/pair_lcbop.html
index 6bdd398d6f..b4877c3866 100644
--- a/doc/pair_lcbop.html
+++ b/doc/pair_lcbop.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lcbop command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_line_lj.html b/doc/pair_line_lj.html
index 72ae332556..fce51ba245 100644
--- a/doc/pair_line_lj.html
+++ b/doc/pair_line_lj.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style line/lj command</a></li>
-<li><a class="reference internal" href="#pair-style-line-lj-omp-command">pair_style line/lj/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_list.html b/doc/pair_list.html
index f0133f7e18..184b2cb1f5 100644
--- a/doc/pair_list.html
+++ b/doc/pair_list.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style list command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj.html b/doc/pair_lj.html
index 8f50bcebf3..e9e911dc33 100644
--- a/doc/pair_lj.html
+++ b/doc/pair_lj.html
@@ -71,51 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-cuda-command">pair_style lj/cut/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-gpu-command">pair_style lj/cut/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-intel-command">pair_style lj/cut/intel command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-kk-command">pair_style lj/cut/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-opt-command">pair_style lj/cut/opt command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-omp-command">pair_style lj/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-cut-command">pair_style lj/cut/coul/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-cut-cuda-command">pair_style lj/cut/coul/cut/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-cut-gpu-command">pair_style lj/cut/coul/cut/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-cut-omp-command">pair_style lj/cut/coul/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-debye-command">pair_style lj/cut/coul/debye command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-debye-cuda-command">pair_style lj/cut/coul/debye/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-debye-gpu-command">pair_style lj/cut/coul/debye/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-debye-kk-command">pair_style lj/cut/coul/debye/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-debye-omp-command">pair_style lj/cut/coul/debye/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-dsf-command">pair_style lj/cut/coul/dsf command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-dsf-gpu-command">pair_style lj/cut/coul/dsf/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-dsf-kk-command">pair_style lj/cut/coul/dsf/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-dsf-omp-command">pair_style lj/cut/coul/dsf/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-command">pair_style lj/cut/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-cuda-command">pair_style lj/cut/coul/long/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-gpu-command">pair_style lj/cut/coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-intel-command">pair_style lj/cut/coul/long/intel command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-opt-command">pair_style lj/cut/coul/long/opt command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-omp-command">pair_style lj/cut/coul/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-msm-command">pair_style lj/cut/coul/msm command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-msm-gpu-command">pair_style lj/cut/coul/msm/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-msm-omp-command">pair_style lj/cut/coul/msm/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-cut-command">pair_style lj/cut/tip4p/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-cut-omp-command">pair_style lj/cut/tip4p/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-long-command">pair_style lj/cut/tip4p/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-long-omp-command">pair_style lj/cut/tip4p/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-long-opt-command">pair_style lj/cut/tip4p/long/opt command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj96.html b/doc/pair_lj96.html
index 74631de313..9abb31482f 100644
--- a/doc/pair_lj96.html
+++ b/doc/pair_lj96.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj96/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-lj96-cut-cuda-command">pair_style lj96/cut/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj96-cut-gpu-command">pair_style lj96/cut/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj96-cut-omp-command">pair_style lj96/cut/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_cubic.html b/doc/pair_lj_cubic.html
index 3b192b6906..5f85a8114f 100644
--- a/doc/pair_lj_cubic.html
+++ b/doc/pair_lj_cubic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/cubic command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cubic-omp-command">pair_style lj/cubic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html
index cc7c27ceb6..ce1f8af3bd 100644
--- a/doc/pair_lj_expand.html
+++ b/doc/pair_lj_expand.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/expand command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-expand-cuda-command">pair_style lj/expand/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-expand-gpu-command">pair_style lj/expand/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-expand-omp-command">pair_style lj/expand/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_long.html b/doc/pair_lj_long.html
index 123a367a63..4b712d2d5c 100644
--- a/doc/pair_lj_long.html
+++ b/doc/pair_lj_long.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/long/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-long-coul-long-omp-command">pair_style lj/long/coul/long/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-long-coul-long-opt-command">pair_style lj/long/coul/long/opt command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-long-tip4p-long-command">pair_style lj/long/tip4p/long command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_sf.html b/doc/pair_lj_sf.html
index d7a8ff42a1..ead29c3165 100644
--- a/doc/pair_lj_sf.html
+++ b/doc/pair_lj_sf.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/sf command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sf-omp-command">pair_style lj/sf/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html
index c71fb41915..4a658275c3 100644
--- a/doc/pair_lj_smooth.html
+++ b/doc/pair_lj_smooth.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/smooth command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-smooth-cuda-command">pair_style lj/smooth/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-smooth-omp-command">pair_style lj/smooth/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_smooth_linear.html b/doc/pair_lj_smooth_linear.html
index c43ed54127..07ec2ddebc 100644
--- a/doc/pair_lj_smooth_linear.html
+++ b/doc/pair_lj_smooth_linear.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/smooth/linear command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-smooth-linear-omp-command">pair_style lj/smooth/linear/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lj_soft.html b/doc/pair_lj_soft.html
index 720060469c..cdf818c955 100644
--- a/doc/pair_lj_soft.html
+++ b/doc/pair_lj_soft.html
@@ -71,33 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/cut/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-soft-omp-command">pair_style lj/cut/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-cut-soft-command">pair_style lj/cut/coul/cut/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-cut-soft-omp-command">pair_style lj/cut/coul/cut/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-soft-command">pair_style lj/cut/coul/long/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-coul-long-soft-omp-command">pair_style lj/cut/coul/long/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-long-soft-command">pair_style lj/cut/tip4p/long/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-cut-tip4p-long-soft-omp-command">pair_style lj/cut/tip4p/long/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-soft-command">pair_style lj/charmm/coul/long/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-charmm-coul-long-soft-omp-command">pair_style lj/charmm/coul/long/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-cut-soft-command">pair_style coul/cut/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-cut-soft-omp-command">pair_style coul/cut/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-soft-command">pair_style coul/long/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-coul-long-soft-omp-command">pair_style coul/long/soft/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-tip4p-long-soft-command">pair_style tip4p/long/soft command</a></li>
-<li><a class="reference internal" href="#pair-style-tip4p-long-soft-omp-command">pair_style tip4p/long/soft/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html
index 630df31f37..ec44958b25 100644
--- a/doc/pair_lubricate.html
+++ b/doc/pair_lubricate.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lubricate command</a></li>
-<li><a class="reference internal" href="#pair-style-lubricate-omp-command">pair_style lubricate/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lubricate-poly-command">pair_style lubricate/poly command</a></li>
-<li><a class="reference internal" href="#pair-style-lubricate-poly-omp-command">pair_style lubricate/poly/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_lubricateU.html b/doc/pair_lubricateU.html
index 15fe534263..5638ed174b 100644
--- a/doc/pair_lubricateU.html
+++ b/doc/pair_lubricateU.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lubricateU command</a></li>
-<li><a class="reference internal" href="#pair-style-lubricateu-poly-command">pair_style lubricateU/poly command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_meam.html b/doc/pair_meam.html
index 168ac42d05..47938aef13 100644
--- a/doc/pair_meam.html
+++ b/doc/pair_meam.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style meam command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_meam_spline.html b/doc/pair_meam_spline.html
index a72f7365e3..a6eeeec968 100644
--- a/doc/pair_meam_spline.html
+++ b/doc/pair_meam_spline.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style meam/spline</a></li>
-<li><a class="reference internal" href="#pair-style-meam-spline-omp">pair_style meam/spline/omp</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_meam_sw_spline.html b/doc/pair_meam_sw_spline.html
index d7f756eab2..fb28bed911 100644
--- a/doc/pair_meam_sw_spline.html
+++ b/doc/pair_meam_sw_spline.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style meam/sw/spline</a></li>
-<li><a class="reference internal" href="#pair-style-meam-sw-spline-omp">pair_style meam/sw/spline/omp</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_mie.html b/doc/pair_mie.html
index f00f3b7951..405c7cfb0c 100644
--- a/doc/pair_mie.html
+++ b/doc/pair_mie.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style mie/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-mie-cut-gpu-command">pair_style mie/cut/gpu command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_modify.html b/doc/pair_modify.html
index bf1f8ac0ce..367799e8c0 100644
--- a/doc/pair_modify.html
+++ b/doc/pair_modify.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a><ul>
-<li><a class="reference internal" href="#use-of-special-keyword">Use of <em>special</em> keyword</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
-</ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_morse.html b/doc/pair_morse.html
index 110fa42dac..1866f54b98 100644
--- a/doc/pair_morse.html
+++ b/doc/pair_morse.html
@@ -71,22 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style morse command</a></li>
-<li><a class="reference internal" href="#pair-style-morse-cuda-command">pair_style morse/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-morse-gpu-command">pair_style morse/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-morse-omp-command">pair_style morse/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-morse-opt-command">pair_style morse/opt command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_nb3b_harmonic.html b/doc/pair_nb3b_harmonic.html
index b856434c94..eb89b4d391 100644
--- a/doc/pair_nb3b_harmonic.html
+++ b/doc/pair_nb3b_harmonic.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style nb3b/harmonic command</a></li>
-<li><a class="reference internal" href="#pair-style-nb3b-harmonic-omp-command">pair_style nb3b/harmonic/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_nm.html b/doc/pair_nm.html
index 22dd832219..424edf7fe5 100644
--- a/doc/pair_nm.html
+++ b/doc/pair_nm.html
@@ -71,23 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style nm/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-nm-cut-coul-cut-command">pair_style nm/cut/coul/cut command</a></li>
-<li><a class="reference internal" href="#pair-style-nm-cut-coul-long-command">pair_style nm/cut/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-nm-cut-omp-command">pair_style nm/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-nm-cut-coul-cut-omp-command">pair_style nm/cut/coul/cut/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-nm-cut-coul-long-omp-command">pair_style nm/cut/coul/long/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_none.html b/doc/pair_none.html
index b16cdd2dd6..fb92136566 100644
--- a/doc/pair_none.html
+++ b/doc/pair_none.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style none command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_peri.html b/doc/pair_peri.html
index 16fac92a60..a6b22224f9 100644
--- a/doc/pair_peri.html
+++ b/doc/pair_peri.html
@@ -71,23 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style peri/pmb command</a></li>
-<li><a class="reference internal" href="#pair-style-peri-pmb-omp-command">pair_style peri/pmb/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-peri-lps-command">pair_style peri/lps command</a></li>
-<li><a class="reference internal" href="#pair-style-peri-lps-omp-command">pair_style peri/lps/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-peri-ves-command">pair_style peri/ves command</a></li>
-<li><a class="reference internal" href="#pair-style-peri-eps-command">pair_style peri/eps command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_polymorphic.html b/doc/pair_polymorphic.html
index 4a16f9245c..57178b2365 100644
--- a/doc/pair_polymorphic.html
+++ b/doc/pair_polymorphic.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style polymorphic command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_quip.html b/doc/pair_quip.html
index a98091c11f..5d2d31bbe8 100644
--- a/doc/pair_quip.html
+++ b/doc/pair_quip.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style quip command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_reax.html b/doc/pair_reax.html
index 558e147c54..6779e45695 100644
--- a/doc/pair_reax.html
+++ b/doc/pair_reax.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style reax command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_reax_c.html b/doc/pair_reax_c.html
index 4d69c2c164..8192eaace6 100644
--- a/doc/pair_reax_c.html
+++ b/doc/pair_reax_c.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style reax/c command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html
index bc1132963f..3afc0b89c9 100644
--- a/doc/pair_resquared.html
+++ b/doc/pair_resquared.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style resquared command</a></li>
-<li><a class="reference internal" href="#pair-style-resquared-gpu-command">pair_style resquared/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-resquared-omp-command">pair_style resquared/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sdk.html b/doc/pair_sdk.html
index 43d49e089e..a548ea27cc 100644
--- a/doc/pair_sdk.html
+++ b/doc/pair_sdk.html
@@ -71,24 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style lj/sdk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sdk-gpu-command">pair_style lj/sdk/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sdk-kk-command">pair_style lj/sdk/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sdk-omp-command">pair_style lj/sdk/omp command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sdk-coul-long-command">pair_style lj/sdk/coul/long command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sdk-coul-long-gpu-command">pair_style lj/sdk/coul/long/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-lj-sdk-coul-long-omp-command">pair_style lj/sdk/coul/long/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_snap.html b/doc/pair_snap.html
index 43bea1e499..0c52e49fc3 100644
--- a/doc/pair_snap.html
+++ b/doc/pair_snap.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style snap command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_soft.html b/doc/pair_soft.html
index 74953e8938..c404b0a08b 100644
--- a/doc/pair_soft.html
+++ b/doc/pair_soft.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style soft command</a></li>
-<li><a class="reference internal" href="#pair-style-soft-gpu-command">pair_style soft/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-soft-omp-command">pair_style soft/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sph_heatconduction.html b/doc/pair_sph_heatconduction.html
index bec49ff69c..a76aedb23b 100644
--- a/doc/pair_sph_heatconduction.html
+++ b/doc/pair_sph_heatconduction.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sph/heatconduction command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sph_idealgas.html b/doc/pair_sph_idealgas.html
index d72481f128..f93bc5e24e 100644
--- a/doc/pair_sph_idealgas.html
+++ b/doc/pair_sph_idealgas.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sph/idealgas command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sph_lj.html b/doc/pair_sph_lj.html
index e4a95c4daf..ea2a9a37fe 100644
--- a/doc/pair_sph_lj.html
+++ b/doc/pair_sph_lj.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sph/lj command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sph_rhosum.html b/doc/pair_sph_rhosum.html
index c1907f2808..31325d3b53 100644
--- a/doc/pair_sph_rhosum.html
+++ b/doc/pair_sph_rhosum.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sph/rhosum command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sph_taitwater.html b/doc/pair_sph_taitwater.html
index c0693b7bd6..f61dc8a2f6 100644
--- a/doc/pair_sph_taitwater.html
+++ b/doc/pair_sph_taitwater.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sph/taitwater command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sph_taitwater_morris.html b/doc/pair_sph_taitwater_morris.html
index 333a36cfde..5838d769e0 100644
--- a/doc/pair_sph_taitwater_morris.html
+++ b/doc/pair_sph_taitwater_morris.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sph/taitwater/morris command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_srp.html b/doc/pair_srp.html
index dd4e0c8d60..5bd6ae4f23 100644
--- a/doc/pair_srp.html
+++ b/doc/pair_srp.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style srp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_style.html b/doc/pair_style.html
index a76441dd85..5c609bb33f 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_sw.html b/doc/pair_sw.html
index 5d6e3b1302..4892074dd3 100644
--- a/doc/pair_sw.html
+++ b/doc/pair_sw.html
@@ -71,23 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style sw command</a></li>
-<li><a class="reference internal" href="#pair-style-sw-cuda-command">pair_style sw/cuda command</a></li>
-<li><a class="reference internal" href="#pair-style-sw-gpu-command">pair_style sw/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-sw-intel-command">pair_style sw/intel command</a></li>
-<li><a class="reference internal" href="#pair-style-sw-kk-command">pair_style sw/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-sw-omp-command">pair_style sw/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_table.html b/doc/pair_table.html
index 96a7cdc10c..7d2c20725e 100644
--- a/doc/pair_table.html
+++ b/doc/pair_table.html
@@ -71,21 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style table command</a></li>
-<li><a class="reference internal" href="#pair-style-table-gpu-command">pair_style table/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-table-kk-command">pair_style table/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-table-omp-command">pair_style table/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html
index 18ed260aac..0ced9f121b 100644
--- a/doc/pair_tersoff.html
+++ b/doc/pair_tersoff.html
@@ -71,23 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style tersoff command</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-table-command">pair_style tersoff/table command</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-cuda">pair_style tersoff/cuda</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-kk">pair_style tersoff/kk</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-omp">pair_style tersoff/omp</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-table-omp-command">pair_style tersoff/table/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_tersoff_mod.html b/doc/pair_tersoff_mod.html
index e629994211..1ef79de50b 100644
--- a/doc/pair_tersoff_mod.html
+++ b/doc/pair_tersoff_mod.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style tersoff/mod command</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-mod-kk-command">pair_style tersoff/mod/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-mod-omp-command">pair_style tersoff/mod/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html
index c7cd3870c0..72106802af 100644
--- a/doc/pair_tersoff_zbl.html
+++ b/doc/pair_tersoff_zbl.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style tersoff/zbl command</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-zbl-kk-command">pair_style tersoff/zbl/kk command</a></li>
-<li><a class="reference internal" href="#pair-style-tersoff-zbl-omp-command">pair_style tersoff/zbl/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_thole.html b/doc/pair_thole.html
index 6c1272f4e9..a9b25e7edd 100644
--- a/doc/pair_thole.html
+++ b/doc/pair_thole.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style thole command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_tri_lj.html b/doc/pair_tri_lj.html
index e8356942cd..780a05d688 100644
--- a/doc/pair_tri_lj.html
+++ b/doc/pair_tri_lj.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style tri/lj command</a></li>
-<li><a class="reference internal" href="#pair-style-tri-lj-omp-command">pair_style tri/lj/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_write.html b/doc/pair_write.html
index 4c323a1882..7bbe5154bd 100644
--- a/doc/pair_write.html
+++ b/doc/pair_write.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_write command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_yukawa.html b/doc/pair_yukawa.html
index a71c1122b2..0e757f551d 100644
--- a/doc/pair_yukawa.html
+++ b/doc/pair_yukawa.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style yukawa command</a></li>
-<li><a class="reference internal" href="#pair-style-yukawa-gpu-command">pair_style yukawa/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-yukawa-omp-command">pair_style yukawa/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_yukawa_colloid.html b/doc/pair_yukawa_colloid.html
index 351c0f5441..4e3eb36bce 100644
--- a/doc/pair_yukawa_colloid.html
+++ b/doc/pair_yukawa_colloid.html
@@ -71,20 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style yukawa/colloid command</a></li>
-<li><a class="reference internal" href="#pair-style-yukawa-colloid-gpu-command">pair_style yukawa/colloid/gpu command</a></li>
-<li><a class="reference internal" href="#pair-style-yukawa-colloid-omp-command">pair_style yukawa/colloid/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/pair_zbl.html b/doc/pair_zbl.html
index c9f17acae0..fd96e2129d 100644
--- a/doc/pair_zbl.html
+++ b/doc/pair_zbl.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">pair_style zbl command</a></li>
-<li><a class="reference internal" href="#pair-style-zbl-omp-command">pair_style zbl/omp command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/partition.html b/doc/partition.html
index 2666e58ab8..7dc37d190e 100644
--- a/doc/partition.html
+++ b/doc/partition.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">partition command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/prd.html b/doc/prd.html
index 106f479d95..cffdd530ab 100644
--- a/doc/prd.html
+++ b/doc/prd.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">prd command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/print.html b/doc/print.html
index 97b495ce3c..c8a3cc9f7d 100644
--- a/doc/print.html
+++ b/doc/print.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">print command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/processors.html b/doc/processors.html
index 8087e76edf..ce086ef402 100644
--- a/doc/processors.html
+++ b/doc/processors.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">processors command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/python.html b/doc/python.html
index 83cdb3dca1..8459a712e9 100644
--- a/doc/python.html
+++ b/doc/python.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">python command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/quit.html b/doc/quit.html
index 1206f4c1ae..4e3309dea5 100644
--- a/doc/quit.html
+++ b/doc/quit.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">quit command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/read_data.html b/doc/read_data.html
index 8a3377705b..8f304177e1 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">read_data command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/read_dump.html b/doc/read_dump.html
index d48f2db406..0da7d5863b 100644
--- a/doc/read_dump.html
+++ b/doc/read_dump.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">read_dump command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/read_restart.html b/doc/read_restart.html
index 341c5cfdab..2746a69dd6 100644
--- a/doc/read_restart.html
+++ b/doc/read_restart.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">read_restart command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/region.html b/doc/region.html
index c1882abe18..e6fca45dac 100644
--- a/doc/region.html
+++ b/doc/region.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">region command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/replicate.html b/doc/replicate.html
index cd929eace1..4a0d76e36c 100644
--- a/doc/replicate.html
+++ b/doc/replicate.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">replicate command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/rerun.html b/doc/rerun.html
index 507f109e63..fbdab497d6 100644
--- a/doc/rerun.html
+++ b/doc/rerun.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">rerun command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/reset_timestep.html b/doc/reset_timestep.html
index 6784989f86..59cc168009 100644
--- a/doc/reset_timestep.html
+++ b/doc/reset_timestep.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">reset_timestep command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/restart.html b/doc/restart.html
index b34eaa1dc3..1b8b86d450 100644
--- a/doc/restart.html
+++ b/doc/restart.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">restart command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/run.html b/doc/run.html
index 8ae57422f0..41595b4dd6 100644
--- a/doc/run.html
+++ b/doc/run.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">run command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/run_style.html b/doc/run_style.html
index 71004e4636..91dab73e54 100644
--- a/doc/run_style.html
+++ b/doc/run_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">run_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/search.html b/doc/search.html
index f0c19a98d7..31a6e1cfd0 100644
--- a/doc/search.html
+++ b/doc/search.html
@@ -71,8 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"></div>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+
           
         
       </div>
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 9902f222da..12821f3cb7 100644
--- a/doc/searchindex.js
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5,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],checkf:164,checkqeq:393,checku:164,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,121,150,151,161,193,198,206,207,214,216,228,229,230,247,248,253,257,260,262,270,274,278,281,282,285,286,287,288,295,304,312,314,318,319,325,328,335,340,344,345,348,349,350,352,353,357,359,360,362,363,369,373,374,377,380,383,384,387,404,411,432,435,437,443],chemic:[9,118,138,143,167,178,179,205,261,266,267,285,319,392,393,400],chemistri:[9,260,261,263,339,357,392,393],chen:290,cheng:348,chenoweth:[392,393],chenoweth_2008:[392,393],chi:[92,133,166,251,261,263,358,360,449],chiefli:391,child:8,chip:[7,12,17,333,436],chipot:193,chiral:312,chmod:[11,12],cho:380,chocol:[7,169],choic:[3,6,12,15,16,18,40,41,54,87,121,123,137,148,164,181,184,185,188,191,194,195,207,213,216,227,229,253,261,270,285,313,319,324,325,328,330,333,364,377,384,388,423,432,433,436,437,442,443,447],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,134,135,168,189,190,191,192,195,202,213,216,227,229,231,232,233,234,235,257,278,282,296,318,319,325,413,418,420,432,438],chose:[408,410],chosen:[2,3,6,12,17,120,144,147,156,164,168,174,179,192,195,202,205,206,214,216,227,229,233,253,256,267,278,282,285,286,291,293,294,300,319,320,325,333,357,361,367,368,371,395,408,418,432,437,443],chri:142,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,124,139,141,181],chute:[4,10,208],ciccotti:273,cieplak:[6,150,435],cii:182,cij:182,circular:[3,6,123,165],circumst:18,circumv:265,citat:[],cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[],classic:[0,3,5,6,7,8,9,203,253,260,265,290,314,357],classifi:[9,405],claus:421,clean:[6,12,14,15,17,431],cleanli:[422,451],clear:[],clearli:7,clebsch:120,clermont:[9,13],clever:427,click:[2,11,22,37,44,55,144,152,163,168,210,305,313,328,346,405],client:[210,212],climb:[228,328,437],clinic:[7,13],clo:[133,166,449],clock:[12,418,437],clockwis:296,close:[3,6,11,12,13,39,41,67,121,147,167,190,191,192,207,214,216,229,247,270,273,296,299,317,319,322,324,325,328,333,335,339,349,350,380,384,410,427,433,443,445],closer:[3,41,116,142,166,167,188,192,196,287,328],closest:[190,251,270,293,360,394,404,413],cloud:443,clovertown:18,clsuter:72,clump1:[255,270],clump2:[255,270],clump3:[255,270],clump:270,cluster:[],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[],cn1:182,cn2:182,cna:[],cnn:182,cnr:[9,13],cnt:[364,427],co2:[40,143,327],coars:[7,9,29,36,40,54,156,255,270,278,362,395,435],coarser:[319,448],coarsest:120,code:[],coeff:[3,7,8,12,21,22,33,44,50,150,151,152,157,304,305,310,346,364,368,384,397,423,425],coeffcient:423,coeffici:[],coefficienct:353,coefficient0:355,coefficient1:355,coeffieci:[6,337],coeffincientn:355,coexist:[9,205,357],cohes:[6,358,380],coincid:[205,299,344,378,379,418],cold:[6,129,209,329,443],coldest:286,coleman8:9,coleman:[9,118,143,271],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,124,132,139,141,144,167,169,181,193,219,225,255,265,268,270,301,318,327,329,347,367,423,430,436,452],collid:[199,278,300],colliex:143,collinear:[3,255],collis:[3,216,278,296,300,354,361,416],colllis:278,colloid:[],colombo:39,colon:[170,301,424],color1:169,color2:169,color:[3,9,41,167,168,169,188,206,260,265],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,120,121,124,132,139,141,142,143,164,167,169,172,180,181,182,183,184,185,186,219,226,227,260,270,279,280,290,300,359,363,392,393,424,438,440,448],colvar:[],colvarmodul:12,com:[],comamnd:194,comand:[191,425],comannd:333,comb3:[],comb:[],comb_1:262,comb_2:262,combiant:350,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,123,137,167,168,178,183,210,219,229,253,259,282,291,299,302,304,318,319,321,325,333,347,349,350,357,358,364,376,377,396,406,408,410,415,426,431,443,448],come:[],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[],comm_styl:[],command:[],comment:[0,2,7,11,12,38,56,150,164,167,214,270,290,327,328,334,355,356,358,368,380,386,393,396,406,407,408,409,410,420,421,423,443,448],commerci:7,commmand:[3,6,12,59,107,248,417,418,420,437,451],common:[],commonli:[3,6,12,17,25,57,59,105,146,167,168,170,314,362,371,396,408,410,423,426,435],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,147,148,168,169,188,189,190,192,193,194,210,212,216,218,219,220,229,252,259,261,262,263,270,278,290,301,318,329,330,331,333,354,388,420,421,425,432,433,450,452],communc:318,comp:[7,212,213,273,319,328,357,384,389,394,403,407,409],compact:[63,172,346,405],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,127,142,143,152,163,169,198,261,301,303,318,319,326,328,380,418,437,438,443,447],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,151,152,163,304,305,313,345,405],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,155,167,170,174,180,181,182,183,184,185,186,188,252,264,282,285,292,295,298,318,333,365,384,407,420,421,448],compens:[6,189,190,268,329,357],compet:289,competit:319,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,142,167,168,170,210,289,319,333,423,424,428],compl:17,complain:[12,17],complement:380,complementari:[7,349,369],complet:[3,6,9,12,15,41,59,71,169,184,188,193,219,253,256,259,278,289,291,303,317,328,333,358,412,418,423,428,431,435,437,440,443,448],complex:[6,8,11,12,13,25,40,42,62,120,132,144,145,216,299,316,328,357,407,421,423,426,448],compli:[285,289],complic:[6,7,9,12,13,179,205,421],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,139,140,141,167,168,169,175,176,180,181,182,183,184,185,186,187,191,192,194,195,200,203,208,212,213,216,219,221,225,226,228,229,230,233,234,235,246,247,249,250,252,253,254,257,268,270,272,273,274,275,278,281,282,283,285,292,293,298,299,300,318,321,325,326,327,328,333,353,357,361,378,379,396,423,424,433,441,448,449],componenet:6,composit:[6,179,216,355],compound:[348,357,358],compres:[71,114,181],compress:[3,6,59,71,114,147,167,168,169,181,194,227,233,257,260],compris:[40,299,367,394,412],compton:[118,143],comptu:[3,6],compuat:319,comput:[],computation:[3,6,189,190,290,339],computational:443,compute_arrai:8,compute_fep:[174,377],compute_group_group:205,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,271],compute_scalar:8,compute_temp:8,compute_ti:174,compute_vector:8,compute_xrd:143,concaten:[2,3,451],concav:299,concentr:355,concept:[6,124,134,181,432],conceptu:[3,6,71,132,192,194,328,349,364,380,428],concern:[6,73,87,206],concis:[11,289],conclud:12,concret:8,concurr:[9,16,319],conden:[290,408,410],condens:[6,126,290,335,351,355,369],condit:[],conducit:6,conduct:[],cone:426,confid:[3,437],config:[12,167,420],configfil:193,configur:[1,6,12,15,17,38,59,146,164,166,167,168,172,192,193,194,195,199,205,212,213,241,253,261,289,316,326,328,335,339,356,380,406,408,410,418,423,425,426,437],confin:[423,437],conflict:[3,40,384,421],conform:[3,6,13,59,191,192,228,269,274,289,312,328,357,435],confus:3,conjuct:353,conjug:[7,8,213,325,357,392,393],conjunct:[6,7,71,86,87,114,127,132,138,144,148,169,173,174,213,216,220,241,256,257,261,262,263,265,270,278,286,293,298,318,319,328,340,342,346,349,353,357,363,369,387,395,411,423,426,430,443,452],connect:[3,6,87,129,147,191,210,255,270,273,275,328,350,361,404,410,420,421,427,443],conput:3,consecut:[3,11,12,39,71,144,169,173,174,195,210,211,349,369,373,418,424,426],consequ:[1,6,290,368,437],conserv:[3,172,179,191,198,199,206,209,213,215,216,220,225,227,229,241,270,273,281,282,286,293,294,298,328,352,353,361,375,432,437],consid:[6,9,70,71,78,87,115,129,130,147,167,169,173,174,180,182,184,188,190,191,195,217,230,252,270,285,286,289,290,293,319,346,357,364,393,394,404,418,419,421,424,425,426,428,431,433,441,443,448],consider:[6,8,213,214,281,282,283,333,432],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,124,127,129,144,156,166,170,175,176,181,194,195,198,200,203,206,213,214,215,226,229,231,232,233,234,235,236,237,239,240,241,242,244,245,246,247,248,249,257,260,265,267,269,270,281,282,283,284,294,318,319,321,327,328,333,335,339,341,347,349,357,360,378,379,380,384,394,407,413,421,423,424,426,427,428,435,443,448],consistent_fe_initi:178,consit:270,constant:[],constitu:[3,6,219,270,295,299,347,394],constrain:[3,6,8,122,123,124,125,127,130,131,132,133,134,136,137,172,181,195,205,206,211,219,223,255,256,268,270,273,276,286,293,326,327,357,428,435,443],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,120,143,192,229,252,269,299,329,333,352,384,404,406,407,426,427,448],constructor:8,consult:393,consum:[1,265,388,448],consumpt:316,contact:[],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,120,124,132,142,143,144,146,150,152,163,164,167,168,169,170,172,173,174,178,180,181,182,183,184,185,186,188,193,195,200,207,211,212,213,214,216,227,241,251,252,255,256,258,260,263,267,270,271,278,285,289,290,299,300,303,317,319,327,328,331,332,334,335,336,339,348,349,352,355,356,357,364,365,380,386,390,391,392,393,396,406,407,408,409,410,411,418,419,420,421,423,424,425,426,428,430,432,435,437,440,441,443,448,450,452],content:[12,18,393,439,441],context:[3,6,8,12,17,117,169,189,190,195,255,267,294,325,415,423,430,439,447,448,449],contibut:70,contigu:420,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,140,169,172,173,174,179,181,182,183,184,185,186,188,191,192,193,194,195,205,206,207,209,210,211,213,214,215,221,226,227,229,231,232,233,234,235,246,247,248,249,254,256,259,260,270,271,274,277,278,280,287,288,290,296,299,303,317,332,333,339,353,354,371,374,392,393,394,409,418,421,423,425,426,431,437,440,441,448,450],continuum:[6,7,9,178,290],contour_integr:178,contract:[59,192,194,229,257,270],contradictori:3,contrain:273,contraint:241,contrari:[207,214],contrast:[1,6,42,55,64,129,194,301,415,451],contrib:290,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,174,179,180,181,182,183,184,185,186,192,205,213,216,219,220,224,230,247,248,255,256,264,267,270,271,273,292,318,326,328,336,353,354,355,357,364,378,379,384,392,393,435,441,443],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,120,153,167,168,172,178,179,188,192,193,194,209,210,213,214,229,231,232,233,234,235,257,262,270,281,282,283,290,294,316,318,330,357,360,392,393,406,410,418,420,432,438,439],control_typ:178,controlfil:393,convect:91,conveni:[6,12,29,167,170,186,271,321,396,448],convent:[3,8,9,29,155,162,163,169,269,275,302,355,357,448],converg:[3,6,41,88,167,168,170,175,188,191,192,200,203,233,260,262,265,269,273,324,325,326,328,348,349,369,418,430,437],convers:[3,8,120,168,169,179,182,257,318,349,350,351,357,369,373,377,387,421,437,447],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,144,151,167,168,169,186,227,301,304,306,309,312,321,328,334,355,408,410,416,421,423,424,425,430,440,443,447,448,450,452],convex:299,convinc:[7,12],cooki:7,cool:[7,134,209,268],cooordin:167,cooper:[5,7],coord123:114,coord1:[3,114,181,184,185],coord2:[3,114,181,184,185],coord3:[3,114,181,184,185],coord:[],coordiat:326,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,120,127,133,139,141,142,144,148,166,167,168,169,170,172,175,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,201,203,205,208,209,210,211,212,213,214,226,228,229,231,232,234,235,247,250,251,252,255,256,257,267,268,270,272,273,274,275,276,277,278,280,288,289,290,297,298,300,301,321,326,327,328,333,334,335,338,356,418,423,424,426,428,431,433,437,443,448,449],coordn:[114,181],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,168,290,328,346,392,421],copper:416,coproccesor:16,coprocessor:[1,4,7,9,16,17,333,436],coproprocessor:17,copy_arrai:8,copyright:[7,8,255],coral:169,core:[],core_shel:126,coreshel:[6,9,342,349,351],cornel:[6,150,435],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,168,299,300,321,412,423],cornflowerblu:169,cornsilk:169,corpor:16,corr:348,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,126,131,138,168,194,207,213,229,230,247,255,257,260,289,295,299,318,328,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,423,438,441,443],correction_max_iter:178,correctli:[3,8,9,11,17,71,81,102,103,122,123,125,127,129,130,131,132,133,136,137,140,167,169,175,195,200,203,214,223,229,230,263,270,273,275,277,296,299,328,329,333,351,379,420,421,423,447,449],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,120,122,123,131,138,143,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,181,183,184,185,187,190,192,194,201,203,204,208,213,216,217,225,226,227,229,231,232,233,234,235,236,241,244,246,247,249,252,253,257,262,270,272,273,281,283,285,294,295,296,298,299,300,302,304,305,306,307,308,309,312,314,319,323,325,327,328,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,418,420,421,423,424,426,436,437,438,440,441,443,448],correspondingli:[378,379,432],cosin:[],cosineshift:27,cosmo:[207,212],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,121,143,168,169,181,184,185,188,189,190,202,229,262,290,318,319,331,349,369,373,384,406,420,432],costheta0:[406,408,410],costheta:390,costli:[11,88,207,329],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,124,134,139,141,157,167,168,169,173,174,179,181,182,184,188,194,203,212,259,260,261,265,268,270,272,278,279,285,289,290,291,295,299,301,303,310,315,317,324,326,329,333,336,359,363,364,392,393,419,420,421,423,425,427,430,431,439,443,448,449],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,121,145,149,261,263,291,318,319,326,333,340,342,343,344,345,348,349,350,351,352,357,361,362,364,369,373,377,384,387,392,393,395,405,410,411,415,428,435,441,443,447],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,132,142,148,175,176,179,181,183,184,185,187,188,195,200,202,205,211,229,241,256,273,281,282,299,319,326,327,328,330,333,359,363,384,441,448],counter:[296,418,429,431,437],counterbal:209,counterpart:[167,270,418],counterproduct:18,coupl:[],cours:[3,8,138,167,173,174,206,269,275,289,295,297,298,300,301,319,378,397,420,423,436,443,448,450],coval:[6,29,357,380,443],covari:207,cover:[6,71,164,169,178,216,357,367,412],coverag:[71,184],cpc:212,cpp:[1,3,6,8,9,11,12,13,87,167,173,174,203,273],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,169,172,198,214,291,316,319,333,346,405,418,436,437,440,441],cpuremain:441,cr2:143,cr3:143,crack:[4,329],crada:[5,7],crai:[5,7,13,18,167],crash:[3,329,443],craympi:333,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:[],creation:[],crimson:169,critchlei:255,criteria:[3,116,145,168,169,189,190,191,224,326,389,412,425,428,448],criterion:[41,142,144,147,179,188,191,205,241,262,296,301,326,328,348,357,361,428,437,438],criterioni:437,critic:[48,49,227,285,290,326],cross:[3,12,22,71,89,123,152,167,168,180,184,190,194,226,228,247,270,275,277,286,293,305,321,328,344,353,354,355,362,363,364,369,371,373,390,395,408,410,423,427,433,450],crossov:1,crossterm:423,crozier:[0,7,13],crucial:260,crystal:[4,6,13,73,251,252,288,329,427,441,443],crystallin:[6,252,321,409,443],crystallis:285,crystallogr:[118,143],crystallograph:[321,441],crystallographi:[118,143,321],cs1:143,cs_chunk:6,cs_im:[40,423],cs_re:[40,423],csanyi:[120,391,396],cscl:380,csequ:6,csh:[11,12,346],cshrc:[11,12],csic:[356,406,408,410],csinfo:6,csisi:[356,406,408,410],csld:[],cst:355,cstherm:6,cstyle:420,csvr:[],ctcm:[334,355],ctemp_cor:198,cterm:274,ctr:9,ctype:11,cu1:143,cu2:143,cu3au:380,cube:[6,41,142,147,188,198,299,321,443],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:339,cummul:[3,6,186,189,190,191,193,202,207,213,215,278,281,282,283,284,286,293,363,441],cumul:[6,179,181,183,184,185,199,205,213,227,229,233,241,270,271,328],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,121,124,132,140,142,145,148,167,168,169,170,173,174,178,179,181,184,185,186,188,189,190,191,192,193,194,195,199,200,203,205,207,210,211,213,219,226,229,230,234,235,241,246,247,249,255,261,262,264,267,268,269,270,273,274,276,277,278,281,282,283,289,290,293,294,295,296,297,298,300,301,303,316,317,318,319,322,323,325,326,327,328,333,339,346,348,352,355,357,358,361,365,368,378,379,380,381,382,384,390,392,393,397,408,410,411,413,418,419,420,421,423,424,425,426,427,429,430,431,433,435,437,438,440,441,448,449,450,451,452],curv:[6,144,205,252],curvatur:[360,394,416],custom:[],cut0:421,cut1:432,cut2:432,cut:[],cuthi:[251,263],cutinn:[341,378,379],cutlo:[251,263],cutmax:390,cutoff1:[345,352,369,373,377,387,395],cutoff2:[340,342,343,345,351,352,369,373,377,387,395],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,120,142,145,147,190,191,196,251,260,261,263,265,267,270,278,291,295,299,301,318,319,326,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,421,425,428,432,443],cutoffa:356,cutoffc:356,cuu3:355,cval:143,cvd:285,cvel:274,cvff:[],cwiggl:[3,226,295,298,300,448],cyan:[2,168,169],cycl:[3,205,227,229,230,233],cyclic:[3,164],cygwin:12,cylind:[3,4,168,211,256,296,299,426],cylindr:[6,211,275,296],cypress:333,cyrot:339,cyrstal:252,d3q15:216,d3q19:216,d_double_doubl:15,d_e:290,d_flag2:259,d_flag:259,d_name:[113,167,259,280,433],d_single_doubl:15,d_single_singl:15,d_sx:259,d_sy:259,d_sz:259,daan:288,dai:12,daili:12,daivi:247,damag:[],dammak:265,damp:[3,6,172,177,213,214,215,220,229,230,233,257,260,265,270,281,282,294,296,297,325,326,328,340,342,344,349,352,357,361,369,377,387,395,405,411,437,443],damp_com:214,damp_drud:214,dampen:[270,443],dampflag:[296,361],dan:17,danger:[3,12,205,301,353,441],dangl:147,daniel:9,darden:[319,352],darkblu:169,darkcyan:169,darken:168,darkgoldenrod:169,darkgrai:169,darkgreen:169,darkkhaki:169,darkmagenta:169,darkolivegreen:169,darkorang:169,darkorchid:169,darkr:169,darksalmon:169,darkseagreen:169,darkslateblu:169,darkslategrai:169,darkturquois:169,darkviolet:169,dasgupta:261,dash:[361,440],dat:[6,91,164,178,419],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,271],dataset:271,datatyp:3,date:[0,6,12,13,392,393,448],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,167,182],davi:295,david:[9,19,318,319,408,410],daw:[355,390],dbg:14,dcd:[3,6,7,167,168,169,170,253,424,428],ddim:166,deactiv:377,dealt:212,debug:[6,7,11,12,13,14,17,118,143,144,253,258,316,318,333,365,384,413,421,422,425,430,433,440,448],deby:[],decai:[349,416],decid:[3,6,12,16,71,226,259,270,291,438],decipher:321,declin:278,decod:168,decompos:[87,396],decomposit:[3,5,7,18,62,178,253],decoupl:[6,443],decreas:[3,167,175,176,191,194,200,203,213,289,318],decrement:274,deepli:315,deeppink:169,deepskyblu:169,def:[12,13,421],defaul:61,defect:[6,70,142],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,150,151,152,153,154,155,156,158,159,161,162,163,164,165,166,167,168,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,203,204,205,208,211,212,213,214,215,216,224,226,228,229,230,231,232,233,234,235,237,238,239,242,244,245,246,247,248,249,251,252,253,255,256,257,259,261,263,268,270,271,272,273,276,278,280,281,282,283,284,286,287,288,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,330,331,332,333,335,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,356,357,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,426,427,428,429,432,433,434,435,437,438,440,441,443,444,445,446,447,448,449],definit:[2,3,6,8,12,13,78,80,116,120,169,181,182,183,184,185,186,194,211,233,271,280,292,295,298,300,302,313,316,327,336,339,347,357,367,390,396,412,421,423,425,432,434,447,448],defint:441,deform:[],deg2theta:143,deg:443,degener:[3,255],degrad:[8,18,252,319,432],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,143,144,150,151,154,155,162,164,166,168,181,191,198,205,207,208,213,214,219,229,230,233,234,235,246,247,249,253,255,269,270,273,281,282,283,288,304,306,309,312,314,326,352,355,363,433,441,443,449],degress:[124,181],del:437,delai:[3,6,12,329,354,441],deleg:364,delet:[2,3,7,8,12,54,57,60,63,142,147,148,172,181,182,183,184,185,186,189,191,202,205,229,271,281,282,301,303,317,327,329,332,384,423,424,426,434,435,440,444,446,448,449],delete_atom:[],delete_bond:[],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[],delta_1:339,delta_3:339,delta_7:339,delta_conf:3,delta_ij:[380,390],delta_mu:[3,179],delta_pi:339,delta_r:390,delta_sigma:339,delx:166,delz:166,demand:265,demo:11,demon:250,demonstr:[260,380],den:256,dendrim:363,denniston:[9,216,218,219,220,252],denomin:[7,149],denot:[118,198,214,252,263,265,349,362,364,393],dens:[71,191,357],densiti:[3,6,7,9,18,40,41,59,100,116,120,130,142,144,173,174,178,181,184,185,188,194,203,216,219,222,223,252,256,257,261,290,295,321,323,327,334,339,355,380,381,382,390,394,399,401,402,403,423,432,433,441,447],depart:[0,7],departur:[227,260],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,120,122,127,131,132,138,144,145,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,168,169,172,173,174,175,176,179,181,183,184,186,187,188,190,192,200,201,204,207,208,209,211,213,214,216,218,219,226,229,231,232,233,234,235,236,244,246,247,249,251,262,265,267,270,272,273,278,281,282,283,285,287,289,290,292,294,295,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,326,327,329,330,331,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,383,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,429,433,435,437,440,441,442,448,449],dependend:6,depflag:12,dephas:[418,437],depos:195,deposit:[],deprec:261,depth:[51,123,168,290,360,394],dequidt:9,der:[87,107,347,348,377,392,393,415,443],deriv:[6,7,8,38,56,63,87,120,138,164,182,192,194,205,213,226,229,231,232,233,234,235,251,257,261,265,287,288,290,295,296,299,325,327,335,339,347,352,357,358,362,371,375,376,380,392,393,405,407,415,443],derjagin:415,derlet:251,descend:169,descent:[7,325],descib:[40,261],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,120,121,123,124,128,129,132,135,137,138,142,143,144,146,147,156,161,164,167,172,173,174,181,182,183,184,185,186,188,191,192,193,194,195,197,198,206,207,210,211,212,213,214,215,216,218,219,220,224,228,229,230,233,240,248,251,253,258,259,260,261,262,263,270,274,275,278,279,280,281,282,283,284,285,286,287,288,293,295,296,298,303,318,319,321,324,325,326,327,328,332,335,336,338,340,341,342,344,345,346,347,348,349,352,355,357,358,360,361,362,364,369,370,371,372,373,374,375,376,377,378,379,380,383,389,390,391,392,393,394,395,396,397,404,405,406,407,408,409,410,411,414,415,416,418,420,421,423,424,426,427,433,436,437,440,448,449,450],descript:[],descriptor:[120,167,365],deserno:319,design:[0,3,6,7,8,11,13,14,15,17,118,126,129,143,178,191,197,198,229,230,251,252,271,285,290,336,337,338,341,344,349,351,357,377,378,379,381,382,390,393,407,432],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,121,126,144,157,166,179,192,194,203,205,206,213,214,215,219,229,247,255,256,257,258,261,265,270,273,278,281,282,283,284,289,296,310,315,318,319,321,324,326,327,328,353,355,363,378,379,406,408,410,419,420,421,423,427,432,437,438,440,441,448,449,450],desk:7,desktop:[4,6,7,10,12,17,168],despit:443,destabil:339,destre:312,destroi:[11,39,189,190],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,120,121,122,123,124,127,137,138,139,141,144,145,148,149,152,163,167,168,169,172,173,174,178,181,182,183,184,186,188,190,191,192,193,194,195,203,205,206,207,208,210,211,213,215,216,220,226,227,228,229,230,231,232,233,234,235,239,241,246,247,248,249,252,255,256,257,259,260,262,263,264,270,273,278,281,282,283,284,285,286,288,289,290,291,292,293,294,301,303,305,313,318,319,322,326,327,329,330,333,334,335,336,338,339,341,343,344,345,346,347,348,349,352,353,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,396,397,405,412,414,415,421,423,424,425,426,428,429,432,433,435,438,441,448,449,452],detect:[2,3,12,61,63,86,204,256,289,328,348,363,368,418,420,423,434,437,448],determ:333,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,121,132,133,142,143,144,166,167,168,169,170,171,175,176,177,180,181,182,183,184,185,186,187,188,192,194,195,198,200,205,208,209,211,213,214,219,224,226,227,229,234,235,246,247,249,251,253,257,260,267,268,269,270,271,272,278,281,282,283,285,291,292,295,296,297,298,299,300,301,313,318,319,321,327,329,330,333,335,336,343,348,352,354,355,359,361,365,373,380,384,393,394,404,407,411,415,420,423,424,426,428,430,433,437,439,440,447,448,449],detil:108,devan:[9,395],devanathan:410,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,210,233,255,260,261,264,335,339,357,382,425],devemi:9,deviat:[227,233,251,359],devic:[1,3,12,15,17,210,333],device_typ:333,devin:[262,348],devis:382,dfactor:168,dff:443,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,319],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,264],dhi:[59,166,194,256],dhug:[227,260],dhugoniot:[227,260],dia:380,diagnost:[],diagon:[3,6,83,120,121,192,229,257,270,293],diagonalstyl:396,diagram:[41,118,143,163,188,253],diallo:363,diam:[168,169,256,327],diamet:[3,6,40,113,144,167,168,169,173,174,213,256,270,278,294,296,327,347,360,361,367,371,394,412,415,423,424,433],diamond:[321,357,380],diamter:[40,256],dick:6,dicsuss:226,dictat:[179,227],did:[3,12,326,353,354,355,361,384,408,410,431],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,140,292,318],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,122,123,124,125,127,130,131,132,133,134,136,137,138,144,145,147,152,163,164,166,167,168,169,172,174,177,179,181,183,188,189,190,191,192,193,194,198,204,205,206,207,208,209,210,213,214,216,226,229,230,231,232,234,235,237,239,242,244,245,246,249,251,253,255,257,260,261,262,265,268,270,273,274,275,276,278,281,282,283,286,287,288,290,293,294,295,296,299,303,304,313,315,317,318,319,321,322,324,325,327,328,330,331,332,333,334,335,339,343,344,346,347,348,353,355,357,360,361,362,364,367,369,370,372,373,380,381,382,383,384,386,390,392,393,394,395,396,397,405,406,407,408,410,412,415,416,417,418,420,421,423,425,426,427,428,431,432,433,435,437,438,440,441,443,447,448,449,450],differenti:[1,3,6,29,164,318,349,390,409],difficult:[192,253,333,363,432],difficulti:392,diffract:[],diffus:[],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[],dim1:3,dim2:3,dim:[3,59,71,122,125,126,127,130,131,132,133,134,136,144,166,184,194,211,296,321,380,426,447,448,449],dimdim:448,dimems:252,dimens:[],dimension:[3,39,112,118,120,122,124,125,126,127,130,131,132,133,134,136,143,165,181,184,228,252,290,321,324,328,390,423,433],dimensionless:[105,120,290,319,396,415],dimer:[6,270,380],dimgrai:169,dimstr:[41,188],dinola:[257,281],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,167,280,443],dir1:434,dir2:434,dir:[1,3,4,8,11,12,227,251,260,277,390,392,393,421,434,448],dirac:120,direc:390,direct:[],directli:[3,6,8,9,11,12,87,113,120,167,168,175,200,207,211,216,252,271,282,294,296,297,298,299,321,325,333,334,335,340,342,343,349,352,355,357,369,373,384,387,395,404,421,433,434,435,441,448],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,170,193,212,255,261,264,278,287,288,328,332,334,335,339,346,348,349,355,356,358,365,366,377,380,381,382,386,390,391,392,393,396,406,408,409,410,421,423,424,425,434,448],disabl:[3,12,16,290,368,421,436],disadvantag:[6,188],disallow:[194,229],disappear:425,discard:[2,3,41,71,184,188,291,299,420,425,426],discontinu:[9,164,326,375],discourag:380,discov:[13,291],discret:[6,8,40,42,168,169,213,216],discuss:[],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[],displace_atom:[],displace_box:59,displacemet:426,displai:[11,13,22,37,44,55,152,163,167,168,305,313,346,405],dispters:3,dissip:[6,206,213,252,287,288,341,353,361,378,379,405],dissolut:189,dist:[6,69,91,108,117,167,253,269,354,404,418,449],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,133,139,142,144,145,146,147,151,166,167,168,169,177,181,184,185,189,190,191,192,194,195,196,199,205,211,216,226,227,228,229,233,241,251,252,256,260,261,268,269,270,273,274,275,276,277,278,285,286,288,289,290,293,295,296,297,298,299,300,304,318,319,321,324,326,328,329,330,333,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,359,360,361,362,363,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,421,423,426,432,433,437,441,443,447,449],distinct:[6,198,267,318,394],distinguish:[6,86,120,219,357],distort:334,distrbut:334,distribut:[],distro:[111,346,389,390],ditto:[8,11,12,14,15,16,17,18,115,190,421],div:8,divd:117,diverg:[3,12,39,270,288,425,443,450],divid:[3,6,16,41,91,112,117,121,141,142,152,163,169,181,182,183,188,194,251,286,293,298,318,326,328,358,393,432,440,448],divis:[6,216,339,367,377,420,423,441,448],dl_poli:7,dlambda:138,dlammps_async_imd:210,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,168],dlammps_gzip:[3,12,167,168,289,423,424,428],dlammps_jpeg:[3,12,168],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,168],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,167],dlen:433,dlmp_intel_offload:[12,16],dlo:[59,166,194,256],dlvo:[7,347,415],dm_lb:216,dmax:[278,324],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,389,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,440,441,448,449,450,451],docuement:394,dodgerblu:169,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,123,124,127,132,134,138,143,144,145,146,148,150,152,157,163,164,166,167,168,169,172,178,179,181,184,187,188,190,191,192,194,198,200,202,205,206,209,211,213,214,216,219,225,229,230,231,232,234,235,246,247,248,249,257,258,259,263,265,268,270,278,281,283,285,286,290,293,294,295,298,299,300,301,306,307,309,310,312,317,318,319,320,321,327,328,329,334,335,336,337,338,339,341,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,364,365,366,367,368,371,372,374,375,376,378,379,380,381,382,384,390,391,392,393,394,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,436,437,440,441,443,448,452],doegenomestolif:7,doesn:[3,7,8,12,144,167,179,184,185,275,327,329,333,335,348,356,366,392,393,406,408,409,410,423,425],dof:[3,8,112,123,124,137,181,270,449],dof_per_atom:[124,181],dof_per_chunk:[124,181],doff:[327,423],doi:[6,193],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,133,143,146,166,168,169,172,179,188,192,194,195,209,212,216,229,230,253,265,270,290,295,296,318,319,328,333,354,384,418,420,423,427,440],domin:[1,357,437],don:[0,8,11,12,13,116,147,175,200,214,259,299,380,421,423],donadio:282,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,138,141,144,147,164,168,169,178,179,181,183,184,185,186,188,189,190,191,192,194,195,203,205,210,211,213,214,221,229,234,235,246,247,249,250,252,253,254,259,267,270,271,273,278,281,282,283,285,287,288,301,303,317,318,319,326,328,329,332,333,335,343,355,364,365,366,373,379,380,384,392,404,407,412,418,419,420,421,424,427,428,431,441,443,448,449],donor:363,dot:[121,140,175,200,208,228],doti:[339,390],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,194,203,258,299,303,317,319,332,333,339,358,362,392,393,419,423,427,431,436,448,449],dover:178,down:[3,6,7,8,11,39,71,192,213,278,294,333,357,384,422],downhil:[324,325],download:[5,7,8,9,11,12,13,17,210,365,391],downsid:6,downward:267,dozen:[8,12,107,172,392,393],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[],dragforc:216,drai:[227,260],drain:[209,294,326],dramat:[59,166,189,190,191,192,194,229,278,281,282,319,333,384,420],drautz:339,draw:168,drawback:259,drawn:[167,168,169,206,418],drayleigh:[227,260],dreid:[],drfourth:105,drho:[113,334,355],drift:[6,103,105,206,207,213,214,225,268,278,432,440,443],drive:[11,12,176,192,194,208,229,251,257,270,297,328],driven:[6,156],driver:[6,12,14,15,172,203,210],drop:[3,169,353],droplet:364,drsquar:105,drude:[],dry:202,dsecriptor:365,dsf:[],dsmc:[],dstyle:256,dt_collis:216,dt_lb:216,dt_md:216,dt_srd:278,dtilt:[59,194],dtneb:437,dtqm:260,dtype:[115,190],dual:[17,278,333],dudarev:143,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,120,121,122,123,125,127,130,131,132,133,134,136,137,139,143,144,147,148,167,168,172,175,176,183,187,189,190,191,192,193,194,195,200,201,202,203,206,207,210,211,213,214,215,216,219,220,221,225,226,227,228,229,233,241,251,254,256,268,269,270,272,275,277,278,279,281,282,283,284,285,287,288,290,294,295,297,298,299,301,319,324,326,328,329,330,350,353,355,359,360,364,378,379,384,390,392,394,395,404,407,408,410,413,415,416,418,420,423,424,425,432,437,440,441,443,448,449],duffi:290,duin:[9,261,266,392,393],duke:319,dummi:[12,29,409],dump1:428,dump2:428,dump:[],dump_atom:8,dump_custom:8,dump_modifi:[],dumpcustom:8,dumptimestep:428,dunbrack:[6,20,150,344,435],dunweg:[213,215],duplic:[2,3,14,15,16,17,18,19,41,42,145,188,207,251,423,447],dupont:[5,7,13],durat:[37,55,122,123,125,126,127,129,130,131,132,133,136,137,163,169,181,205,265,290,313,361,405],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,145,148,164,167,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,319,326,328,332,333,353,377,384,393,407,418,419,421,423,426,428,430,431,433,435,437,438,441,448,451,452],dvector:8,dvlo:415,dvx:6,dx_lb:216,dy3:143,dyamic:12,dyanam:6,dyanmic:437,dynam:[],dynamo:[5,334,355,380],dyne:447,dyre:374,dysam:426,e28637:29,e_1:339,e_2:339,e_b:358,e_e:357,e_hbond:363,e_i:[6,339,358],e_j:[6,339],e_k:[339,357],e_kl:6,e_lj:[335,352],e_n:[339,357],e_nn:357,e_pr:357,e_rebo:335,e_tors:335,eaa:304,eaat:151,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,131,132,133,134,136,137,138,139,140,141,142,143,144,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,261,262,263,265,267,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,291,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,313,314,317,318,319,321,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,440,441,443,447,448,449,450,452],eacn:[41,188],eam0d:252,eam3d:252,eam:[],eam_databas:13,eam_gener:13,eangl:441,earli:[41,181,183,184,185,186,188,264,271],earlier:[7,8,12,59,169,328,361,380,384,437],earliest:437,earth:357,easi:[6,7,8,11,13,87,121,167,173,174,175,176,184,187,200,208,209,211,213,214,272,281,282,283,295,298,300,327,423,426,431,433,449],easier:[8,9,13,16,167,168,252],easili:[8,11,168,169,294,328,420,430,439,448],eastwood:[318,319],eat:151,eatom:301,eaxmpl:6,eba:21,ebb13:151,ebb:21,ebond:[198,214,440,441],ebt:151,ec_ii:380,ec_ij:380,ec_jj:380,echo:[],eco:[392,393],ecoa:[392,393],ecoul:[107,198,214,392,393,441],ecp:[357,423],edg:[2,3,6,41,59,71,118,142,143,146,147,168,177,184,211,272,295,298,299,300,301,321,423,426,433],edge_histo:142,edge_threshold:142,edih:441,edim:286,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,443],editor:13,edu:[7,9,11,13,355,378,389,392,393],edward:[9,17],eebt:151,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,109,112,121,122,126,131,132,139,142,148,150,151,153,154,155,156,158,159,161,162,163,164,166,167,168,169,173,174,175,178,182,185,186,187,189,190,191,192,194,195,201,204,206,207,208,209,210,211,213,214,228,229,231,232,233,234,235,236,244,246,247,249,250,251,253,256,257,259,260,261,262,265,269,270,272,273,277,278,281,282,283,285,286,288,290,293,294,295,296,297,299,300,301,304,306,307,308,309,312,314,318,319,321,325,326,327,328,329,334,335,337,339,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,425,426,428,432,433,435,441,447,448,450],efffect:427,efficaci:39,effici:[0,1,3,6,7,8,10,12,15,17,18,39,58,61,67,112,167,168,169,192,194,198,207,229,253,255,265,270,273,278,318,319,324,329,333,339,347,349,364,369,373,394,430,452],effort:[5,7,424],efftemp:[96,97,130],efi:[392,393],efield:[],eflux:209,eggebrecht:349,ehb:[392,393],eigensolv:3,eigenvalu:[252,253,318],eigtol:3,eik:138,eim:[],eimp:441,einstein:[265,288],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,41,44,50,59,63,71,107,113,116,118,120,121,124,126,127,143,144,147,152,157,164,167,168,169,172,180,182,183,185,186,188,191,192,193,194,195,205,211,212,216,220,226,227,229,230,233,247,251,267,270,272,273,274,275,278,285,292,296,299,303,305,316,318,319,321,325,326,330,333,339,341,347,355,364,365,367,378,379,380,384,388,390,408,410,412,418,421,423,425,426,427,430,432,435,438,440,448],ejtehadi:[347,360,394],elaplong:[173,174,211,426,441,448],elaps:[3,173,174,175,176,187,194,200,208,209,211,213,214,226,256,272,281,282,283,295,296,298,300,397,418,426,428,429,433,437,441,448],elast:[],elba:29,electr:[6,172,178,200,214,318,319,358,392,393,416,443,447],electrolyt:[9,415],electron:[3,6,7,9,13,40,96,97,113,118,128,130,135,172,178,197,198,214,215,230,240,248,263,284,290,325,327,334,336,348,352,355,357,358,380,390,391,410,416,423,443,447],electron_integr:178,electron_temperatur:178,electron_unit:357,electroneg:[6,261,262,263,348,358],electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,179,205,261,263,264,291,318,319,347,352,357,369,377,379,393,415],eleftheri:270,elem1:[358,380,396],elem2:[358,380,396],element1:[267,334,355],element2:[267,334,355],element:[3,6,7,8,13,63,81,89,103,105,112,117,119,120,121,122,123,124,125,126,127,131,132,133,134,136,137,140,167,168,169,170,172,178,182,183,186,252,267,285,292,334,335,339,348,355,356,357,358,364,365,366,380,381,382,386,390,391,392,393,396,406,408,409,410,443,448,451],elementn:[334,355],elementset:178,elev:437,elif:[120,303],elig:[3,179,189,190,202,205,363],elimin:[3,6,71,206,213,214,270,273,287,288,418],elj:352,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,82,123,165],ellipsoid:[3,4,6,7,13,40,42,82,113,123,144,165,167,213,231,234,237,238,246,270,278,323,326,360,379,394,405,423,433,450],ellipsoidflag:423,elong:[198,214,441],elp:[392,393],els:[3,7,8,12,71,107,116,117,119,168,180,181,182,183,184,185,186,205,229,270,278,290,291,292,301,303,318,364,422,434,448,451],elsewher:[8,226,278,380,391,392,393,435,441,448],elt:380,emac:[],email:[0,3,5,7,8,11,358],emb:[3,9,299],emb_lin_neg:380,embed:[3,5,7,11,12,13,29,88,142,290,334,355,358,377,380,381,382,390,405,413,421],embt:151,emi:[7,9],emol:[392,393,441],emphas:361,empir:[178,282,335,357],emploi:[9,252,265,409],empti:[3,57,71,146,270,318,329,368,423,434,435,448],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,83,87,96,97,98,99,100,101,105,109,111,112,120,122,123,126,128,130,131,135,136,138,142,150,151,153,154,155,156,157,158,159,161,162,163,164,167,169,170,172,173,174,175,176,177,179,185,187,189,190,191,193,195,200,201,202,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,222,223,225,227,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,260,261,262,263,264,265,266,267,269,270,272,273,274,275,277,278,281,283,284,285,286,287,288,290,291,293,294,295,296,297,299,302,304,306,307,308,309,310,312,313,314,319,326,328,332,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,421,424,425,430,432,448,452],enclos:[2,6,12,146,167,258,303,380,419,421,431,448],encod:[13,39,42,167,168,169,259,364],encompass:[3,6,40,57,59,116,145,292,405,426],encount:[3,8,12,59,183,332,428,448],encourag:[7,8,264,276],end12i:113,end12x:113,end12z:113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,147,148,151,166,167,168,169,170,173,174,182,183,185,186,191,194,198,206,211,213,214,215,228,229,230,241,257,269,270,274,278,281,282,283,284,286,289,290,293,297,300,301,317,318,327,328,332,333,353,355,360,394,396,397,411,413,418,421,423,424,425,426,428,430,431,435,439,441,443,448,452],end_of_step:8,endbondtors:[3,151,157,423],endif:8,energet:[191,335,393],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,167,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,318,319,324,325,326,328,329,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,404,405,406,407,408,409,410,412,413,414,415,416,418,421,423,428,432,433,435,437,439,440,441,443,447,448,451],energy_update_freq:393,enforc:[6,57,58,104,166,167,168,170,172,179,191,194,229,250,252,262,270,273,303,318,369,420,448,449],enforce2d:[],eng:[11,65,69,108,167,203,301,303,348,382],eng_previ:303,engin:[178,194,255,274,287,355,381],engr:[392,393],enhanc:[174,178,418],enlarg:[59,168],enough:[3,40,61,86,144,145,147,188,214,256,260,265,270,291,295,296,299,329,333,349,388,423,427,428],enpub:355,ensembl:[],ensight:6,ensur:[3,6,120,167,179,192,205,206,229,289,319,339,354,377,404,406],enter:[57,134,358,437],enthalpi:[231,232,355,440,441,448],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,121,124,143,144,169,172,173,174,181,184,185,188,191,193,202,205,206,209,213,214,225,229,231,232,233,234,235,251,253,255,268,270,276,290,292,303,333,352,373,384,407,423,431,432],entireti:[367,412],entiti:[6,8,40,42,167,270],entri:[3,8,38,42,56,65,69,79,92,108,115,118,142,164,169,183,184,185,193,260,301,327,339,356,380,386,393,396,406,407,408,409,410],entropi:437,entry1:[38,56,169,346,407],entry2:169,entryn:169,enumer:[145,167],enumuer:6,env:333,environ:[1,3,6,11,12,16,17,18,168,207,212,251,333,334,339,346,348,356,357,390,408,420,434,448],epair:[107,169,359,363,392,393,441],epen:[392,393],epfl:[207,212],epp:352,epq:352,eps0:415,eps14:377,epsilon0:410,epsilon:[3,6,36,45,46,50,53,54,87,150,173,174,205,270,278,295,299,324,326,338,344,345,347,349,350,351,352,360,362,363,364,367,368,369,370,371,372,373,374,375,376,377,383,387,394,395,400,406,412,414,415,432,443,447],epsilon_0:416,epsilon_14:344,epsilon_:394,epsilon_d:350,epsilon_i:[360,384,394],epsilon_i_:394,epsilon_i_a:[360,394],epsilon_i_b:[360,394],epsilon_i_c:[360,394],epsilon_ij:384,epsilon_j:[360,384,394],epsilon_j_:394,epsilon_j_a:[360,394],epsilon_j_b:[360,394],epsilon_j_c:[360,394],epsilon_lj:394,epton:389,eqch:139,eqeq:[392,393],eqp:352,eqq:352,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,121,123,138,140,144,168,169,172,173,174,175,176,179,182,183,186,187,188,192,194,195,200,205,206,208,209,211,213,214,216,219,220,226,227,233,243,251,253,256,258,260,261,262,265,267,269,270,272,274,281,282,283,286,287,288,290,292,293,295,298,300,301,303,317,326,328,329,330,332,333,348,353,359,360,363,378,383,390,392,393,394,396,397,407,412,416,419,420,421,423,425,426,430,431,434,437,439,441,448,449],equat:[3,6,7,8,9,91,112,118,143,152,163,172,192,198,199,207,213,214,216,219,227,228,229,230,233,247,251,253,260,261,265,273,278,286,290,293,295,296,298,300,312,318,319,347,352,353,357,358,361,366,378,379,380,384,394,399,400,402,403,411,416,443],equi:230,equidist:228,equil:[3,261,322,430,452],equilater:433,equilibr:[3,4,5,6,7,9,59,91,144,172,179,182,191,192,205,227,229,230,247,248,260,261,262,263,286,287,288,293,348,349,392,393,419,433],equilibria:293,equilibribum:[189,190],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,127,128,151,153,192,194,205,206,207,214,216,229,233,247,260,265,269,273,274,275,278,285,286,288,293,304,306,309,312,348,380,386,443],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:178,equival:[6,12,13,59,142,146,169,183,186,192,194,205,213,229,247,257,269,270,298,353,357,408,410,423,426,431,432,441,443],equlibrium:6,equliibr:[261,263],er3:143,eradiu:[40,113,357,423],eras:[272,287],erat:[194,379],erc:349,erfc:[349,369,384],erforc:113,erg:447,erhart:[179,355,408,410],ermscal:336,ernst:9,eror:3,eros:380,erose_form:380,erot:[],errata:[408,410],erratum:295,erron:3,error:[],erta:361,ervel:[113,423],escap:[195,443],especi:[8,11,16,132,144,172,179,188,205,260,265,268,269,333,420],espresso:[9,264],essenti:[8,11,12,27,88,125,126,127,130,131,132,133,134,136,153,182,233,252,294,319,335,349,369,410,428,441],essex:29,establish:[87,209],estim:[1,3,6,10,12,38,41,56,91,121,178,188,199,227,278,285,318,319,324,384,393,407,437,441],esu:447,esub:380,eta:[6,216,229,260,261,263,294,356,358,360,390,409,447],eta_dot:229,eta_ij:390,eta_ji:358,etag:[40,423],etail:441,etap:229,etap_dot:229,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,121,122,124,125,126,127,128,130,131,132,133,134,136,138,144,146,147,148,157,167,168,169,172,178,179,180,181,183,184,185,186,189,190,194,195,203,205,206,213,229,256,267,271,290,291,299,303,317,318,326,327,328,329,331,355,356,364,377,379,388,392,393,406,408,410,418,421,423,424,425,430,432,433,437,439,440,441,443,447,448,450,452],ethernet:18,etol:[326,328,418,437],etot0:260,etot:[6,94,96,97,110,121,130,169,198,214,227,260,440,441],eu2:143,eu3:143,euler:[326,328],eulerian:178,euqat:398,europhi:216,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,120,124,134,142,144,167,168,169,173,174,175,176,178,180,181,182,183,184,185,186,187,194,200,206,208,209,211,212,213,214,252,258,261,272,281,282,283,292,295,298,300,301,303,318,319,324,326,333,384,390,407,418,419,421,425,426,428,430,431,432,433,437,439,441,448,449],evalut:[303,421],evan:[132,247],evanseck:[6,20,150,344,435],evapor:[],evaul:[8,326],evdwl:[107,392,393,441],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,145,146,160,164,167,169,172,173,174,179,180,181,183,184,185,186,188,189,190,192,194,195,198,211,214,227,229,230,252,265,267,270,271,278,286,290,293,295,299,301,311,318,324,326,328,333,338,357,358,361,364,384,394,413,423,424,426,428,429,430,432,433,435,438,440,441,443,452],evenli:[3,41,121,164,188,216,367,413,423],event:[],eventu:[3,6,12,15,146,261,437],ever:[54,56,212,278],evera:[347,360,394,405],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,132,147,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,202,203,205,207,209,210,211,216,217,225,229,230,233,250,251,252,256,257,258,259,260,261,262,263,265,267,268,270,271,273,274,278,280,281,282,283,284,285,286,289,290,291,292,293,301,303,317,319,328,329,330,333,353,354,364,377,392,393,401,417,418,419,423,425,427,428,430,431,432,437,438,439,441,448,452],everyth:[8,107],everywher:[116,371],eviri:357,evolut:[207,216,253,418],evolv:[216,253,291],ewald:[2,3,5,6,7,8,12,88,110,118,121,291,318,319,326,340,342,343,349,352,357,369,373,387,395,405,407,425],ewald_disp:352,ewalddisp:3,exact:[22,41,44,71,138,147,152,188,191,206,207,213,214,215,256,265,266,278,290,305,318,346,425,430,437,450,452],exactli:[3,6,12,14,17,38,41,56,59,71,91,123,128,135,144,164,173,174,183,188,194,199,206,213,214,215,230,240,241,248,252,260,278,283,284,297,333,346,353,355,361,364,367,378,384,407,425,426,433,437,448],exager:443,examin:[6,8,191,252],examp:[421,448],exampl:[],exce:[3,6,16,17,18,41,58,71,146,181,184,185,188,192,194,199,202,229,252,278,326,333,423,448],exceed:[3,41,59,188,194,229,278,431],excel:357,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,169,172,175,181,182,183,187,188,192,194,201,204,205,208,211,213,215,229,230,231,232,233,234,235,236,240,241,244,246,247,248,249,253,262,263,270,272,273,275,278,281,283,284,290,294,301,303,304,305,306,307,308,309,312,313,314,318,319,321,323,327,328,329,331,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,385,386,387,389,392,393,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],excess:357,exchang:[2,3,6,8,9,61,62,172,178,179,205,213,262,270,286,290,293,318,333,357,438],exchange:318,excit:[9,357],exclud:[3,6,9,12,16,17,63,71,112,120,124,131,132,148,167,181,184,189,190,217,225,255,268,270,285,296,301,326,327,329,341,361,364,378,379,384,404,435],exclus:[1,3,9,12,16,87,333,348,432],excurs:418,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,145,168,210,264,303,317,320,332,419,421,431,434,437,448],exemplari:206,exemplifi:357,exert:[6,211,214,265,297,298,299,319],exhaust:[178,332,448],exhibit:[229,325,357,432],exist:[3,6,7,8,11,12,13,37,55,59,68,70,144,145,163,168,169,172,177,187,190,192,195,205,255,256,258,301,304,306,307,309,313,322,327,333,364,392,413,419,421,423,424,425,434,435,436,448,449,450],exit:[2,3,11,12,41,57,167,188,317,332,421,422,431,440,448],exlanatori:3,exp:[],expand:[],expans:[12,120,167,434],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,125,136,142,164,188,200,205,207,226,251,257,259,260,265,270,301,319,329,346,380,384,418,421,423,425,428,432,437,448],expens:[6,10,71,169,251,255,270,290,301,318,319,329,333,421],experi:[6,13,15,17,187,195,210,219,228,257,269,270,324,328,353,384,432,437],experienc:[6,12,218,219],experiment:[318,333,437],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,124,132,164,167,168,169,172,181,182,186,188,190,192,194,229,251,259,270,275,301,303,317,318,321,327,328,332,338,355,367,397,412,416,421,424,425,428,430,433,443,448,452],explan:[3,6,59,113,120,167,181,228,251,364,417,420,421,423,432],explanatori:[3,8,117,167,180,181,183,184,185,270,327,420,448],explantori:[3,266],explic:383,explicit:[6,9,11,22,44,77,87,113,116,138,152,173,174,194,305,323,335,336,339,344,346,355,357,368,378,411,417,420,424,427],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,134,142,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,184,187,194,201,204,206,208,213,229,231,232,233,234,235,236,244,246,247,249,259,260,262,270,272,273,281,283,284,290,294,304,306,307,308,309,312,314,327,333,334,335,337,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,414,415,416,423,425,432,433,435,436,443],explictli:[16,436],exploit:[9,15,17,253],explor:[118,143],expon:[3,261,263,355,360,363,377,383,395],exponenti:[87,390,406,416,437,448],expos:11,exposit:[178,353,354],express:[6,120,130,144,173,174,192,226,251,261,290,296,303,339,355,357,371,380,396,405,448],expressiont:339,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,172,175,176,179,186,187,193,196,200,203,204,205,207,208,209,211,213,215,227,229,233,241,251,252,268,269,270,272,274,275,277,281,282,283,284,285,287,288,290,292,295,299,300,360,380,393,394,396,440,441],extent:[1,3,41,45,57,71,142,146,167,177,184,188,211,297,300,318,321,335,407,420,423,426],exterior:[3,6,299],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,121,122,123,125,127,130,131,132,133,134,136,137,143,144,145,146,150,169,183,188,190,229,258,259,260,270,278,326,327,330,331,352,361,364,367,380,384,420,421,423,426,435,443,448],extract:[3,6,11,13,36,63,87,107,115,117,119,173,174,263,328,349,358,380,396,421,428,440],extract_atom:11,extract_comput:[11,421],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,168,192,194,229,288,357,409,443],extrema:377,extrins:178,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[140,292],f_a:[408,409,410],f_ave:117,f_c:409,f_f:410,f_fix_id:260,f_harm:288,f_i:390,f_id:[6,71,117,119,167,172,180,181,182,183,184,185,186,224,280,292,441,448],f_ij:390,f_indent:186,f_int:287,f_jj:91,f_k:390,f_langevin:290,f_max:[260,265],f_msst:227,f_r:[214,408,409,410],f_sigma:339,f_solid:288,f_ss:6,f_temp:214,face:[3,6,57,59,71,132,142,146,177,184,185,295,297,298,299,300,321,360,380,394,423,426],face_threshold:142,facet:142,facil:[0,12],facilit:[6,13],fact:[6,8,16,207,278,288,361,435],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],factori:[3,421],factoriz:318,fail:[3,11,12,59,148,192,195,318,326,328,351,393,421],fairli:[11,384,432,437],faken:73,falcon:210,fall:[3,6,169,183,256,421],fals:[86,301,303,448],fame:8,famili:420,familiar:[0,11],fan:390,far:[3,6,12,17,57,59,61,86,167,169,170,188,189,190,192,195,205,229,251,269,270,278,295,306,309,324,328,329,412,421,423,428,441],farago:213,farrel:[408,410],farther:167,fashion:[6,8,41,71,144,169,172,173,174,179,184,188,190,195,205,207,211,226,227,229,231,232,233,234,235,243,246,247,248,249,259,260,262,270,274,277,280,288,290,294,295,296,298,300,328,364,378,426,435,448,451],fasolino:366,fast:[6,7,9,12,13,17,39,167,238,260,291,318,319,341,378,379,405,407,425,430,432,441,449,452],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,187,188,201,204,208,212,213,229,231,232,233,234,235,236,244,246,247,249,257,261,262,270,272,273,278,281,283,285,287,290,294,304,306,307,308,309,312,314,318,319,330,331,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,432,436,443],fastest:[6,14,17,132,184,290,291,333,420],fatal:[3,440],fault:[70,393],faulti:12,fava:360,favor:191,favorit:7,fbmc:285,fcc:[],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[],fennel:[349,369],fep:[],ferguson:[6,150,435],fermi:[1,12,15,130,333,410],fermion:[9,357],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,170,180,181,182,183,184,185,186,214,229,256,259,261,273,292,318,326,327,328,335,420,423,428,432,434,448,450],fewer:[1,3,11,15,16,61,219,432],fewest:3,fextern:203,feynman:253,fff:421,ffield:[348,358,392,393],ffmpeg:[3,12,168],ffplai:168,fft:[1,3,7,12,14,15,88,109,110,121,252,318,319,432],fft_inc:[12,319],fft_lib:12,fft_path:12,fftbench:318,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,175,176,200,203,207,253,269,349,369,373,404],field1:[424,428],field2:424,field:[],fifth:[275,386],figur:[1,3,8,11,12,260,420,421],fij:352,file0:251,file1:[11,13,251,289,303,327,428,430,434],file2:[11,13,289,303,327,428,430,434],file:[],filenam:[3,12,13,38,41,56,164,167,168,169,170,178,181,182,183,184,185,186,188,193,251,255,258,261,262,263,266,267,270,271,289,290,315,316,317,328,334,335,339,349,355,356,358,366,380,381,382,386,390,391,392,393,396,406,407,408,409,410,419,420,421,424,425,430,434,441,448,450,451,452],filennam:430,filep:[3,167,169,425,430,452],filepo:267,fill:[7,144,168,256,290,321,329,339,393,426],filter:[169,178],final_integr:8,final_integrate_respa:8,finchham:[6,126,351],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,147,164,170,179,191,192,202,205,228,251,257,265,269,324,326,328,329,349,364,369,373,380,405,407,443,448],find_custom:8,fine:[16,17,148,175,200,288,329,333,448],finer:[120,144,448],finest:318,finger:[144,166,226,426],finish:[6,11,41,188,303,315,317,318,330,332,333,412,428,448,449],finit:[],finni:[7,355,405],finvers:198,fiorin:[9,193],fire:[324,325,326,328,437],firebrick:169,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,121,129,132,138,140,142,143,145,146,147,151,164,167,168,169,170,172,179,181,182,183,184,185,186,188,191,194,205,206,211,216,226,227,228,229,251,253,258,259,260,262,267,270,273,274,275,276,278,279,280,287,288,289,290,292,296,301,303,304,310,321,326,327,328,329,332,333,334,335,338,339,340,342,344,346,348,349,355,357,358,361,362,365,366,368,369,373,378,379,380,382,384,386,390,392,393,396,404,406,407,408,409,410,418,419,420,421,423,424,425,428,430,432,435,436,437,440,441,443,448,449,450,452],fischer:[6,9,19,20,150,344,435],fit:[3,6,9,12,38,56,164,269,278,335,339,366,380,384,400,407,409,431,448],five:[73,130,260,327,339,381,423,437],fix:[],fix_adapt:[138,174,377],fix_atom_swap:205,fix_bal:62,fix_deposit:[3,179,205,256],fix_evapor:[179,205],fix_flux:178,fix_gcmc:[179,327],fix_gl:207,fix_gld:207,fix_grav:256,fix_id:[3,192,227,229,231,232,233,234,235,257,260],fix_modifi:[],fix_mov:[166,296],fix_nh:8,fix_npt:207,fix_nvt:[179,205],fix_poem:[3,6],fix_pour:[3,195],fix_qbmsst:9,fix_qeq:[3,348],fix_rattl:273,fix_reax_bond:392,fix_rigid:[219,338],fix_saed_vtk:271,fix_setforc:8,fix_shak:273,fix_srd:3,fix_styl:233,fix_temp_rescal:284,fixedpoint:[192,229],fixextern:203,fixid:178,fji:352,flag1:[197,331],flag2:[197,331],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,404,418,420,421,423,424,425,427,428,429,433,448],flag_buck:343,flag_coul:[343,352,373],flag_lj:[352,373],flagfld:[341,378,379],flaghi:[3,341,378,379],flaglog:[341,378,379],flagn:197,flagvf:[341,378,379],flat:[6,290,295,296,300],flavor:[2,7,12,384],fld:[9,295,341,378,379],flen:336,flex_press:336,flexibl:[3,6,8,145,168,181,184,193,207,230,286,293,357,409,441],flip:[3,6,194,229,297,298],floor:448,flop:12,floralwhit:169,flow:[],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[],fluid_veloc:220,flush:[3,169,440],flux:[],flv:168,fly:[7,9,12,41,168,172,178,195,198,270,273,291,339,441,443],fmackai:9,fmag:196,fmass:253,fmax:[326,441],fmomentum:198,fmsec:[2,169,213,214,226,229,257,270,281,282,432,442,447,449],fname:317,fno:12,fnorm:[326,441],fnpt:198,fnvt:198,foce:364,fock:336,focu:273,fogarti:[9,263,393],foil:[120,251,396],fold:[276,432],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,39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379,392,393,421,448],interf:333,interfac:[],interfer:[229,335],interg:[6,443],intergr:[432,436],interi:379,interior:[3,6,41,299,426],interlac:380,interleav:[6,144,431],intermedi:[6,12,59,168,228,251,312,328,421,422,431,435],intermix:418,intermolecular:335,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,121,124,126,143,151,164,168,169,172,173,174,178,190,194,198,210,222,223,227,229,233,252,270,274,304,306,309,312,316,326,327,398,399,407,421,423,425,428,437,440,441,447,448,449,450],internal_element_set:178,internal_quadratur:178,internet:212,interpenetr:380,interpentr:[399,400,402],interpol:[6,15,38,56,100,164,168,169,178,216,251,318,319,328,339,384,393,401,407,408],interpret:[2,6,11,168,183,361,397,418,421,437,448],interrupt:260,intersect:[3,6,118,169,299,301,426],intersert:299,interspers:326,interstiti:142,intertia:[3,93],interv:[3,6,91,182,213,260,265,266,401,418,437,448],intestieti:118,intial:[6,333,335],intiial:[41,428],intiti:[3,277],intra:270,intra_energi:205,intramolecular:[29,205],introduc:[6,9,168,229,260,265,270,312,318,334,349,357,369,373,377,406,437],introduct:[],intsal:16,intuit:321,inv:[118,143,271],invalid:[3,12,71,89,147,241,328,378,379,425],invari:120,invent:273,invers:[],invert:[6,148,252],invis:299,invoc:[142,191,333,421],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,122,131,138,139,142,144,145,147,148,150,151,153,154,155,156,158,159,161,162,164,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,317,318,319,320,321,326,328,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,381,384,385,386,387,389,394,395,396,397,406,407,408,409,410,412,413,414,415,416,417,420,421,422,424,426,428,431,432,434,435,437,440,441,443,448,449],invokd:3,involv:[3,6,7,8,12,63,108,115,116,117,124,148,172,189,205,216,255,258,263,278,318,325,326,328,338,354,360,406,408,410,419,420,426,428,432,437],ioff:[327,423],ion:[6,7,250,275,290,319,339,350,358,359,380,405,410,416,423,443],ionic:[6,9,340,342,350,357,358,387,443],ioniz:[9,348,357],iparam:[3,190],ipi:[],ipp:[],ir3:143,ir4:143,irregular:[6,41,58,188,192,194,229,270],irrelev:386,irrespect:[378,379],irrevers:198,isbn:415,isel:[318,319],isenthalp:[229,230,231,232],ismail:[318,319,343,373],isn:[3,8,11,12,209],iso:[3,192,198,214,229,230,231,232,233,234,235,257,265,270,443],isobar:[229,230,234,235],isodem:357,isol:[3,147,301],isomorph:253,isotherm:[205,229,230,234,235,257],isotrop:[6,213,257,318,319,341,360,378,379],isovolum:271,isralewitz:274,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,59,71,73,81,103,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,168,175,178,187,191,192,195,200,201,204,205,208,213,227,229,231,232,233,234,235,236,244,246,247,249,253,257,259,262,270,272,273,277,281,282,283,288,294,300,303,304,306,307,308,309,312,314,319,327,328,331,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,404,406,407,408,409,410,412,414,415,416,423,425,432,435,440,441,448,449],ital:[392,393],itali:13,item:[6,7,8,41,167,169,188],iter:[3,6,12,39,41,63,175,176,187,188,192,198,200,203,211,252,261,262,270,273,285,301,303,317,324,325,326,328,332,418,428,432,437,441,448],ith:[71,117,119,180,181,182,183,184,185,186,280,292,441,448],itself:[2,3,4,6,7,8,9,11,12,13,18,42,59,91,107,135,167,168,169,170,182,193,198,214,224,228,264,270,290,301,303,327,328,349,358,360,364,365,407,421,427,430,431,435,448,452],ityp:[3,115,116,144,177,190,263,413],itype1:116,itype2:116,itypen:116,ivector:8,ivori:169,ixcm:270,ixi:[42,93,270,327,448],ixx:[42,93,270,327,448],ixz:[42,93,270,327,448],iycm:270,iyi:[42,93,270,327,448],iyz:[42,93,270,327,448],izcm:270,izrailev:274,izumi:409,izz:[42,93,270,327,448],j0jt:91,j20:182,j_m:120,jac:[6,150,435],jackson:383,jacobi:3,jacobsen:325,jagreat:13,jame:[9,19],janssen:251,januari:380,jaramillo:[7,9,13,357],jarzynski:274,jatempl:9,jcc:9,jcp:295,jec:13,jeff:13,jello:229,jensen:[213,318],jeremi:[9,382],jerom:9,jewett:13,jiang:[214,443],jiao:[9,13],jiht:[7,9],jik:339,jim:7,jku:7,jmake:12,jmm:120,joannopoulo:227,job:[12,60,273,431],jochim:[229,230],john:[7,13],johnson:13,join:[6,426],joint:[3,255,363],jon:[9,70],jonathan:9,jone:[1,3,6,7,9,10,12,13,45,46,64,87,107,110,172,1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:[3,420],topolgi:40,topolog:[2,3,6,7,8,12,13,39,40,87,108,115,147,148,169,189,190,210,255,327,364,384,420,423,424,425,427,428,435],topwal:187,torder:270,torqu:[],torsion:[6,151,152,163,335,392,393],torsion_flag:335,tosi:340,tot:265,total:[3,6,11,12,14,15,16,17,18,39,41,63,71,81,88,89,90,91,98,102,103,104,105,107,109,110,117,120,121,122,124,125,126,127,130,131,132,133,134,136,138,140,141,142,167,172,175,176,179,181,183,184,185,187,188,190,196,198,200,203,204,205,206,211,213,214,215,216,217,219,227,230,233,243,252,253,255,256,260,265,267,269,270,271,272,274,275,277,286,287,288,290,293,295,299,318,326,327,328,329,330,333,334,336,338,339,348,355,357,361,380,381,382,390,392,393,396,412,418,420,421,425,431,432,437,438,441,448],touch:[12,211,296],toukmaji:[319,352],toward:[9,29,142,168,172,195,196,211,216,228,233,251,268,275,289,291,312,328],toxvaerd:374,tpa:333,tparam:270,tpartial:124,tpc:333,tpcpu:441,tperiod:270,tptask:[16,333],tqx:[113,167,280],tqy:[113,167,280],tqz:[113,167,280],trace:357,track:[3,7,12,190,194,216,290,300,418,423,429,437,441,448],track_displac:178,tracker:210,trade:[6,12,262,318,319,349,369,373,432,437],tradeoff:384,tradit:[6,319],traffic:12,trail:[2,22,44,77,87,116,138,148,152,169,173,174,270,305,323,327,328,346,358,380,393,396,417,423,431,433],train:393,traj:193,traj_titl:393,trajectori:[3,6,12,39,87,167,210,229,231,232,234,235,236,237,239,240,242,244,245,246,247,248,249,253,270,273,274,291,300,353,384,393,425,433,443,447],tran:[155,156],transfer:[1,6,16,178,198,210,212,286,290,293,318,333,339,443],transform:[],transit:[6,86,228,274,289,328,350,377,382,410,418,437],translat:[3,6,61,63,94,95,96,97,98,123,124,128,137,181,205,209,213,214,219,229,234,235,246,249,253,270,281,282,283,285,321,357,423,441],transmiss:210,transmit:[6,210],transpar:[14,17],transport:[178,290,398],transpos:12,trap:[3,6,91,140,182,211,292,448],trapezoid:[182,448],trate:[3,194,210],travel:278,treat:[2,3,6,8,17,40,42,71,82,84,85,121,123,137,148,165,181,182,183,186,195,204,230,252,255,256,270,278,290,292,299,303,317,318,326,327,329,338,351,357,358,360,363,367,381,382,394,412,423,426,428,431,433,443,448],treatment:[9,265,351],tree:[3,255,377],tref:354,tri:[],trial:[195,205,336,432],triangl:[3,6,7,40,42,82,113,142,172,245,270,278,405,412,423,433],triangleflag:423,triangul:[6,13],triangular:[4,6,42,82,113,192,245,423],tricki:[420,443],triclin:[],triflag:6,trigger:[3,11,12,62,86,188,191,205,326,441],trigon:25,trilinear:216,trilino:17,trim:[3,424],tripflag:392,tripl:[2,120,194,339,392,419,421],triplet:[3,34,37,356,386,390,406,408,409,410],trivial:[8,11],trj:393,trott:[7,9,14,17,120,396],troubl:[11,12],truli:8,truncat:[3,5,6,12,71,259,265,295,299,325,337,349,357,361,369,371,374,384,389,433],trung:15,tscale:[3,227,260],tschopp:67,tsige:343,tsrd:[278,300],tstart:[206,207,213,215,229,230,270,281,282,283,284,353,429],tstat:[],tstop:[206,207,213,215,229,230,270,281,282,283,284,353,429,437],tsuzuki:73,ttm:[],ttm_mod:290,tucker:[120,396],tuckerman2006:229,tuckerman:[229,230,248,253,270,432],tune:[],tunnel:253,turn:[3,4,6,12,22,33,37,39,44,50,54,55,59,65,69,71,108,115,120,143,148,152,157,163,168,169,172,179,189,190,191,192,205,210,229,241,255,258,259,270,278,305,310,313,318,326,328,329,331,333,335,351,363,364,380,384,393,404,405,419,423,425,430,435,436,441,445,450],turquois:169,tutein:335,tutori:[6,9],tweak:[12,144,210],twice:[3,6,16,17,63,88,150,169,172,173,174,192,226,229,263,333,364,421,423,430],twin:67,twist:[378,379],two:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,22,38,39,41,42,44,54,56,57,59,61,63,65,68,69,71,76,77,79,87,88,92,107,108,113,114,115,116,117,118,120,123,126,127,129,130,132,138,142,143,144,145,147,152,166,167,168,169,172,173,174,179,180,181,182,183,184,185,186,188,189,190,191,192,195,198,202,205,206,207,209,211,212,213,214,216,219,228,229,230,233,251,252,253,256,257,259,260,261,265,267,270,274,275,278,285,286,288,290,293,296,299,301,303,305,314,318,319,321,323,324,326,327,328,331,333,334,335,336,338,339,340,341,342,343,346,347,348,349,351,352,353,354,355,356,357,358,360,361,364,367,368,369,373,377,378,379,380,384,387,390,391,392,393,394,396,397,404,405,406,408,409,410,411,412,415,416,417,418,420,421,423,424,425,426,427,430,433,435,437,438,440,441,443,447,448,449,450,451,452],two_temperatur:178,twobodi:[408,410],twogrid:3,twojmax:[120,396],twolevel:[3,420],txt2html:8,txt:[8,12,13,167,170,258,259,290,316,327,368,413,428,448],typcial:[41,188],type1:[77,118,143],type2:[77,118,143],type:[],typen:[77,118,143],typic:[1,2,3,6,7,8,10,11,12,13,14,15,16,17,18,29,39,40,41,45,46,55,57,59,61,63,70,71,86,87,102,107,119,138,142,144,145,147,167,168,169,172,173,174,175,177,178,181,188,189,190,191,192,194,195,200,202,203,205,208,214,229,241,252,255,256,259,261,263,269,270,273,278,285,293,294,300,318,321,325,326,327,328,329,330,333,344,346,347,349,359,360,363,364,368,369,373,378,379,380,384,394,405,407,410,418,419,421,423,424,425,426,432,435,437,438,440,447,448,450,452],typicali:12,tzou:290,u_f:216,u_ij:390,u_prom:339,uberuaga:[228,328],u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Documentation","Accelerating LAMMPS performance","Commands","Errors","Example problems","Future and history","How-to discussions","Introduction","Modifying &amp; extending LAMMPS","Packages","Performance &amp; scalability","Python interface to LAMMPS","Getting Started","Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","&lt;no title&gt;","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":189,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,120,124,132,133,137,143,144,147,149,163,165,166,167,168,169,170,171,173,174,175,177,178,179,181,184,185,186,189,190,192,193,194,195,199,202,205,206,211,213,214,215,216,217,219,224,227,229,230,233,247,248,252,253,256,257,258,259,260,262,265,267,268,270,271,278,280,285,286,287,288,291,293,295,297,301,313,316,318,319,321,322,324,325,327,329,330,331,333,336,339,341,357,378,379,384,392,393,404,405,418,419,420,423,424,426,428,430,431,432,435,437,439,440,441,442,447,449,450,451],"function":448,"long":[340,342,343,344,345,349,351,352,369,373,377,387,395],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[173,174],addforc:175,addit:[12,13],addtorqu:176,adiabat:6,adp:334,airebo:335,alloi:355,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:177,arrai:6,aspher:[6,82,123,231,234,237,238,246],atc:[9,178],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,120,121,142,177,179,180,259,448],atom_modifi:39,atom_styl:40,attract:5,aveforc:187,awpmd:[9,336],balanc:[41,188],barostat:6,basal:67,beck:337,berendsen:[257,281],between:6,binary2txt:13,bodi:[6,8,42,68,239,338],bond:[8,13,69,189,190,191,266],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:339,born:[340,351],boundari:[7,57],box:[6,58,192],brownian:341,buck:[342,343,351],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,150,344,377],chunk:[6,66,71,75,90,93,104,106,114,124,139,141,181],citat:7,class2:[21,43,151,304,345],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[295,347,415],colvar:[9,13,193],com:[74,75,125],comb3:348,comb:[262,348],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,448],compute_modifi:102,condit:7,conduct:[6,286],constant:6,constraint:7,contact:76,coord:77,core:6,correl:182,cosin:[23,24,25,26,27,28,153],cossq:306,coul:[340,342,343,344,345,349,350,351,362,369,373,377,387,395],coupl:6,creat:190,create_atom:144,create_bond:145,create_box:146,createatom:13,creation:7,csld:282,csvr:282,cubic:371,cuda:[9,14,109,112,122,131,175,187,201,204,208,229,236,272,273,281,283,294,340,342,344,345,355,361,362,369,370,372,375,385,406,408],custom:8,cut:[49,336,342,345,349,352,357,359,369,370,377,383,387],cvff:307,damag:78,data2xmovi:13,data:6,databas:13,deby:[349,369],deform:[127,128,194],delete_atom:147,delete_bond:148,delta:24,deposit:195,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,16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\ No newline at end of file
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5,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],checkf:164,checkqeq:393,checku:164,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,121,150,151,161,193,198,206,207,214,216,228,229,230,247,248,253,257,260,262,270,274,278,281,282,285,286,287,288,295,304,312,314,318,319,325,328,335,340,344,345,348,349,350,352,353,357,359,360,362,363,369,373,374,377,380,383,384,387,404,411,432,435,437,443],chemic:[9,118,138,143,167,178,179,205,261,266,267,285,319,392,393,400],chemistri:[9,260,261,263,339,357,392,393],chen:290,cheng:348,chenoweth:[392,393],chenoweth_2008:[392,393],chi:[92,133,166,251,261,263,358,360,449],chiefli:391,child:8,chip:[7,12,17,333,436],chipot:193,chiral:312,chmod:[11,12],cho:380,chocol:[7,169],choic:[3,6,12,15,16,18,40,41,54,87,121,123,137,148,164,181,184,185,188,191,194,195,207,213,216,227,229,253,261,270,285,313,319,324,325,328,330,333,364,377,384,388,423,432,433,436,437,442,443,447],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,134,135,168,189,190,191,192,195,202,213,216,227,229,231,232,233,234,235,257,278,282,296,318,319,325,413,418,420,432,438],chose:[408,410],chosen:[2,3,6,12,17,120,144,147,156,164,168,174,179,192,195,202,205,206,214,216,227,229,233,253,256,267,278,282,285,286,291,293,294,300,319,320,325,333,357,361,367,368,371,395,408,418,432,437,443],chri:142,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,124,139,141,181],chute:[4,10,208],ciccotti:273,cieplak:[6,150,435],cii:182,cij:182,circular:[3,6,123,165],circumst:18,circumv:265,citat:[],cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[],classic:[0,3,5,6,7,8,9,203,253,260,265,290,314,357],classifi:[9,405],claus:421,clean:[6,12,14,15,17,431],cleanli:[422,451],clear:[],clearli:7,clebsch:120,clermont:[9,13],clever:427,click:[2,11,22,37,44,55,144,152,163,168,210,305,313,328,346,405],client:[210,212],climb:[228,328,437],clinic:[7,13],clo:[133,166,449],clock:[12,418,437],clockwis:296,close:[3,6,11,12,13,39,41,67,121,147,167,190,191,192,207,214,216,229,247,270,273,296,299,317,319,322,324,325,328,333,335,339,349,350,380,384,410,427,433,443,445],closer:[3,41,116,142,166,167,188,192,196,287,328],closest:[190,251,270,293,360,394,404,413],cloud:443,clovertown:18,clsuter:72,clump1:[255,270],clump2:[255,270],clump3:[255,270],clump:270,cluster:[],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[],cn1:182,cn2:182,cna:[],cnn:182,cnr:[9,13],cnt:[364,427],co2:[40,143,327],coars:[7,9,29,36,40,54,156,255,270,278,362,395,435],coarser:[319,448],coarsest:120,code:[],coeff:[3,7,8,12,21,22,33,44,50,150,151,152,157,304,305,310,346,364,368,384,397,423,425],coeffcient:423,coeffici:[],coefficienct:353,coefficient0:355,coefficient1:355,coeffieci:[6,337],coeffincientn:355,coexist:[9,205,357],cohes:[6,358,380],coincid:[205,299,344,378,379,418],cold:[6,129,209,329,443],coldest:286,coleman8:9,coleman:[9,118,143,271],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,124,132,139,141,144,167,169,181,193,219,225,255,265,268,270,301,318,327,329,347,367,423,430,436,452],collid:[199,278,300],colliex:143,collinear:[3,255],collis:[3,216,278,296,300,354,361,416],colllis:278,colloid:[],colombo:39,colon:[170,301,424],color1:169,color2:169,color:[3,9,41,167,168,169,188,206,260,265],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,120,121,124,132,139,141,142,143,164,167,169,172,180,181,182,183,184,185,186,219,226,227,260,270,279,280,290,300,359,363,392,393,424,438,440,448],colvar:[],colvarmodul:12,com:[],comamnd:194,comand:[191,425],comannd:333,comb3:[],comb:[],comb_1:262,comb_2:262,combiant:350,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,123,137,167,168,178,183,210,219,229,253,259,282,291,299,302,304,318,319,321,325,333,347,349,350,357,358,364,376,377,396,406,408,410,415,426,431,443,448],come:[],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,150,164,167,214,270,290,327,328,334,355,356,358,368,380,386,393,396,406,407,408,409,410,420,421,423,443,448],commerci:7,commmand:[3,6,12,59,107,248,417,418,420,437,451],common:[],commonli:[3,6,12,17,25,57,59,105,146,167,168,170,314,362,371,396,408,410,423,426,435],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,147,148,168,169,188,189,190,192,193,194,210,212,216,218,219,220,229,252,259,261,262,263,270,278,290,301,318,329,330,331,333,354,388,420,421,425,432,433,450,452],communc:318,comp:[7,212,213,273,319,328,357,384,389,394,403,407,409],compact:[63,172,346,405],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,127,142,143,152,163,169,198,261,301,303,318,319,326,328,380,418,437,438,443,447],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,151,152,163,304,305,313,345,405],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,155,167,170,174,180,181,182,183,184,185,186,188,252,264,282,285,292,295,298,318,333,365,384,407,420,421,448],compens:[6,189,190,268,329,357],compet:289,competit:319,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,142,167,168,170,210,289,319,333,423,424,428],compl:17,complain:[12,17],complement:380,complementari:[7,349,369],complet:[3,6,9,12,15,41,59,71,169,184,188,193,219,253,256,259,278,289,291,303,317,328,333,358,412,418,423,428,431,435,437,440,443,448],complex:[6,8,11,12,13,25,40,42,62,120,132,144,145,216,299,316,328,357,407,421,423,426,448],compli:[285,289],complic:[6,7,9,12,13,179,205,421],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,139,140,141,167,168,169,175,176,180,181,182,183,184,185,186,187,191,192,194,195,200,203,208,212,213,216,219,221,225,226,228,229,230,233,234,235,246,247,249,250,252,253,254,257,268,270,272,273,274,275,278,281,282,283,285,292,293,298,299,300,318,321,325,326,327,328,333,353,357,361,378,379,396,423,424,433,441,448,449],componenet:6,composit:[6,179,216,355],compound:[348,357,358],compres:[71,114,181],compress:[3,6,59,71,114,147,167,168,169,181,194,227,233,257,260],compris:[40,299,367,394,412],compton:[118,143],comptu:[3,6],compuat:319,comput:[],computation:[3,6,189,190,290,339],computational:443,compute_arrai:8,compute_fep:[174,377],compute_group_group:205,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,271],compute_scalar:8,compute_temp:8,compute_ti:174,compute_vector:8,compute_xrd:143,concaten:[2,3,451],concav:299,concentr:355,concept:[6,124,134,181,432],conceptu:[3,6,71,132,192,194,328,349,364,380,428],concern:[6,73,87,206],concis:[11,289],conclud:12,concret:8,concurr:[9,16,319],conden:[290,408,410],condens:[6,126,290,335,351,355,369],condit:[],conducit:6,conduct:[],cone:426,confid:[3,437],config:[12,167,420],configfil:193,configur:[1,6,12,15,17,38,59,146,164,166,167,168,172,192,193,194,195,199,205,212,213,241,253,261,289,316,326,328,335,339,356,380,406,408,410,418,423,425,426,437],confin:[423,437],conflict:[3,40,384,421],conform:[3,6,13,59,191,192,228,269,274,289,312,328,357,435],confus:3,conjuct:353,conjug:[7,8,213,325,357,392,393],conjunct:[6,7,71,86,87,114,127,132,138,144,148,169,173,174,213,216,220,241,256,257,261,262,263,265,270,278,286,293,298,318,319,328,340,342,346,349,353,357,363,369,387,395,411,423,426,430,443,452],connect:[3,6,87,129,147,191,210,255,270,273,275,328,350,361,404,410,420,421,427,443],conput:3,consecut:[3,11,12,39,71,144,169,173,174,195,210,211,349,369,373,418,424,426],consequ:[1,6,290,368,437],conserv:[3,172,179,191,198,199,206,209,213,215,216,220,225,227,229,241,270,273,281,282,286,293,294,298,328,352,353,361,375,432,437],consid:[6,9,70,71,78,87,115,129,130,147,167,169,173,174,180,182,184,188,190,191,195,217,230,252,270,285,286,289,290,293,319,346,357,364,393,394,404,418,419,421,424,425,426,428,431,433,441,443,448],consider:[6,8,213,214,281,282,283,333,432],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,124,127,129,144,156,166,170,175,176,181,194,195,198,200,203,206,213,214,215,226,229,231,232,233,234,235,236,237,239,240,241,242,244,245,246,247,248,249,257,260,265,267,269,270,281,282,283,284,294,318,319,321,327,328,333,335,339,341,347,349,357,360,378,379,380,384,394,407,413,421,423,424,426,427,428,435,443,448],consistent_fe_initi:178,consit:270,constant:[],constitu:[3,6,219,270,295,299,347,394],constrain:[3,6,8,122,123,124,125,127,130,131,132,133,134,136,137,172,181,195,205,206,211,219,223,255,256,268,270,273,276,286,293,326,327,357,428,435,443],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,120,143,192,229,252,269,299,329,333,352,384,404,406,407,426,427,448],constructor:8,consult:393,consum:[1,265,388,448],consumpt:316,contact:[],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,120,124,132,142,143,144,146,150,152,163,164,167,168,169,170,172,173,174,178,180,181,182,183,184,185,186,188,193,195,200,207,211,212,213,214,216,227,241,251,252,255,256,258,260,263,267,270,271,278,285,289,290,299,300,303,317,319,327,328,331,332,334,335,336,339,348,349,352,355,356,357,364,365,380,386,390,391,392,393,396,406,407,408,409,410,411,418,419,420,421,423,424,425,426,428,430,432,435,437,440,441,443,448,450,452],content:[12,18,393,439,441],context:[3,6,8,12,17,117,169,189,190,195,255,267,294,325,415,423,430,439,447,448,449],contibut:70,contigu:420,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,140,169,172,173,174,179,181,182,183,184,185,186,188,191,192,193,194,195,205,206,207,209,210,211,213,214,215,221,226,227,229,231,232,233,234,235,246,247,248,249,254,256,259,260,270,271,274,277,278,280,287,288,290,296,299,303,317,332,333,339,353,354,371,374,392,393,394,409,418,421,423,425,426,431,437,440,441,448,450],continuum:[6,7,9,178,290],contour_integr:178,contract:[59,192,194,229,257,270],contradictori:3,contrain:273,contraint:241,contrari:[207,214],contrast:[1,6,42,55,64,129,194,301,415,451],contrib:290,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,174,179,180,181,182,183,184,185,186,192,205,213,216,219,220,224,230,247,248,255,256,264,267,270,271,273,292,318,326,328,336,353,354,355,357,364,378,379,384,392,393,435,441,443],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,120,153,167,168,172,178,179,188,192,193,194,209,210,213,214,229,231,232,233,234,235,257,262,270,281,282,283,290,294,316,318,330,357,360,392,393,406,410,418,420,432,438,439],control_typ:178,controlfil:393,convect:91,conveni:[6,12,29,167,170,186,271,321,396,448],convent:[3,8,9,29,155,162,163,169,269,275,302,355,357,448],converg:[3,6,41,88,167,168,170,175,188,191,192,200,203,233,260,262,265,269,273,324,325,326,328,348,349,369,418,430,437],convers:[3,8,120,168,169,179,182,257,318,349,350,351,357,369,373,377,387,421,437,447],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,144,151,167,168,169,186,227,301,304,306,309,312,321,328,334,355,408,410,416,421,423,424,425,430,440,443,447,448,450,452],convex:299,convinc:[7,12],cooki:7,cool:[7,134,209,268],cooordin:167,cooper:[5,7],coord123:114,coord1:[3,114,181,184,185],coord2:[3,114,181,184,185],coord3:[3,114,181,184,185],coord:[],coordiat:326,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,120,127,133,139,141,142,144,148,166,167,168,169,170,172,175,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,201,203,205,208,209,210,211,212,213,214,226,228,229,231,232,234,235,247,250,251,252,255,256,257,267,268,270,272,273,274,275,276,277,278,280,288,289,290,297,298,300,301,321,326,327,328,333,334,335,338,356,418,423,424,426,428,431,433,437,443,448,449],coordn:[114,181],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,168,290,328,346,392,421],copper:416,coproccesor:16,coprocessor:[1,4,7,9,16,17,333,436],coproprocessor:17,copy_arrai:8,copyright:[7,8,255],coral:169,core:[],core_shel:126,coreshel:[6,9,342,349,351],cornel:[6,150,435],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,168,299,300,321,412,423],cornflowerblu:169,cornsilk:169,corpor:16,corr:348,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,126,131,138,168,194,207,213,229,230,247,255,257,260,289,295,299,318,328,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,423,438,441,443],correction_max_iter:178,correctli:[3,8,9,11,17,71,81,102,103,122,123,125,127,129,130,131,132,133,136,137,140,167,169,175,195,200,203,214,223,229,230,263,270,273,275,277,296,299,328,329,333,351,379,420,421,423,447,449],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,120,122,123,131,138,143,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,181,183,184,185,187,190,192,194,201,203,204,208,213,216,217,225,226,227,229,231,232,233,234,235,236,241,244,246,247,249,252,253,257,262,270,272,273,281,283,285,294,295,296,298,299,300,302,304,305,306,307,308,309,312,314,319,323,325,327,328,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,418,420,421,423,424,426,436,437,438,440,441,443,448],correspondingli:[378,379,432],cosin:[],cosineshift:27,cosmo:[207,212],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,121,143,168,169,181,184,185,188,189,190,202,229,262,290,318,319,331,349,369,373,384,406,420,432],costheta0:[406,408,410],costheta:390,costli:[11,88,207,329],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,124,134,139,141,157,167,168,169,173,174,179,181,182,184,188,194,203,212,259,260,261,265,268,270,272,278,279,285,289,290,291,295,299,301,303,310,315,317,324,326,329,333,336,359,363,364,392,393,419,420,421,423,425,427,430,431,439,443,448,449],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,121,145,149,261,263,291,318,319,326,333,340,342,343,344,345,348,349,350,351,352,357,361,362,364,369,373,377,384,387,392,393,395,405,410,411,415,428,435,441,443,447],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,132,142,148,175,176,179,181,183,184,185,187,188,195,200,202,205,211,229,241,256,273,281,282,299,319,326,327,328,330,333,359,363,384,441,448],counter:[296,418,429,431,437],counterbal:209,counterpart:[167,270,418],counterproduct:18,coupl:[],cours:[3,8,138,167,173,174,206,269,275,289,295,297,298,300,301,319,378,397,420,423,436,443,448,450],coval:[6,29,357,380,443],covari:207,cover:[6,71,164,169,178,216,357,367,412],coverag:[71,184],cpc:212,cpp:[1,3,6,8,9,11,12,13,87,167,173,174,203,273],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,169,172,198,214,291,316,319,333,346,405,418,436,437,440,441],cpuremain:441,cr2:143,cr3:143,crack:[4,329],crada:[5,7],crai:[5,7,13,18,167],crash:[3,329,443],craympi:333,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:[],creation:[],crimson:169,critchlei:255,criteria:[3,116,145,168,169,189,190,191,224,326,389,412,425,428,448],criterion:[41,142,144,147,179,188,191,205,241,262,296,301,326,328,348,357,361,428,437,438],criterioni:437,critic:[48,49,227,285,290,326],cross:[3,12,22,71,89,123,152,167,168,180,184,190,194,226,228,247,270,275,277,286,293,305,321,328,344,353,354,355,362,363,364,369,371,373,390,395,408,410,423,427,433,450],crossov:1,crossterm:423,crozier:[0,7,13],crucial:260,crystal:[4,6,13,73,251,252,288,329,427,441,443],crystallin:[6,252,321,409,443],crystallis:285,crystallogr:[118,143],crystallograph:[321,441],crystallographi:[118,143,321],cs1:143,cs_chunk:6,cs_im:[40,423],cs_re:[40,423],csanyi:[120,391,396],cscl:380,csequ:6,csh:[11,12,346],cshrc:[11,12],csic:[356,406,408,410],csinfo:6,csisi:[356,406,408,410],csld:[],cst:355,cstherm:6,cstyle:420,csvr:[],ctcm:[334,355],ctemp_cor:198,cterm:274,ctr:9,ctype:11,cu1:143,cu2:143,cu3au:380,cube:[6,41,142,147,188,198,299,321,443],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:339,cummul:[3,6,186,189,190,191,193,202,207,213,215,278,281,282,283,284,286,293,363,441],cumul:[6,179,181,183,184,185,199,205,213,227,229,233,241,270,271,328],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,121,124,132,140,142,145,148,167,168,169,170,173,174,178,179,181,184,185,186,188,189,190,191,192,193,194,195,199,200,203,205,207,210,211,213,219,226,229,230,234,235,241,246,247,249,255,261,262,264,267,268,269,270,273,274,276,277,278,281,282,283,289,290,293,294,295,296,297,298,300,301,303,316,317,318,319,322,323,325,326,327,328,333,339,346,348,352,355,357,358,361,365,368,378,379,380,381,382,384,390,392,393,397,408,410,411,413,418,419,420,421,423,424,425,426,427,429,430,431,433,435,437,438,440,441,448,449,450,451,452],curv:[6,144,205,252],curvatur:[360,394,416],custom:[],cut0:421,cut1:432,cut2:432,cut:[],cuthi:[251,263],cutinn:[341,378,379],cutlo:[251,263],cutmax:390,cutoff1:[345,352,369,373,377,387,395],cutoff2:[340,342,343,345,351,352,369,373,377,387,395],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,120,142,145,147,190,191,196,251,260,261,263,265,267,270,278,291,295,299,301,318,319,326,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,421,425,428,432,443],cutoffa:356,cutoffc:356,cuu3:355,cval:143,cvd:285,cvel:274,cvff:[],cwiggl:[3,226,295,298,300,448],cyan:[2,168,169],cycl:[3,205,227,229,230,233],cyclic:[3,164],cygwin:12,cylind:[3,4,168,211,256,296,299,426],cylindr:[6,211,275,296],cypress:333,cyrot:339,cyrstal:252,d3q15:216,d3q19:216,d_double_doubl:15,d_e:290,d_flag2:259,d_flag:259,d_name:[113,167,259,280,433],d_single_doubl:15,d_single_singl:15,d_sx:259,d_sy:259,d_sz:259,daan:288,dai:12,daili:12,daivi:247,damag:[],dammak:265,damp:[3,6,172,177,213,214,215,220,229,230,233,257,260,265,270,281,282,294,296,297,325,326,328,340,342,344,349,352,357,361,369,377,387,395,405,411,437,443],damp_com:214,damp_drud:214,dampen:[270,443],dampflag:[296,361],dan:17,danger:[3,12,205,301,353,441],dangl:147,daniel:9,darden:[319,352],darkblu:169,darkcyan:169,darken:168,darkgoldenrod:169,darkgrai:169,darkgreen:169,darkkhaki:169,darkmagenta:169,darkolivegreen:169,darkorang:169,darkorchid:169,darkr:169,darksalmon:169,darkseagreen:169,darkslateblu:169,darkslategrai:169,darkturquois:169,darkviolet:169,dasgupta:261,dash:[361,440],dat:[6,91,164,178,419],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,271],dataset:271,datatyp:3,date:[0,6,12,13,392,393,448],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,167,182],davi:295,david:[9,19,318,319,408,410],daw:[355,390],dbg:14,dcd:[3,6,7,167,168,169,170,253,424,428],ddim:166,deactiv:377,dealt:212,debug:[6,7,11,12,13,14,17,118,143,144,253,258,316,318,333,365,384,413,421,422,425,430,433,440,448],deby:[],decai:[349,416],decid:[3,6,12,16,71,226,259,270,291,438],decipher:321,declin:278,decod:168,decompos:[87,396],decomposit:[3,5,7,18,62,178,253],decoupl:[6,443],decreas:[3,167,175,176,191,194,200,203,213,289,318],decrement:274,deepli:315,deeppink:169,deepskyblu:169,def:[12,13,421],defaul:61,defect:[6,70,142],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,150,151,152,153,154,155,156,158,159,161,162,163,164,165,166,167,168,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,203,204,205,208,211,212,213,214,215,216,224,226,228,229,230,231,232,233,234,235,237,238,239,242,244,245,246,247,248,249,251,252,253,255,256,257,259,261,263,268,270,271,272,273,276,278,280,281,282,283,284,286,287,288,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,330,331,332,333,335,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,356,357,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,426,427,428,429,432,433,434,435,437,438,440,441,443,444,445,446,447,448,449],definit:[2,3,6,8,12,13,78,80,116,120,169,181,182,183,184,185,186,194,211,233,271,280,292,295,298,300,302,313,316,327,336,339,347,357,367,390,396,412,421,423,425,432,434,447,448],defint:441,deform:[],deg2theta:143,deg:443,degener:[3,255],degrad:[8,18,252,319,432],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,143,144,150,151,154,155,162,164,166,168,181,191,198,205,207,208,213,214,219,229,230,233,234,235,246,247,249,253,255,269,270,273,281,282,283,288,304,306,309,312,314,326,352,355,363,433,441,443,449],degress:[124,181],del:437,delai:[3,6,12,329,354,441],deleg:364,delet:[2,3,7,8,12,54,57,60,63,142,147,148,172,181,182,183,184,185,186,189,191,202,205,229,271,281,282,301,303,317,327,329,332,384,423,424,426,434,435,440,444,446,448,449],delete_atom:[],delete_bond:[],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[],delta_1:339,delta_3:339,delta_7:339,delta_conf:3,delta_ij:[380,390],delta_mu:[3,179],delta_pi:339,delta_r:390,delta_sigma:339,delx:166,delz:166,demand:265,demo:11,demon:250,demonstr:[260,380],den:256,dendrim:363,denniston:[9,216,218,219,220,252],denomin:[7,149],denot:[118,198,214,252,263,265,349,362,364,393],dens:[71,191,357],densiti:[3,6,7,9,18,40,41,59,100,116,120,130,142,144,173,174,178,181,184,185,188,194,203,216,219,222,223,252,256,257,261,290,295,321,323,327,334,339,355,380,381,382,390,394,399,401,402,403,423,432,433,441,447],depart:[0,7],departur:[227,260],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,120,122,127,131,132,138,144,145,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,168,169,172,173,174,175,176,179,181,183,184,186,187,188,190,192,200,201,204,207,208,209,211,213,214,216,218,219,226,229,231,232,233,234,235,236,244,246,247,249,251,262,265,267,270,272,273,278,281,282,283,285,287,289,290,292,294,295,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,326,327,329,330,331,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,383,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,429,433,435,437,440,441,442,448,449],dependend:6,depflag:12,dephas:[418,437],depos:195,deposit:[],deprec:261,depth:[51,123,168,290,360,394],dequidt:9,der:[87,107,347,348,377,392,393,415,443],deriv:[6,7,8,38,56,63,87,120,138,164,182,192,194,205,213,226,229,231,232,233,234,235,251,257,261,265,287,288,290,295,296,299,325,327,335,339,347,352,357,358,362,371,375,376,380,392,393,405,407,415,443],derjagin:415,derlet:251,descend:169,descent:[7,325],descib:[40,261],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,120,121,123,124,128,129,132,135,137,138,142,143,144,146,147,156,161,164,167,172,173,174,181,182,183,184,185,186,188,191,192,193,194,195,197,198,206,207,210,211,212,213,214,215,216,218,219,220,224,228,229,230,233,240,248,251,253,258,259,260,261,262,263,270,274,275,278,279,280,281,282,283,284,285,286,287,288,293,295,296,298,303,318,319,321,324,325,326,327,328,332,335,336,338,340,341,342,344,345,346,347,348,349,352,355,357,358,360,361,362,364,369,370,371,372,373,374,375,376,377,378,379,380,383,389,390,391,392,393,394,395,396,397,404,405,406,407,408,409,410,411,414,415,416,418,420,421,423,424,426,427,433,436,437,440,448,449,450],descript:[],descriptor:[120,167,365],deserno:319,design:[0,3,6,7,8,11,13,14,15,17,118,126,129,143,178,191,197,198,229,230,251,252,271,285,290,336,337,338,341,344,349,351,357,377,378,379,381,382,390,393,407,432],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,121,126,144,157,166,179,192,194,203,205,206,213,214,215,219,229,247,255,256,257,258,261,265,270,273,278,281,282,283,284,289,296,310,315,318,319,321,324,326,327,328,353,355,363,378,379,406,408,410,419,420,421,423,427,432,437,438,440,441,448,449,450],desk:7,desktop:[4,6,7,10,12,17,168],despit:443,destabil:339,destre:312,destroi:[11,39,189,190],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,120,121,122,123,124,127,137,138,139,141,144,145,148,149,152,163,167,168,169,172,173,174,178,181,182,183,184,186,188,190,191,192,193,194,195,203,205,206,207,208,210,211,213,215,216,220,226,227,228,229,230,231,232,233,234,235,239,241,246,247,248,249,252,255,256,257,259,260,262,263,264,270,273,278,281,282,283,284,285,286,288,289,290,291,292,293,294,301,303,305,313,318,319,322,326,327,329,330,333,334,335,336,338,339,341,343,344,345,346,347,348,349,352,353,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,396,397,405,412,414,415,421,423,424,425,426,428,429,432,433,435,438,441,448,449,452],detect:[2,3,12,61,63,86,204,256,289,328,348,363,368,418,420,423,434,437,448],determ:333,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,121,132,133,142,143,144,166,167,168,169,170,171,175,176,177,180,181,182,183,184,185,186,187,188,192,194,195,198,200,205,208,209,211,213,214,219,224,226,227,229,234,235,246,247,249,251,253,257,260,267,268,269,270,271,272,278,281,282,283,285,291,292,295,296,297,298,299,300,301,313,318,319,321,327,329,330,333,335,336,343,348,352,354,355,359,361,365,373,380,384,393,394,404,407,411,415,420,423,424,426,428,430,433,437,439,440,447,448,449],detil:108,devan:[9,395],devanathan:410,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,210,233,255,260,261,264,335,339,357,382,425],devemi:9,deviat:[227,233,251,359],devic:[1,3,12,15,17,210,333],device_typ:333,devin:[262,348],devis:382,dfactor:168,dff:443,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,319],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,264],dhi:[59,166,194,256],dhug:[227,260],dhugoniot:[227,260],dia:380,diagnost:[],diagon:[3,6,83,120,121,192,229,257,270,293],diagonalstyl:396,diagram:[41,118,143,163,188,253],diallo:363,diam:[168,169,256,327],diamet:[3,6,40,113,144,167,168,169,173,174,213,256,270,278,294,296,327,347,360,361,367,371,394,412,415,423,424,433],diamond:[321,357,380],diamter:[40,256],dick:6,dicsuss:226,dictat:[179,227],did:[3,12,326,353,354,355,361,384,408,410,431],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,140,292,318],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,122,123,124,125,127,130,131,132,133,134,136,137,138,144,145,147,152,163,164,166,167,168,169,172,174,177,179,181,183,188,189,190,191,192,193,194,198,204,205,206,207,208,209,210,213,214,216,226,229,230,231,232,234,235,237,239,242,244,245,246,249,251,253,255,257,260,261,262,265,268,270,273,274,275,276,278,281,282,283,286,287,288,290,293,294,295,296,299,303,304,313,315,317,318,319,321,322,324,325,327,328,330,331,332,333,334,335,339,343,344,346,347,348,353,355,357,360,361,362,364,367,369,370,372,373,380,381,382,383,384,386,390,392,393,394,395,396,397,405,406,407,408,410,412,415,416,417,418,420,421,423,425,426,427,428,431,432,433,435,437,438,440,441,443,447,448,449,450],differenti:[1,3,6,29,164,318,349,390,409],difficult:[192,253,333,363,432],difficulti:392,diffract:[],diffus:[],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[],dim1:3,dim2:3,dim:[3,59,71,122,125,126,127,130,131,132,133,134,136,144,166,184,194,211,296,321,380,426,447,448,449],dimdim:448,dimems:252,dimens:[],dimension:[3,39,112,118,120,122,124,125,126,127,130,131,132,133,134,136,143,165,181,184,228,252,290,321,324,328,390,423,433],dimensionless:[105,120,290,319,396,415],dimer:[6,270,380],dimgrai:169,dimstr:[41,188],dinola:[257,281],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,167,280,443],dir1:434,dir2:434,dir:[1,3,4,8,11,12,227,251,260,277,390,392,393,421,434,448],dirac:120,direc:390,direct:[],directli:[3,6,8,9,11,12,87,113,120,167,168,175,200,207,211,216,252,271,282,294,296,297,298,299,321,325,333,334,335,340,342,343,349,352,355,357,369,373,384,387,395,404,421,433,434,435,441,448],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,170,193,212,255,261,264,278,287,288,328,332,334,335,339,346,348,349,355,356,358,365,366,377,380,381,382,386,390,391,392,393,396,406,408,409,410,421,423,424,425,434,448],disabl:[3,12,16,290,368,421,436],disadvantag:[6,188],disallow:[194,229],disappear:425,discard:[2,3,41,71,184,188,291,299,420,425,426],discontinu:[9,164,326,375],discourag:380,discov:[13,291],discret:[6,8,40,42,168,169,213,216],discuss:[],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[],displace_atom:[],displace_box:59,displacemet:426,displai:[11,13,22,37,44,55,152,163,167,168,305,313,346,405],dispters:3,dissip:[6,206,213,252,287,288,341,353,361,378,379,405],dissolut:189,dist:[6,69,91,108,117,167,253,269,354,404,418,449],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,133,139,142,144,145,146,147,151,166,167,168,169,177,181,184,185,189,190,191,192,194,195,196,199,205,211,216,226,227,228,229,233,241,251,252,256,260,261,268,269,270,273,274,275,276,277,278,285,286,288,289,290,293,295,296,297,298,299,300,304,318,319,321,324,326,328,329,330,333,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,359,360,361,362,363,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,421,423,426,432,433,437,441,443,447,449],distinct:[6,198,267,318,394],distinguish:[6,86,120,219,357],distort:334,distrbut:334,distribut:[],distro:[111,346,389,390],ditto:[8,11,12,14,15,16,17,18,115,190,421],div:8,divd:117,diverg:[3,12,39,270,288,425,443,450],divid:[3,6,16,41,91,112,117,121,141,142,152,163,169,181,182,183,188,194,251,286,293,298,318,326,328,358,393,432,440,448],divis:[6,216,339,367,377,420,423,441,448],dl_poli:7,dlambda:138,dlammps_async_imd:210,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,168],dlammps_gzip:[3,12,167,168,289,423,424,428],dlammps_jpeg:[3,12,168],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,168],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,167],dlen:433,dlmp_intel_offload:[12,16],dlo:[59,166,194,256],dlvo:[7,347,415],dm_lb:216,dmax:[278,324],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,389,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,440,441,448,449,450,451],docuement:394,dodgerblu:169,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,123,124,127,132,134,138,143,144,145,146,148,150,152,157,163,164,166,167,168,169,172,178,179,181,184,187,188,190,191,192,194,198,200,202,205,206,209,211,213,214,216,219,225,229,230,231,232,234,235,246,247,248,249,257,258,259,263,265,268,270,278,281,283,285,286,290,293,294,295,298,299,300,301,306,307,309,310,312,317,318,319,320,321,327,328,329,334,335,336,337,338,339,341,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,364,365,366,367,368,371,372,374,375,376,378,379,380,381,382,384,390,391,392,393,394,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,436,437,440,441,443,448,452],doegenomestolif:7,doesn:[3,7,8,12,144,167,179,184,185,275,327,329,333,335,348,356,366,392,393,406,408,409,410,423,425],dof:[3,8,112,123,124,137,181,270,449],dof_per_atom:[124,181],dof_per_chunk:[124,181],doff:[327,423],doi:[6,193],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,133,143,146,166,168,169,172,179,188,192,194,195,209,212,216,229,230,253,265,270,290,295,296,318,319,328,333,354,384,418,420,423,427,440],domin:[1,357,437],don:[0,8,11,12,13,116,147,175,200,214,259,299,380,421,423],donadio:282,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,138,141,144,147,164,168,169,178,179,181,183,184,185,186,188,189,190,191,192,194,195,203,205,210,211,213,214,221,229,234,235,246,247,249,250,252,253,254,259,267,270,271,273,278,281,282,283,285,287,288,301,303,317,318,319,326,328,329,332,333,335,343,355,364,365,366,373,379,380,384,392,404,407,412,418,419,420,421,424,427,428,431,441,443,448,449],donor:363,dot:[121,140,175,200,208,228],doti:[339,390],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,194,203,258,299,303,317,319,332,333,339,358,362,392,393,419,423,427,431,436,448,449],dover:178,down:[3,6,7,8,11,39,71,192,213,278,294,333,357,384,422],downhil:[324,325],download:[5,7,8,9,11,12,13,17,210,365,391],downsid:6,downward:267,dozen:[8,12,107,172,392,393],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[],dragforc:216,drai:[227,260],drain:[209,294,326],dramat:[59,166,189,190,191,192,194,229,278,281,282,319,333,384,420],drautz:339,draw:168,drawback:259,drawn:[167,168,169,206,418],drayleigh:[227,260],dreid:[],drfourth:105,drho:[113,334,355],drift:[6,103,105,206,207,213,214,225,268,278,432,440,443],drive:[11,12,176,192,194,208,229,251,257,270,297,328],driven:[6,156],driver:[6,12,14,15,172,203,210],drop:[3,169,353],droplet:364,drsquar:105,drude:[],dry:202,dsecriptor:365,dsf:[],dsmc:[],dstyle:256,dt_collis:216,dt_lb:216,dt_md:216,dt_srd:278,dtilt:[59,194],dtneb:437,dtqm:260,dtype:[115,190],dual:[17,278,333],dudarev:143,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,120,121,122,123,125,127,130,131,132,133,134,136,137,139,143,144,147,148,167,168,172,175,176,183,187,189,190,191,192,193,194,195,200,201,202,203,206,207,210,211,213,214,215,216,219,220,221,225,226,227,228,229,233,241,251,254,256,268,269,270,272,275,277,278,279,281,282,283,284,285,287,288,290,294,295,297,298,299,301,319,324,326,328,329,330,350,353,355,359,360,364,378,379,384,390,392,394,395,404,407,408,410,413,415,416,418,420,423,424,425,432,437,440,441,443,448,449],duffi:290,duin:[9,261,266,392,393],duke:319,dummi:[12,29,409],dump1:428,dump2:428,dump:[],dump_atom:8,dump_custom:8,dump_modifi:[],dumpcustom:8,dumptimestep:428,dunbrack:[6,20,150,344,435],dunweg:[213,215],duplic:[2,3,14,15,16,17,18,19,41,42,145,188,207,251,423,447],dupont:[5,7,13],durat:[37,55,122,123,125,126,127,129,130,131,132,133,136,137,163,169,181,205,265,290,313,361,405],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,145,148,164,167,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,319,326,328,332,333,353,377,384,393,407,418,419,421,423,426,428,430,431,433,435,437,438,441,448,451,452],dvector:8,dvlo:415,dvx:6,dx_lb:216,dy3:143,dyamic:12,dyanam:6,dyanmic:437,dynam:[],dynamo:[5,334,355,380],dyne:447,dyre:374,dysam:426,e28637:29,e_1:339,e_2:339,e_b:358,e_e:357,e_hbond:363,e_i:[6,339,358],e_j:[6,339],e_k:[339,357],e_kl:6,e_lj:[335,352],e_n:[339,357],e_nn:357,e_pr:357,e_rebo:335,e_tors:335,eaa:304,eaat:151,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,131,132,133,134,136,137,138,139,140,141,142,143,144,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,261,262,263,265,267,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,291,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,313,314,317,318,319,321,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,440,441,443,447,448,449,450,452],eacn:[41,188],eam0d:252,eam3d:252,eam:[],eam_databas:13,eam_gener:13,eangl:441,earli:[41,181,183,184,185,186,188,264,271],earlier:[7,8,12,59,169,328,361,380,384,437],earliest:437,earth:357,easi:[6,7,8,11,13,87,121,167,173,174,175,176,184,187,200,208,209,211,213,214,272,281,282,283,295,298,300,327,423,426,431,433,449],easier:[8,9,13,16,167,168,252],easili:[8,11,168,169,294,328,420,430,439,448],eastwood:[318,319],eat:151,eatom:301,eaxmpl:6,eba:21,ebb13:151,ebb:21,ebond:[198,214,440,441],ebt:151,ec_ii:380,ec_ij:380,ec_jj:380,echo:[],eco:[392,393],ecoa:[392,393],ecoul:[107,198,214,392,393,441],ecp:[357,423],edg:[2,3,6,41,59,71,118,142,143,146,147,168,177,184,211,272,295,298,299,300,301,321,423,426,433],edge_histo:142,edge_threshold:142,edih:441,edim:286,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,443],editor:13,edu:[7,9,11,13,355,378,389,392,393],edward:[9,17],eebt:151,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,109,112,121,122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297,300,301,317,318,327,328,332,333,353,355,360,394,396,397,411,413,418,421,423,424,425,426,428,430,431,435,439,441,443,448,452],end_of_step:8,endbondtors:[3,151,157,423],endif:8,energet:[191,335,393],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,167,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,318,319,324,325,326,328,329,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,404,405,406,407,408,409,410,412,413,414,415,416,418,421,423,428,432,433,435,437,439,440,441,443,447,448,451],energy_update_freq:393,enforc:[6,57,58,104,166,167,168,170,172,179,191,194,229,250,252,262,270,273,303,318,369,420,448,449],enforce2d:[],eng:[11,65,69,108,167,203,301,303,348,382],eng_previ:303,engin:[178,194,255,274,287,355,381],engr:[392,393],enhanc:[174,178,418],enlarg:[59,168],enough:[3,40,61,86,144,145,147,188,214,256,260,265,270,291,295,296,299,329,333,349,388,423,427,428],enpub:355,ensembl:[],ensight:6,ensur:[3,6,120,167,179,192,205,206,229,289,319,339,354,377,404,406],enter:[57,134,358,437],enthalpi:[231,232,355,440,441,448],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,121,124,143,144,169,172,173,174,181,184,185,188,191,193,202,205,206,209,213,214,225,229,231,232,233,234,235,251,253,255,268,270,276,290,292,303,333,352,373,384,407,423,431,432],entireti:[367,412],entiti:[6,8,40,42,167,270],entri:[3,8,38,42,56,65,69,79,92,108,115,118,142,164,169,183,184,185,193,260,301,327,339,356,380,386,393,396,406,407,408,409,410],entropi:437,entry1:[38,56,169,346,407],entry2:169,entryn:169,enumer:[145,167],enumuer:6,env:333,environ:[1,3,6,11,12,16,17,18,168,207,212,251,333,334,339,346,348,356,357,390,408,420,434,448],epair:[107,169,359,363,392,393,441],epen:[392,393],epfl:[207,212],epp:352,epq:352,eps0:415,eps14:377,epsilon0:410,epsilon:[3,6,36,45,46,50,53,54,87,150,173,174,205,270,278,295,299,324,326,338,344,345,347,349,350,351,352,360,362,363,364,367,368,369,370,371,372,373,374,375,376,377,383,387,394,395,400,406,412,414,415,432,443,447],epsilon_0:416,epsilon_14:344,epsilon_:394,epsilon_d:350,epsilon_i:[360,384,394],epsilon_i_:394,epsilon_i_a:[360,394],epsilon_i_b:[360,394],epsilon_i_c:[360,394],epsilon_ij:384,epsilon_j:[360,384,394],epsilon_j_:394,epsilon_j_a:[360,394],epsilon_j_b:[360,394],epsilon_j_c:[360,394],epsilon_lj:394,epton:389,eqch:139,eqeq:[392,393],eqp:352,eqq:352,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,121,123,138,140,144,168,169,172,173,174,175,176,179,182,183,186,187,188,192,194,195,200,205,206,208,209,211,213,214,216,219,220,226,227,233,243,251,253,256,258,260,261,262,265,267,269,270,272,274,281,282,283,286,287,288,290,292,293,295,298,300,301,303,317,326,328,329,330,332,333,348,353,359,360,363,378,383,390,392,393,394,396,397,407,412,416,419,420,421,423,425,426,430,431,434,437,439,441,448,449],equat:[3,6,7,8,9,91,112,118,143,152,163,172,192,198,199,207,213,214,216,219,227,228,229,230,233,247,251,253,260,261,265,273,278,286,290,293,295,296,298,300,312,318,319,347,352,353,357,358,361,366,378,379,380,384,394,399,400,402,403,411,416,443],equi:230,equidist:228,equil:[3,261,322,430,452],equilater:433,equilibr:[3,4,5,6,7,9,59,91,144,172,179,182,191,192,205,227,229,230,247,248,260,261,262,263,286,287,288,293,348,349,392,393,419,433],equilibria:293,equilibribum:[189,190],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,127,128,151,153,192,194,205,206,207,214,216,229,233,247,260,265,269,273,274,275,278,285,286,288,293,304,306,309,312,348,380,386,443],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:178,equival:[6,12,13,59,142,146,169,183,186,192,194,205,213,229,247,257,269,270,298,353,357,408,410,423,426,431,432,441,443],equlibrium:6,equliibr:[261,263],er3:143,eradiu:[40,113,357,423],eras:[272,287],erat:[194,379],erc:349,erfc:[349,369,384],erforc:113,erg:447,erhart:[179,355,408,410],ermscal:336,ernst:9,eror:3,eros:380,erose_form:380,erot:[],errata:[408,410],erratum:295,erron:3,error:[],erta:361,ervel:[113,423],escap:[195,443],especi:[8,11,16,132,144,172,179,188,205,260,265,268,269,333,420],espresso:[9,264],essenti:[8,11,12,27,88,125,126,127,130,131,132,133,134,136,153,182,233,252,294,319,335,349,369,410,428,441],essex:29,establish:[87,209],estim:[1,3,6,10,12,38,41,56,91,121,178,188,199,227,278,285,318,319,324,384,393,407,437,441],esu:447,esub:380,eta:[6,216,229,260,261,263,294,356,358,360,390,409,447],eta_dot:229,eta_ij:390,eta_ji:358,etag:[40,423],etail:441,etap:229,etap_dot:229,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,121,122,124,125,126,127,128,130,131,132,133,134,136,138,144,146,147,148,157,167,168,169,172,178,179,180,181,183,184,185,186,189,190,194,195,203,205,206,213,229,256,267,271,290,291,299,303,317,318,326,327,328,329,331,355,356,364,377,379,388,392,393,406,408,410,418,421,423,424,425,430,432,433,437,439,440,441,443,447,448,450,452],ethernet:18,etol:[326,328,418,437],etot0:260,etot:[6,94,96,97,110,121,130,169,198,214,227,260,440,441],eu2:143,eu3:143,euler:[326,328],eulerian:178,euqat:398,europhi:216,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,120,124,134,142,144,167,168,169,173,174,175,176,178,180,181,182,183,184,185,186,187,194,200,206,208,209,211,212,213,214,252,258,261,272,281,282,283,292,295,298,300,301,303,318,319,324,326,333,384,390,407,418,419,421,425,426,428,430,431,432,433,437,439,441,448,449],evalut:[303,421],evan:[132,247],evanseck:[6,20,150,344,435],evapor:[],evaul:[8,326],evdwl:[107,392,393,441],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,145,146,160,164,167,169,172,173,174,179,180,181,183,184,185,186,188,189,190,192,194,195,198,211,214,227,229,230,252,265,267,270,271,278,286,290,293,295,299,301,311,318,324,326,328,333,338,357,358,361,364,384,394,413,423,424,426,428,429,430,432,433,435,438,440,441,443,452],evenli:[3,41,121,164,188,216,367,413,423],event:[],eventu:[3,6,12,15,146,261,437],ever:[54,56,212,278],evera:[347,360,394,405],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,132,147,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,202,203,205,207,209,210,211,216,217,225,229,230,233,250,251,252,256,257,258,259,260,261,262,263,265,267,268,270,271,273,274,278,280,281,282,283,284,285,286,289,290,291,292,293,301,303,317,319,328,329,330,333,353,354,364,377,392,393,401,417,418,419,423,425,427,428,430,431,432,437,438,439,441,448,452],everyth:[8,107],everywher:[116,371],eviri:357,evolut:[207,216,253,418],evolv:[216,253,291],ewald:[2,3,5,6,7,8,12,88,110,118,121,291,318,319,326,340,342,343,349,352,357,369,373,387,395,405,407,425],ewald_disp:352,ewalddisp:3,exact:[22,41,44,71,138,147,152,188,191,206,207,213,214,215,256,265,266,278,290,305,318,346,425,430,437,450,452],exactli:[3,6,12,14,17,38,41,56,59,71,91,123,128,135,144,164,173,174,183,188,194,199,206,213,214,215,230,240,241,248,252,260,278,283,284,297,333,346,353,355,361,364,367,378,384,407,425,426,433,437,448],exager:443,examin:[6,8,191,252],examp:[421,448],exampl:[],exce:[3,6,16,17,18,41,58,71,146,181,184,185,188,192,194,199,202,229,252,278,326,333,423,448],exceed:[3,41,59,188,194,229,278,431],excel:357,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,169,172,175,181,182,183,187,188,192,194,201,204,205,208,211,213,215,229,230,231,232,233,234,235,236,240,241,244,246,247,248,249,253,262,263,270,272,273,275,278,281,283,284,290,294,301,303,304,305,306,307,308,309,312,313,314,318,319,321,323,327,328,329,331,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,385,386,387,389,392,393,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],excess:357,exchang:[2,3,6,8,9,61,62,172,178,179,205,213,262,270,286,290,293,318,333,357,438],exchange:318,excit:[9,357],exclud:[3,6,9,12,16,17,63,71,112,120,124,131,132,148,167,181,184,189,190,217,225,255,268,270,285,296,301,326,327,329,341,361,364,378,379,384,404,435],exclus:[1,3,9,12,16,87,333,348,432],excurs:418,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,145,168,210,264,303,317,320,332,419,421,431,434,437,448],exemplari:206,exemplifi:357,exert:[6,211,214,265,297,298,299,319],exhaust:[178,332,448],exhibit:[229,325,357,432],exist:[3,6,7,8,11,12,13,37,55,59,68,70,144,145,163,168,169,172,177,187,190,192,195,205,255,256,258,301,304,306,307,309,313,322,327,333,364,392,413,419,421,423,424,425,434,435,436,448,449,450],exit:[2,3,11,12,41,57,167,188,317,332,421,422,431,440,448],exlanatori:3,exp:[],expand:[],expans:[12,120,167,434],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,125,136,142,164,188,200,205,207,226,251,257,259,260,265,270,301,319,329,346,380,384,418,421,423,425,428,432,437,448],expens:[6,10,71,169,251,255,270,290,301,318,319,329,333,421],experi:[6,13,15,17,187,195,210,219,228,257,269,270,324,328,353,384,432,437],experienc:[6,12,218,219],experiment:[318,333,437],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,124,132,164,167,168,169,172,181,182,186,188,190,192,194,229,251,259,270,275,301,303,317,318,321,327,328,332,338,355,367,397,412,416,421,424,425,428,430,433,443,448,452],explan:[3,6,59,113,120,167,181,228,251,364,417,420,421,423,432],explanatori:[3,8,117,167,180,181,183,184,185,270,327,420,448],explantori:[3,266],explic:383,explicit:[6,9,11,22,44,77,87,113,116,138,152,173,174,194,305,323,335,336,339,344,346,355,357,368,378,411,417,420,424,427],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,134,142,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,184,187,194,201,204,206,208,213,229,231,232,233,234,235,236,244,246,247,249,259,260,262,270,272,273,281,283,284,290,294,304,306,307,308,309,312,314,327,333,334,335,337,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,414,415,416,423,425,432,433,435,436,443],explictli:[16,436],exploit:[9,15,17,253],explor:[118,143],expon:[3,261,263,355,360,363,377,383,395],exponenti:[87,390,406,416,437,448],expos:11,exposit:[178,353,354],express:[6,120,130,144,173,174,192,226,251,261,290,296,303,339,355,357,371,380,396,405,448],expressiont:339,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,172,175,176,179,186,187,193,196,200,203,204,205,207,208,209,211,213,215,227,229,233,241,251,252,268,269,270,272,274,275,277,281,282,283,284,285,287,288,290,292,295,299,300,360,380,393,394,396,440,441],extent:[1,3,41,45,57,71,142,146,167,177,184,188,211,297,300,318,321,335,407,420,423,426],exterior:[3,6,299],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,121,122,123,125,127,130,131,132,133,134,136,137,143,144,145,146,150,169,183,188,190,229,258,259,260,270,278,326,327,330,331,352,361,364,367,380,384,420,421,423,426,435,443,448],extract:[3,6,11,13,36,63,87,107,115,117,119,173,174,263,328,349,358,380,396,421,428,440],extract_atom:11,extract_comput:[11,421],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,168,192,194,229,288,357,409,443],extrema:377,extrins:178,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[140,292],f_a:[408,409,410],f_ave:117,f_c:409,f_f:410,f_fix_id:260,f_harm:288,f_i:390,f_id:[6,71,117,119,167,172,180,181,182,183,184,185,186,224,280,292,441,448],f_ij:390,f_indent:186,f_int:287,f_jj:91,f_k:390,f_langevin:290,f_max:[260,265],f_msst:227,f_r:[214,408,409,410],f_sigma:339,f_solid:288,f_ss:6,f_temp:214,face:[3,6,57,59,71,132,142,146,177,184,185,295,297,298,299,300,321,360,380,394,423,426],face_threshold:142,facet:142,facil:[0,12],facilit:[6,13],fact:[6,8,16,207,278,288,361,435],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],factori:[3,421],factoriz:318,fail:[3,11,12,59,148,192,195,318,326,328,351,393,421],fairli:[11,384,432,437],faken:73,falcon:210,fall:[3,6,169,183,256,421],fals:[86,301,303,448],fame:8,famili:420,familiar:[0,11],fan:390,far:[3,6,12,17,57,59,61,86,167,169,170,188,189,190,192,195,205,229,251,269,270,278,295,306,309,324,328,329,412,421,423,428,441],farago:213,farrel:[408,410],farther:167,fashion:[6,8,41,71,144,169,172,173,174,179,184,188,190,195,205,207,211,226,227,229,231,232,233,234,235,243,246,247,248,249,259,260,262,270,274,277,280,288,290,294,295,296,298,300,328,364,378,426,435,448,451],fasolino:366,fast:[6,7,9,12,13,17,39,167,238,260,291,318,319,341,378,379,405,407,425,430,432,441,449,452],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,187,188,201,204,208,212,213,229,231,232,233,234,235,236,244,246,247,249,257,261,262,270,272,273,278,281,283,285,287,290,294,304,306,307,308,309,312,314,318,319,330,331,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,432,436,443],fastest:[6,14,17,132,184,290,291,333,420],fatal:[3,440],fault:[70,393],faulti:12,fava:360,favor:191,favorit:7,fbmc:285,fcc:[],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[],fennel:[349,369],fep:[],ferguson:[6,150,435],fermi:[1,12,15,130,333,410],fermion:[9,357],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,170,180,181,182,183,184,185,186,214,229,256,259,261,273,292,318,326,327,328,335,420,423,428,432,434,448,450],fewer:[1,3,11,15,16,61,219,432],fewest:3,fextern:203,feynman:253,fff:421,ffield:[348,358,392,393],ffmpeg:[3,12,168],ffplai:168,fft:[1,3,7,12,14,15,88,109,110,121,252,318,319,432],fft_inc:[12,319],fft_lib:12,fft_path:12,fftbench:318,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,175,176,200,203,207,253,269,349,369,373,404],field1:[424,428],field2:424,field:[],fifth:[275,386],figur:[1,3,8,11,12,260,420,421],fij:352,file0:251,file1:[11,13,251,289,303,327,428,430,434],file2:[11,13,289,303,327,428,430,434],file:[],filenam:[3,12,13,38,41,56,164,167,168,169,170,178,181,182,183,184,185,186,188,193,251,255,258,261,262,263,266,267,270,271,289,290,315,316,317,328,334,335,339,349,355,356,358,366,380,381,382,386,390,391,392,393,396,406,407,408,409,410,419,420,421,424,425,430,434,441,448,450,451,452],filennam:430,filep:[3,167,169,425,430,452],filepo:267,fill:[7,144,168,256,290,321,329,339,393,426],filter:[169,178],final_integr:8,final_integrate_respa:8,finchham:[6,126,351],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,147,164,170,179,191,192,202,205,228,251,257,265,269,324,326,328,329,349,364,369,373,380,405,407,443,448],find_custom:8,fine:[16,17,148,175,200,288,329,333,448],finer:[120,144,448],finest:318,finger:[144,166,226,426],finish:[6,11,41,188,303,315,317,318,330,332,333,412,428,448,449],finit:[],finni:[7,355,405],finvers:198,fiorin:[9,193],fire:[324,325,326,328,437],firebrick:169,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,121,129,132,138,140,142,143,145,146,147,151,164,167,168,169,170,172,179,181,182,183,184,185,186,188,191,194,205,206,211,216,226,227,228,229,251,253,258,259,260,262,267,270,273,274,275,276,278,279,280,287,288,289,290,292,296,301,303,304,310,321,326,327,328,329,332,333,334,335,338,339,340,342,344,346,348,349,355,357,358,361,362,365,366,368,369,373,378,379,380,382,384,386,390,392,393,396,404,406,407,408,409,410,418,419,420,421,423,424,425,428,430,432,435,436,437,440,441,443,448,449,450,452],fischer:[6,9,19,20,150,344,435],fit:[3,6,9,12,38,56,164,269,278,335,339,366,380,384,400,407,409,431,448],five:[73,130,260,327,339,381,423,437],fix:[],fix_adapt:[138,174,377],fix_atom_swap:205,fix_bal:62,fix_deposit:[3,179,205,256],fix_evapor:[179,205],fix_flux:178,fix_gcmc:[179,327],fix_gl:207,fix_gld:207,fix_grav:256,fix_id:[3,192,227,229,231,232,233,234,235,257,260],fix_modifi:[],fix_mov:[166,296],fix_nh:8,fix_npt:207,fix_nvt:[179,205],fix_poem:[3,6],fix_pour:[3,195],fix_qbmsst:9,fix_qeq:[3,348],fix_rattl:273,fix_reax_bond:392,fix_rigid:[219,338],fix_saed_vtk:271,fix_setforc:8,fix_shak:273,fix_srd:3,fix_styl:233,fix_temp_rescal:284,fixedpoint:[192,229],fixextern:203,fixid:178,fji:352,flag1:[197,331],flag2:[197,331],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,404,418,420,421,423,424,425,427,428,429,433,448],flag_buck:343,flag_coul:[343,352,373],flag_lj:[352,373],flagfld:[341,378,379],flaghi:[3,341,378,379],flaglog:[341,378,379],flagn:197,flagvf:[341,378,379],flat:[6,290,295,296,300],flavor:[2,7,12,384],fld:[9,295,341,378,379],flen:336,flex_press:336,flexibl:[3,6,8,145,168,181,184,193,207,230,286,293,357,409,441],flip:[3,6,194,229,297,298],floor:448,flop:12,floralwhit:169,flow:[],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[],fluid_veloc:220,flush:[3,169,440],flux:[],flv:168,fly:[7,9,12,41,168,172,178,195,198,270,273,291,339,441,443],fmackai:9,fmag:196,fmass:253,fmax:[326,441],fmomentum:198,fmsec:[2,169,213,214,226,229,257,270,281,282,432,442,447,449],fname:317,fno:12,fnorm:[326,441],fnpt:198,fnvt:198,foce:364,fock:336,focu:273,fogarti:[9,263,393],foil:[120,251,396],fold:[276,432],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","&lt;no title&gt;","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":189,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,120,124,132,133,137,143,144,147,149,163,165,166,167,168,169,170,171,173,174,175,177,178,179,181,184,185,186,189,190,192,193,194,195,199,202,205,206,211,213,214,215,216,217,219,224,227,229,230,233,247,248,252,253,256,257,258,259,260,262,265,267,268,270,271,278,280,285,286,287,288,291,293,295,297,301,313,316,318,319,321,322,324,325,327,329,330,331,333,336,339,341,357,378,379,384,392,393,404,405,418,419,420,423,424,426,428,430,431,432,435,437,439,440,441,442,447,449,450,451],"function":448,"long":[340,342,343,344,345,349,351,352,369,373,377,387,395],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[173,174],addforc:175,addit:[12,13],addtorqu:176,adiabat:6,adp:334,airebo:335,alloi:355,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:177,arrai:6,aspher:[6,82,123,231,234,237,238,246],atc:[9,178],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,120,121,142,177,179,180,259,448],atom_modifi:39,atom_styl:40,attract:5,aveforc:187,awpmd:[9,336],balanc:[41,188],barostat:6,basal:67,beck:337,berendsen:[257,281],between:6,binary2txt:13,bodi:[6,8,42,68,239,338],bond:[8,13,69,189,190,191,266],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:339,born:[340,351],boundari:[7,57],box:[6,58,192],brownian:341,buck:[342,343,351],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,150,344,377],chunk:[6,66,71,75,90,93,104,106,114,124,139,141,181],citat:7,class2:[21,43,151,304,345],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[295,347,415],colvar:[9,13,193],com:[74,75,125],comb3:348,comb:[262,348],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,448],compute_modifi:102,condit:7,conduct:[6,286],constant:6,constraint:7,contact:76,coord:77,core:6,correl:182,cosin:[23,24,25,26,27,28,153],cossq:306,coul:[340,342,343,344,345,349,350,351,362,369,373,377,387,395],coupl:6,creat:190,create_atom:144,create_bond:145,create_box:146,createatom:13,creation:7,csld:282,csvr:282,cubic:371,cuda:[9,14,109,112,122,131,175,187,201,204,208,229,236,272,273,281,283,294,340,342,344,345,355,361,362,369,370,372,375,385,406,408],custom:8,cut:[49,336,342,345,349,352,357,359,369,370,377,383,387],cvff:307,damag:78,data2xmovi:13,data:6,databas:13,deby:[349,369],deform:[127,128,194],delete_atom:147,delete_bond:148,delta:24,deposit:195,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,16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86,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],state:280,stationari:223,stop:[173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],store:[279,280],strategi:1,streitz:349,stress:121,structur:2,style:[1,2,6,8],submit:8,suffix:436,summari:6,swap:[179,191],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],system:6,tabl:[0,6,38,56,164,407,408],tad:437,taitwat:[402,403],temp:[122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,281,282,283,284],temper:438,temperatur:6,tersoff:[408,409,410],test:11,tfmc:285,thermal:[6,286],thermo:[6,439],thermo_modifi:440,thermo_styl:441,thermodynam:[6,8],thermostat:6,thole:411,time:[6,186],timestep:442,tip3p:6,tip4p:[6,349,369,373,377],tip:12,tmd:289,tool:13,torqu:139,transform:198,tri:[245,412],triclin:6,tstat:353,ttm:290,tune:291,type:7,umbrella:314,uncomput:444,undump:445,unfix:446,unit:447,user:[9,12,14,16,18],vacf:140,valu:[6,448],variabl:[6,8,448],variou:1,vcm:141,vector:[6,292,448],veloc:449,version:[0,5,12],via:12,vim:13,viscos:[6,293],viscou:[220,294],visual:6,voronoi:142,vtk:271,wall:[6,295,296,297,298,299,300],warn:3,water:6,weight:183,what:[7,12],wolf:[340,349],wrapper:11,write:6,write_data:450,write_dump:451,write_restart:452,xmgrace:13,xmovi:13,xrd:143,yukawa:[414,415],zbl:[410,416]}})
\ No newline at end of file
diff --git a/doc/set.html b/doc/set.html
index d11e85c32d..a11c8db6ca 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">set command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/shell.html b/doc/shell.html
index c88acda775..9d94d9da48 100644
--- a/doc/shell.html
+++ b/doc/shell.html
@@ -71,17 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">shell command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/special_bonds.html b/doc/special_bonds.html
index 27bcb1a79c..2680144fcd 100644
--- a/doc/special_bonds.html
+++ b/doc/special_bonds.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">special_bonds command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/suffix.html b/doc/suffix.html
index da1e75e122..6ba28b1419 100644
--- a/doc/suffix.html
+++ b/doc/suffix.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">suffix command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/tad.html b/doc/tad.html
index 9b93620057..88d95cc678 100644
--- a/doc/tad.html
+++ b/doc/tad.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">tad command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/temper.html b/doc/temper.html
index 90a4376a74..6b85f9b5be 100644
--- a/doc/temper.html
+++ b/doc/temper.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">temper command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/thermo.html b/doc/thermo.html
index be54e7bebb..4d167e8596 100644
--- a/doc/thermo.html
+++ b/doc/thermo.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">thermo command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html
index e5533d60cf..8ae6cd9694 100644
--- a/doc/thermo_modify.html
+++ b/doc/thermo_modify.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">thermo_modify command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 4c049f0786..3d6356aa3c 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">thermo_style command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/timestep.html b/doc/timestep.html
index d424cc4603..0a1e588a24 100644
--- a/doc/timestep.html
+++ b/doc/timestep.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">timestep command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/tutorial_drude.html b/doc/tutorial_drude.html
index b1e38a2f60..8e135dc2ee 100644
--- a/doc/tutorial_drude.html
+++ b/doc/tutorial_drude.html
@@ -71,10 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul class="simple">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</div>
+
           
         
       </div>
diff --git a/doc/uncompute.html b/doc/uncompute.html
index 7b9e016424..c2e18b140b 100644
--- a/doc/uncompute.html
+++ b/doc/uncompute.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">uncompute command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/undump.html b/doc/undump.html
index 2ffbd741a8..f345273c34 100644
--- a/doc/undump.html
+++ b/doc/undump.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">undump command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/unfix.html b/doc/unfix.html
index efc91cc3d3..8ffc184119 100644
--- a/doc/unfix.html
+++ b/doc/unfix.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">unfix command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/units.html b/doc/units.html
index 8475208ca5..f7fa0f3a52 100644
--- a/doc/units.html
+++ b/doc/units.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">units command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/variable.html b/doc/variable.html
index e0a1d1cb15..d76ee57022 100644
--- a/doc/variable.html
+++ b/doc/variable.html
@@ -71,28 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">variable command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a><ul>
-<li><a class="reference internal" href="#math-operators">Math Operators</a></li>
-<li><a class="reference internal" href="#math-functions">Math Functions</a></li>
-<li><a class="reference internal" href="#group-and-region-functions">Group and Region Functions</a></li>
-<li><a class="reference internal" href="#special-functions">Special Functions</a></li>
-<li><a class="reference internal" href="#atom-values-and-vectors">Atom Values and Vectors</a></li>
-<li><a class="reference internal" href="#compute-references">Compute References</a></li>
-<li><a class="reference internal" href="#fix-references">Fix References</a></li>
-<li><a class="reference internal" href="#variable-references">Variable References</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-</ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/velocity.html b/doc/velocity.html
index f23a490f5e..7b492cc11b 100644
--- a/doc/velocity.html
+++ b/doc/velocity.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">velocity command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/write_data.html b/doc/write_data.html
index c828ed96e0..1fed354d06 100644
--- a/doc/write_data.html
+++ b/doc/write_data.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">write_data command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/write_dump.html b/doc/write_dump.html
index 1a8238384d..29bdfb7200 100644
--- a/doc/write_dump.html
+++ b/doc/write_dump.html
@@ -71,19 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">write_dump command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
-<li><a class="reference internal" href="#default">Default</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>
diff --git a/doc/write_restart.html b/doc/write_restart.html
index 27cb53137c..d6863eb7c8 100644
--- a/doc/write_restart.html
+++ b/doc/write_restart.html
@@ -71,18 +71,22 @@
         
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">write_restart command</a><ul>
-<li><a class="reference internal" href="#syntax">Syntax</a></li>
-<li><a class="reference internal" href="#examples">Examples</a></li>
-<li><a class="reference internal" href="#description">Description</a></li>
-<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
-<li><a class="reference internal" href="#related-commands">Related commands</a></li>
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
 </ul>
-</li>
-</ul>
-</div>
+
           
         
       </div>